VRPT/OWL The OWL ontology for VRPT/RDF, generated from the VRPT PDBML Schema. Category Abstract class for category holders. CategoryElement Abstract class for category elements. categoryItem Abstract datatype property for category items. Abstract property for cross-references within VRPT. Abstract property for cross-references between categories. Abstract property for cross-references between categories. Abstract property for external links. Abstract property for external RDF links. Abstract property for external HTML links. link to PDBML-all file. link to PDBML-noatom file. link to PDBML-extatom file. link to wwPDB validation report (XML). link to PDBML formatted validation report (full). link to PDBML formatted validation report (alternative). link to associated PDB entry. link to related PDB entry. link to split PDB entry. link to associated BMRB entry. link to associated EMDB entry. link to associated SASBDB entry. external link to PubMed. external link to sequence databases. external link to UniProt. external link to GenBank. external link to EMBL. external link to NORINE. external link to PIR. external link to RefSeq. external link to glycoinfo.org. external link to DOI (digital object identifier). external link to NCBI taxonomy. external link to NCBI taxonomy (source organism). external link to NCBI taxonomy (host organism). external link to EC (enzyme commission) number. external link to GO (gene ontology). external link to InterPro. external link to Pfam. external link to CATH. external link to SCOP, SCOP2, and SCOP2B. external link to Ensembl (Eukaryotic Genome). external link to chemical component in CCD. external link to peptide reference in PRD (a part of BIRD, Biologically Interesting molecules Reference Dictionary). external link to CCDC (Cambridge Crystallographic Data Centre). external link to PubChem Substance. external link to ChemSpider. external link to CAS. external link to ChEBI. external link to MeSH. external link to ChemIDplus. external link to ChEMBL. external link to BindingDB. external link to DrugBank. external link to KEGG Compound. external link to KEGG Drug. external link to ChemDB. datablock The datablock class holds all categories of wwPDB validation information. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 VRPT PDBML Schema translated from wwPDB Validation Information Dictionary v4.399, which is backward compatible with the PDBx/mmCIF Dictionary v5.370: http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic Abstract property pointing to category. Abstract property pointing to category element. link_to_datablock Link to the base datablock of category elements. 0 diffrn Data items in the DIFFRN category record details about the diffraction data and their measurement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:diffrnCategory> <VRPTx:diffrn id="Set1"> <VRPTx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</VRPTx:ambient_environment> <VRPTx:ambient_temp>293.0</VRPTx:ambient_temp> <VRPTx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</VRPTx:crystal_support> <VRPTx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection</VRPTx:crystal_treatment> </VRPTx:diffrn> </VRPTx:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <VRPTx:diffrnCategory> <VRPTx:diffrn id="d1"> <VRPTx:ambient_temp>293</VRPTx:ambient_temp> <VRPTx:details> \q scan width (1.0 + 0.14tan\q)\&#37;, \q scan rate 1.2\&#37; per min. Background counts for 5 sec on each side every scan.</VRPTx:details> </VRPTx:diffrn> </VRPTx:diffrnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 1 diffrnCategory This property indicates that datablock has a category holder diffrnCategory. diffrnCategory This property indicates that diffrnCategory. has a category diffrn. diffrnItem Abstract datatype property for diffrn items. reference_to_diffrn cross-reference to diffrn. referenced_by_diffrn cross-reference from diffrn. diffrn.ambient_environment The gas or liquid surrounding the sample, if not air. diffrn.ambient_pressure The mean hydrostatic pressure in kilopascals at which the intensities were measured. diffrn.ambient_pressure_esd The estimated standard deviation of attribute ambient_pressure in category diffrn. diffrn.ambient_pressure_gt The mean hydrostatic pressure in kilopascals above which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_pressure_lt The mean hydrostatic pressure in kilopascals below which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_temp The mean temperature in kelvins at which the intensities were measured. diffrn.ambient_temp_details A description of special aspects of temperature control during data collection. diffrn.ambient_temp_esd The standard uncertainty (estimated standard deviation) of attribute ambient_temp in category diffrn. diffrn.ambient_temp_gt The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_temp_lt The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. diffrn.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. diffrn.crystal_support The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop diffrn.crystal_treatment Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. equilibrated in hutch for 24 hours flash frozen in liquid nitrogen slow cooled with direct air stream diffrn.details Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. Y N Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment. Y N diffrn.id This data item uniquely identifies a set of diffraction data. 0 diffrn_attenuator Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:diffrn_attenuatorCategory> <VRPTx:diffrn_attenuator code="1"> <VRPTx:scale>16.976</VRPTx:scale> </VRPTx:diffrn_attenuator> </VRPTx:diffrn_attenuatorCategory> 0 1 0 1 1 diffrn_attenuatorCategory This property indicates that datablock has a category holder diffrn_attenuatorCategory. diffrn_attenuatorCategory This property indicates that diffrn_attenuatorCategory. has a category diffrn_attenuator. diffrn_attenuatorItem Abstract datatype property for diffrn_attenuator items. reference_to_diffrn_attenuator cross-reference to diffrn_attenuator. referenced_by_diffrn_attenuator cross-reference from diffrn_attenuator. diffrn_attenuator.material Material from which the attenuator is made. diffrn_attenuator.scale The scale factor applied when an intensity measurement is reduced by an attenuator identified by attribute code. in category diffrn_attenuator The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities. diffrn_attenuator.code A code associated with a particular attenuator setting. This code is referenced by the attribute attenuator_code in category diffrn_refln which is stored with the diffraction data. See attribute scale in category diffrn_attenuator. 0 diffrn_detector Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:diffrn_detectorCategory> <VRPTx:diffrn_detector diffrn_id="d1"> <VRPTx:detector>multiwire</VRPTx:detector> <VRPTx:type>Siemens</VRPTx:type> </VRPTx:diffrn_detector> </VRPTx:diffrn_detectorCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_detectorCategory This property indicates that datablock has a category holder diffrn_detectorCategory. diffrn_detectorCategory This property indicates that diffrn_detectorCategory. has a category diffrn_detector. diffrn_detectorItem Abstract datatype property for diffrn_detector items. reference_to_diffrn_detector cross-reference to diffrn_detector. referenced_by_diffrn_detector cross-reference from diffrn_detector. diffrn_detector.area_resol_mean The resolution of an area detector, in pixels/mm. diffrn_detector.details A description of special aspects of the radiation detector. diffrn_detector.detector The general class of the radiation detector. photographic film scintillation counter CCD plate BF~3~ counter diffrn_detector.dtime The deadtime in microseconds of the detector used to measure the diffraction intensities. diffrn_detector.pdbx_collection_date The date of data collection. 1996-12-25 diffrn_detector.pdbx_collection_time_total The total number of seconds required to measure this data set. 120.0 diffrn_detector.pdbx_frames_total The total number of data frames collected for this data set. 20 100 diffrn_detector.pdbx_frequency The operating frequency of the detector (Hz) used in data collection. diffrn_detector.type The make, model or name of the detector device used. diffrn_detector.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_measurement Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:diffrn_measurementCategory> <VRPTx:diffrn_measurement diffrn_id="d1"> <VRPTx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</VRPTx:details> <VRPTx:device>3-circle camera</VRPTx:device> <VRPTx:device_details>none</VRPTx:device_details> <VRPTx:device_type>Supper model x</VRPTx:device_type> <VRPTx:method>omega scan</VRPTx:method> </VRPTx:diffrn_measurement> </VRPTx:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:diffrn_measurementCategory> <VRPTx:diffrn_measurement diffrn_id="s1"> <VRPTx:device_type>Philips PW1100/20 diffractometer</VRPTx:device_type> <VRPTx:method>\q/2\q</VRPTx:method> </VRPTx:diffrn_measurement> </VRPTx:diffrn_measurementCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_measurementCategory This property indicates that datablock has a category holder diffrn_measurementCategory. diffrn_measurementCategory This property indicates that diffrn_measurementCategory. has a category diffrn_measurement. diffrn_measurementItem Abstract datatype property for diffrn_measurement items. reference_to_diffrn_measurement cross-reference to diffrn_measurement. referenced_by_diffrn_measurement cross-reference from diffrn_measurement. diffrn_measurement.details A description of special aspects of the intensity measurement. 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees diffrn_measurement.device The general class of goniometer or device used to support and orient the specimen. 3-circle camera 4-circle camera kappa-geometry camera oscillation camera precession camera diffrn_measurement.device_details A description of special aspects of the device used to measure the diffraction intensities. commercial goniometer modified locally to allow for 90\% \t arc diffrn_measurement.device_type The make, model or name of the measurement device (goniometer) used. Supper model q Huber model r Enraf-Nonius model s homemade diffrn_measurement.method Method used to measure intensities. profile data from theta/2theta scans diffrn_measurement.specimen_support The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop diffrn_measurement.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_orient_matrix Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <VRPTx:diffrn_orient_matrixCategory> <VRPTx:diffrn_orient_matrix diffrn_id="set1"> <VRPTx:UB11>-0.071479</VRPTx:UB11> <VRPTx:UB12>0.020208</VRPTx:UB12> <VRPTx:UB13>0.039076</VRPTx:UB13> <VRPTx:UB21>0.035372</VRPTx:UB21> <VRPTx:UB22>0.056209</VRPTx:UB22> <VRPTx:UB23>0.078324</VRPTx:UB23> <VRPTx:UB31>-0.007470</VRPTx:UB31> <VRPTx:UB32>0.067854</VRPTx:UB32> <VRPTx:UB33>-0.017832</VRPTx:UB33> <VRPTx:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</VRPTx:type> </VRPTx:diffrn_orient_matrix> </VRPTx:diffrn_orient_matrixCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_orient_matrixCategory This property indicates that datablock has a category holder diffrn_orient_matrixCategory. diffrn_orient_matrixCategory This property indicates that diffrn_orient_matrixCategory. has a category diffrn_orient_matrix. diffrn_orient_matrixItem Abstract datatype property for diffrn_orient_matrix items. reference_to_diffrn_orient_matrix cross-reference to diffrn_orient_matrix. referenced_by_diffrn_orient_matrix cross-reference from diffrn_orient_matrix. diffrn_orient_matrix.UB11 The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB12 The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB13 The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB21 The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB22 The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB23 The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB31 The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB32 The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB33 The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.type A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. diffrn_orient_matrix.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_orient_refln Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <VRPTx:diffrn_orient_reflnCategory> <VRPTx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <VRPTx:angle_chi>-28.45</VRPTx:angle_chi> <VRPTx:angle_kappa>-11.32</VRPTx:angle_kappa> <VRPTx:angle_omega>5.33</VRPTx:angle_omega> <VRPTx:angle_phi>101.78</VRPTx:angle_phi> <VRPTx:angle_psi>0.00</VRPTx:angle_psi> <VRPTx:angle_theta>10.66</VRPTx:angle_theta> </VRPTx:diffrn_orient_refln> </VRPTx:diffrn_orient_reflnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 diffrn_orient_reflnCategory This property indicates that datablock has a category holder diffrn_orient_reflnCategory. diffrn_orient_reflnCategory This property indicates that diffrn_orient_reflnCategory. has a category diffrn_orient_refln. diffrn_orient_reflnItem Abstract datatype property for diffrn_orient_refln items. reference_to_diffrn_orient_refln cross-reference to diffrn_orient_refln. referenced_by_diffrn_orient_refln cross-reference from diffrn_orient_refln. diffrn_orient_refln.angle_chi Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_kappa Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_omega Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_phi Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_psi Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_theta Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. diffrn_orient_refln.index_h Miller index h of a reflection used to define the orientation matrix. diffrn_orient_refln.index_k Miller index k of a reflection used to define the orientation matrix. diffrn_orient_refln.index_l Miller index l of a reflection used to define the orientation matrix. 0 diffrn_radiation Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:diffrn_radiationCategory> <VRPTx:diffrn_radiation diffrn_id="set1"> <VRPTx:collimation>0.3 mm double pinhole</VRPTx:collimation> <VRPTx:monochromator>graphite</VRPTx:monochromator> <VRPTx:type>Cu K\a</VRPTx:type> <VRPTx:wavelength_id>1</VRPTx:wavelength_id> </VRPTx:diffrn_radiation> </VRPTx:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:diffrn_radiationCategory> <VRPTx:diffrn_radiation diffrn_id="set1"> <VRPTx:monochromator>graphite</VRPTx:monochromator> <VRPTx:type>Cu K\a</VRPTx:type> <VRPTx:wavelength_id>1</VRPTx:wavelength_id> </VRPTx:diffrn_radiation> </VRPTx:diffrn_radiationCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_radiationCategory This property indicates that datablock has a category holder diffrn_radiationCategory. diffrn_radiationCategory This property indicates that diffrn_radiationCategory. has a category diffrn_radiation. diffrn_radiationItem Abstract datatype property for diffrn_radiation items. reference_to_diffrn_radiation cross-reference to diffrn_radiation. referenced_by_diffrn_radiation cross-reference from diffrn_radiation. diffrn_radiation.collimation The collimation or focusing applied to the radiation. 0.3 mm double-pinhole 0.5 mm focusing mirrors diffrn_radiation.filter_edge Absorption edge in angstroms of the radiation filter used. diffrn_radiation.inhomogeneity Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. diffrn_radiation.monochromator The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. Zr filter Ge 220 none equatorial mounted graphite diffrn_radiation.pdbx_analyzer Indicates the method used to obtain monochromatic radiation. attribute monochromator in category diffrn_radiation describes the primary beam monochromator (pre-specimen monochromation). attribute pdbx_analyzer in category diffrn_radiation specifies the post-diffraction analyser (post-specimen) monochromation. Note that monochromators may have either 'parallel' or 'antiparallel' orientation. It is assumed that the geometry is parallel unless specified otherwise. In a parallel geometry, the position of the monochromator allows the incident beam and the final post-specimen and post-monochromator beam to be as close to parallel as possible. In a parallel geometry, the diffracting planes in the specimen and monochromator will be parallel when 2*theta(monochromator) is equal to 2*theta (specimen). For further discussion see R. Jenkins and R. Snyder, Introduction to X-ray Powder Diffraction, Wiley (1996), pp. 164-5. GE(111) Zr filter Ge 220 none equatorial mounted graphite (0001) Si (111), antiparallel diffrn_radiation.pdbx_diffrn_protocol SINGLE WAVELENGTH, LAUE, or MAD. SINGLE WAVELENGTH MONOCHROMATIC LAUE MAD OTHER M L Monochromatic or Laue. M L x-ray neutron electron The radiation scattering type for this diffraction data set. diffrn_radiation.pdbx_wavelength Wavelength of radiation. diffrn_radiation.pdbx_wavelength_list Comma separated list of wavelengths or wavelength range. diffrn_radiation.polarisn_norm The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See attribute polarisn_ratio in category diffrn_radiation. diffrn_radiation.polarisn_ratio Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized component of the radiation. The perpendicular component forms an angle of attribute polarisn_norm in category diffrn_radiation to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). x-ray neutron electron gamma The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined. diffrn_radiation.type The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. CuK\a Cu K\a~1~ Cu K-L~2,3~ white-beam diffrn_radiation.wavelength_id This data item is a pointer to attribute id in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category. K-L~3~ K-L~2~ K-M~3~ K-L~2,3~ The IUPAC symbol for the X-ray wavelength for the probe radiation. diffrn_radiation.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_radiation_wavelength Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:diffrn_radiation_wavelengthCategory> <VRPTx:diffrn_radiation_wavelength id="1"> <VRPTx:wavelength>1.54</VRPTx:wavelength> <VRPTx:wt>1.0</VRPTx:wt> </VRPTx:diffrn_radiation_wavelength> </VRPTx:diffrn_radiation_wavelengthCategory> 1 1 0 1 1 diffrn_radiation_wavelengthCategory This property indicates that datablock has a category holder diffrn_radiation_wavelengthCategory. diffrn_radiation_wavelengthCategory This property indicates that diffrn_radiation_wavelengthCategory. has a category diffrn_radiation_wavelength. diffrn_radiation_wavelengthItem Abstract datatype property for diffrn_radiation_wavelength items. reference_to_diffrn_radiation_wavelength cross-reference to diffrn_radiation_wavelength. referenced_by_diffrn_radiation_wavelength cross-reference from diffrn_radiation_wavelength. diffrn_radiation_wavelength.wavelength The radiation wavelength in angstroms. diffrn_radiation_wavelength.wt The relative weight of a wavelength identified by the code attribute id in category diffrn_radiation_wavelength in the list of wavelengths. diffrn_radiation_wavelength.id The code identifying each value of attribute wavelength. in category diffrn_radiation_wavelength Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The attribute wavelength_id in category diffrn_refln codes must match one of the codes defined in this category. x1 x2 neut 0 diffrn_refln Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by attribute diffrn_id. in category diffrn_refln The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by attribute diffrn_id in category diffrn_reflns. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102. <VRPTx:diffrn_reflnCategory> <VRPTx:diffrn_refln diffrn_id="set1" id="1102"> <VRPTx:angle_chi>32.21</VRPTx:angle_chi> <VRPTx:angle_kappa>20.12</VRPTx:angle_kappa> <VRPTx:angle_omega>11.54</VRPTx:angle_omega> <VRPTx:angle_phi>176.02</VRPTx:angle_phi> <VRPTx:angle_psi>0.00</VRPTx:angle_psi> <VRPTx:angle_theta>23.08</VRPTx:angle_theta> <VRPTx:attenuator_code>Ni.005</VRPTx:attenuator_code> <VRPTx:counts_bg_1>22</VRPTx:counts_bg_1> <VRPTx:counts_bg_2>25</VRPTx:counts_bg_2> <VRPTx:counts_net>3450</VRPTx:counts_net> <VRPTx:counts_peak>321</VRPTx:counts_peak> <VRPTx:counts_total>3499</VRPTx:counts_total> <VRPTx:detect_slit_horiz>0.04</VRPTx:detect_slit_horiz> <VRPTx:detect_slit_vert>0.02</VRPTx:detect_slit_vert> <VRPTx:elapsed_time>1.00</VRPTx:elapsed_time> <VRPTx:index_h>4</VRPTx:index_h> <VRPTx:index_k>0</VRPTx:index_k> <VRPTx:index_l>2</VRPTx:index_l> <VRPTx:intensity_net>202.56</VRPTx:intensity_net> <VRPTx:intensity_sigma>2.18</VRPTx:intensity_sigma> <VRPTx:scale_group_code>A24</VRPTx:scale_group_code> <VRPTx:scan_mode>om</VRPTx:scan_mode> <VRPTx:scan_mode_backgd>mo</VRPTx:scan_mode_backgd> <VRPTx:scan_rate>1.2</VRPTx:scan_rate> <VRPTx:scan_time_backgd>900.00</VRPTx:scan_time_backgd> <VRPTx:scan_width>1.0</VRPTx:scan_width> <VRPTx:sint_over_lambda>0.25426</VRPTx:sint_over_lambda> <VRPTx:standard_code>1</VRPTx:standard_code> <VRPTx:wavelength>1.54184</VRPTx:wavelength> <VRPTx:wavelength_id>Cu1fixed</VRPTx:wavelength_id> </VRPTx:diffrn_refln> </VRPTx:diffrn_reflnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 diffrn_reflnCategory This property indicates that datablock has a category holder diffrn_reflnCategory. diffrn_reflnCategory This property indicates that diffrn_reflnCategory. has a category diffrn_refln. diffrn_reflnItem Abstract datatype property for diffrn_refln items. reference_to_diffrn_refln cross-reference to diffrn_refln. referenced_by_diffrn_refln cross-reference from diffrn_refln. diffrn_refln.angle_chi The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_kappa The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_omega The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_phi The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_psi The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_theta The diffractometer angle theta of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.attenuator_code The code identifying the attenuator setting for this reflection. This code must match one of the attribute code in category diffrn_attenuator values. diffrn_refln.class_code The code identifying the class to which this reflection has been assigned. This code must match a value of attribute code in category diffrn_reflns_class. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. diffrn_refln.counts_bg_1 The diffractometer counts for the measurement of the background before the peak. diffrn_refln.counts_bg_2 The diffractometer counts for the measurement of the background after the peak. diffrn_refln.counts_net The diffractometer counts for the measurement of net counts after background removal. diffrn_refln.counts_peak The diffractometer counts for the measurement of counts for the peak scan or position. diffrn_refln.counts_total The diffractometer counts for the measurement of total counts (background plus peak). diffrn_refln.detect_slit_horiz Total slit aperture in degrees in the diffraction plane. diffrn_refln.detect_slit_vert Total slit aperture in degrees perpendicular to the diffraction plane. diffrn_refln.elapsed_time Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity. diffrn_refln.index_h Miller index h of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. diffrn_refln.index_k Miller index k of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. diffrn_refln.index_l Miller index l of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. diffrn_refln.intensity_net Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. diffrn_refln.intensity_sigma Standard uncertainty (estimated standard deviation) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. diffrn_refln.intensity_u Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. diffrn_refln.pdbx_detector_x Detector coordinate (in pixels) along the X-direction for this reflection. This is often the position where the calculated reflection centroid is predicted to occur. The detector X-direction is most often along the fast changing array index of the 2D diffraction array, while the Y-coordinate is along the slow changing array index. diffrn_refln.pdbx_detector_y Detector coordinate (in pixels) along the Y-direction for this reflection. This is often the position where the calculated reflection centroid is predicted to occur. The detector X-direction is most often along the fast changing array index of the 2D diffraction array, while the Y-coordinate is along the slow changing array index. diffrn_refln.pdbx_image_id The identifier of the diffraction image this reflection is associated with. This is often the image where the calculated reflection centroid is predicted to occur. diffrn_refln.pdbx_rotation_angle The value of the angle around the scan axis for this reflection. This is often the scan angle at which the calculated reflection centroid is predicted to occur. diffrn_refln.pdbx_scale_value The scale factor applied to an individual reflection intensity at the last scaling step before merging all measurements belonging to symmetry-unique reflections into a merged intensity. diffrn_refln.pdbx_scan_angle The value of the angle around the scan axis for this reflection. This is often the scan angle at which the calculated reflection centroid is predicted to occur. diffrn_refln.scale_group_code The code identifying the scale applying to this reflection. This data item is a pointer to attribute code in category diffrn_scale_group in the DIFFRN_SCALE_GROUP category. om ot q The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. st mo The code identifying the mode of scanning a reflection to measure the background intensity. diffrn_refln.scan_rate The rate of scanning a reflection in degrees per minute to measure the intensity. diffrn_refln.scan_time_backgd The time spent measuring each background in seconds. diffrn_refln.scan_width The scan width in degrees of the scan mode defined by the code attribute scan_mode in category diffrn_refln. diffrn_refln.sint_over_lambda The (sin theta)/lambda value in reciprocal angstroms for this reflection. diffrn_refln.standard_code The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to attribute code in category diffrn_standard_refln in the DIFFRN_STANDARD_REFLN category. diffrn_refln.wavelength The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. diffrn_refln.wavelength_id This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. diffrn_refln.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. diffrn_refln.id The value of attribute id in category diffrn_refln must uniquely identify the reflection in the data set identified by the item attribute diffrn_id. in category diffrn_refln Note that this item need not be a number; it can be any unique identifier. 0 diffrn_reflns Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_reflnsCategory This property indicates that datablock has a category holder diffrn_reflnsCategory. diffrn_reflnsCategory This property indicates that diffrn_reflnsCategory. has a category diffrn_reflns. diffrn_reflnsItem Abstract datatype property for diffrn_reflns items. reference_to_diffrn_reflns cross-reference to diffrn_reflns. referenced_by_diffrn_reflns cross-reference from diffrn_reflns. diffrn_reflns.av_R_equivalents The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average absolute difference between av(I) and the individual symmetry-equivalent intensities. diffrn_reflns.av_sigmaI_over_netI Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. diffrn_reflns.av_unetI_over_netI Measure [sum u(net I)|/sum|net I|] for all measured reflections. diffrn_reflns.limit_h_max The maximum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. diffrn_reflns.limit_h_min The minimum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. diffrn_reflns.limit_k_max The maximum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. diffrn_reflns.limit_k_min The minimum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. diffrn_reflns.limit_l_max The maximum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. diffrn_reflns.limit_l_min The minimum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. diffrn_reflns.number The total number of measured intensities, excluding reflections that are classified as systematically absent. diffrn_reflns.pdbx_Rmerge_I_obs The R factor for merging the reflections that satisfy the resolution limits established by attribute d_resolution_high in category diffrn_reflns and attribute d_resolution_low in category diffrn_reflns and the observation limit established by attribute observed_criterion. in category diffrn_reflns Rmerge(I) = [sum~i~(sum~j~|I~j~ - |)] / [sum~i~(sum~j~)] I~j~ = the intensity of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection diffrn_reflns.pdbx_Rsym_value The R factor for averaging the symmetry related reflections to a unique data set. diffrn_reflns.pdbx_chi_squared Overall Chi-squared statistic for the data set. diffrn_reflns.pdbx_d_res_high The highest resolution for the interplanar spacings in the reflection data set. This is the smallest d value. diffrn_reflns.pdbx_d_res_low The lowest resolution for the interplanar spacings in the reflection data set. This is the largest d value. diffrn_reflns.pdbx_number_obs The number of reflections satisfying the observation criterion as in attribute pdbx_observed_criterion in category diffrn_reflns diffrn_reflns.pdbx_observed_criterion The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. diffrn_reflns.pdbx_percent_possible_obs The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _diffrn_reflns.d_resolution_high and _diffrn_reflns.d_resolution_low and the observation limit established by attribute observed_criterion in category diffrn_reflns. diffrn_reflns.pdbx_redundancy The overall redundancy for the data set. diffrn_reflns.pdbx_rejects The number of rejected reflections in the data set. The reflections may be rejected by setting the observation criterion, attribute observed_criterion in category diffrn_reflns. diffrn_reflns.reduction_process A description of the process used to reduce the intensity data into structure-factor magnitudes. data averaged using Fisher test diffrn_reflns.theta_max Maximum theta angle in degrees for the measured diffraction intensities. diffrn_reflns.theta_min Minimum theta angle in degrees for the measured diffraction intensities. diffrn_reflns.transf_matrix11 The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix12 The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix13 The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix21 The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix22 The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix23 The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix31 The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix32 The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix33 The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_reflns_class Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment. Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. <VRPTx:diffrn_reflns_classCategory> <VRPTx:diffrn_reflns_class code="Main"> <VRPTx:av_R_eq>0.015</VRPTx:av_R_eq> <VRPTx:d_res_high>0.551</VRPTx:d_res_high> <VRPTx:d_res_low>6.136</VRPTx:d_res_low> <VRPTx:description>m=0; main reflections</VRPTx:description> <VRPTx:number>1580</VRPTx:number> </VRPTx:diffrn_reflns_class> <VRPTx:diffrn_reflns_class code="Sat1"> <VRPTx:av_R_eq>0.010</VRPTx:av_R_eq> <VRPTx:d_res_high>0.551</VRPTx:d_res_high> <VRPTx:d_res_low>6.136</VRPTx:d_res_low> <VRPTx:description>m=1; first-order satellites</VRPTx:description> <VRPTx:number>1045</VRPTx:number> </VRPTx:diffrn_reflns_class> </VRPTx:diffrn_reflns_classCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_reflns_classCategory This property indicates that datablock has a category holder diffrn_reflns_classCategory. diffrn_reflns_classCategory This property indicates that diffrn_reflns_classCategory. has a category diffrn_reflns_class. diffrn_reflns_classItem Abstract datatype property for diffrn_reflns_class items. reference_to_diffrn_reflns_class cross-reference to diffrn_reflns_class. referenced_by_diffrn_reflns_class cross-reference from diffrn_reflns_class. diffrn_reflns_class.av_R_eq For each reflection class, the residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The av|del(I)| term is the average absolute difference between av(I) and the individual intensities. diffrn_reflns_class.av_sgI_over_I Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities in a reflection class. diffrn_reflns_class.av_uI_over_I Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. diffrn_reflns_class.d_res_high The smallest value in angstroms for the interplanar spacings for the reflections in each measured reflection class. This is called the highest resolution for this reflection class. diffrn_reflns_class.d_res_low The largest value in angstroms of the interplanar spacings for the reflections for each measured reflection class. This is called the lowest resolution for this reflection class. diffrn_reflns_class.description Description of each reflection class. m=1 first order satellites H0L0 common projection reflections diffrn_reflns_class.number The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations. diffrn_reflns_class.code The code identifying a certain reflection class. 1 m1 s2 0 diffrn_scale_group Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <VRPTx:diffrn_scale_groupCategory> <VRPTx:diffrn_scale_group code="A24"> <VRPTx:I_net>1.021</VRPTx:I_net> </VRPTx:diffrn_scale_group> </VRPTx:diffrn_scale_groupCategory> 0 1 1 diffrn_scale_groupCategory This property indicates that datablock has a category holder diffrn_scale_groupCategory. diffrn_scale_groupCategory This property indicates that diffrn_scale_groupCategory. has a category diffrn_scale_group. diffrn_scale_groupItem Abstract datatype property for diffrn_scale_group items. reference_to_diffrn_scale_group cross-reference to diffrn_scale_group. referenced_by_diffrn_scale_group cross-reference from diffrn_scale_group. diffrn_scale_group.I_net The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale. diffrn_scale_group.code The value of attribute code in category diffrn_scale_group must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. 1 2 c1 c2 0 diffrn_source Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:diffrn_sourceCategory> <VRPTx:diffrn_source diffrn_id="s1"> <VRPTx:current>180</VRPTx:current> <VRPTx:power>50</VRPTx:power> <VRPTx:size>8mm x 0.4 mm broad-focus</VRPTx:size> <VRPTx:source>rotating anode</VRPTx:source> <VRPTx:type>Rigaku RU-200</VRPTx:type> </VRPTx:diffrn_source> </VRPTx:diffrn_sourceCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_sourceCategory This property indicates that datablock has a category holder diffrn_sourceCategory. diffrn_sourceCategory This property indicates that diffrn_sourceCategory. has a category diffrn_source. diffrn_sourceItem Abstract datatype property for diffrn_source items. reference_to_diffrn_source cross-reference to diffrn_source. referenced_by_diffrn_source cross-reference from diffrn_source. diffrn_source.current The current in milliamperes at which the radiation source was operated. diffrn_source.details A description of special aspects of the radiation source used. diffrn_source.pdbx_synchrotron_beamline Synchrotron beamline. diffrn_source.pdbx_synchrotron_site Synchrotron site. diffrn_source.pdbx_wavelength Wavelength of radiation. diffrn_source.pdbx_wavelength_list Comma separated list of wavelengths or wavelength range. diffrn_source.power The power in kilowatts at which the radiation source was operated. diffrn_source.size The dimensions of the source as viewed from the sample. 8mm x 0.4 mm fine-focus broad focus diffrn_source.source The general class of the radiation source. sealed X-ray tube nuclear reactor spallation source electron microscope rotating-anode X-ray tube synchrotron diffrn_source.take-off_angle The complement of the angle in degrees between the normal to the surface of the X-ray tube target and the primary X-ray beam for beams generated by traditional X-ray tubes. 1.5 H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources. diffrn_source.type The make, model or name of the source of radiation. NSLS beamline X8C Rigaku RU200 diffrn_source.voltage The voltage in kilovolts at which the radiation source was operated. diffrn_source.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_standard_refln Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:diffrn_standard_reflnCategory> <VRPTx:diffrn_standard_refln code="1" diffrn_id="s1"> <VRPTx:index_h>3</VRPTx:index_h> <VRPTx:index_k>2</VRPTx:index_k> <VRPTx:index_l>4</VRPTx:index_l> </VRPTx:diffrn_standard_refln> <VRPTx:diffrn_standard_refln code="1" diffrn_id="s1"> <VRPTx:index_h>1</VRPTx:index_h> <VRPTx:index_k>9</VRPTx:index_k> <VRPTx:index_l>1</VRPTx:index_l> </VRPTx:diffrn_standard_refln> <VRPTx:diffrn_standard_refln code="1" diffrn_id="s1"> <VRPTx:index_h>3</VRPTx:index_h> <VRPTx:index_k>0</VRPTx:index_k> <VRPTx:index_l>10</VRPTx:index_l> </VRPTx:diffrn_standard_refln> </VRPTx:diffrn_standard_reflnCategory> 1 1 1 1 1 1 1 1 diffrn_standard_reflnCategory This property indicates that datablock has a category holder diffrn_standard_reflnCategory. diffrn_standard_reflnCategory This property indicates that diffrn_standard_reflnCategory. has a category diffrn_standard_refln. diffrn_standard_reflnItem Abstract datatype property for diffrn_standard_refln items. reference_to_diffrn_standard_refln cross-reference to diffrn_standard_refln. referenced_by_diffrn_standard_refln cross-reference from diffrn_standard_refln. diffrn_standard_refln.index_h Miller index h of a standard reflection used in the diffraction measurement process. diffrn_standard_refln.index_k Miller index k of a standard reflection used in the diffraction measurement process. diffrn_standard_refln.index_l Miller index l of a standard reflection used in the diffraction measurement process. diffrn_standard_refln.code The code identifying a reflection measured as a standard reflection with the indices attribute index_h, in category diffrn_standard_refln attribute index_k in category diffrn_standard_refln and attribute index_l in category diffrn_standard_refln. This is the same code as the attribute standard_code in category diffrn_refln in the DIFFRN_REFLN list. 1 2 c1 c2 diffrn_standard_refln.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_standards Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:diffrn_standardsCategory> <VRPTx:diffrn_standards diffrn_id="s1"> <VRPTx:decay_>0</VRPTx:decay_> <VRPTx:interval_time>120</VRPTx:interval_time> <VRPTx:number>3</VRPTx:number> </VRPTx:diffrn_standards> </VRPTx:diffrn_standardsCategory> 0 1 0 1 0 1 0 1 0 1 1 diffrn_standardsCategory This property indicates that datablock has a category holder diffrn_standardsCategory. diffrn_standardsCategory This property indicates that diffrn_standardsCategory. has a category diffrn_standards. diffrn_standardsItem Abstract datatype property for diffrn_standards items. reference_to_diffrn_standards cross-reference to diffrn_standards. referenced_by_diffrn_standards cross-reference from diffrn_standards. diffrn_standards.decay_ The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. diffrn_standards.interval_count The number of reflection intensities between the measurement of standard reflection intensities. diffrn_standards.interval_time The time in minutes between the measurement of standard reflection intensities. diffrn_standards.number The number of unique standard reflections used during the measurement of the diffraction intensities. diffrn_standards.scale_sigma The standard uncertainty (estimated standard deviation) of the individual mean standard scales applied to the intensity data. diffrn_standards.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 em_2d_crystal_entity Data items in the EM_SYMMETRY_2DX category record 2D crystal symmetry parameters utilized in a 3DEM reconstruction. 1 1 0 1 1 1 1 1 1 1 1 1 1 1 em_2d_crystal_entityCategory This property indicates that datablock has a category holder em_2d_crystal_entityCategory. em_2d_crystal_entityCategory This property indicates that em_2d_crystal_entityCategory. has a category em_2d_crystal_entity. em_2d_crystal_entityItem Abstract datatype property for em_2d_crystal_entity items. reference_to_em_2d_crystal_entity cross-reference to em_2d_crystal_entity. referenced_by_em_2d_crystal_entity cross-reference from em_2d_crystal_entity. em_2d_crystal_entity.angle_gamma Unit-cell angle gamma in degrees. em_2d_crystal_entity.c_sampling_length Length used to sample the reciprocal lattice lines in the c-direction. em_2d_crystal_entity.length_a Unit-cell length a in angstroms. 62.4 em_2d_crystal_entity.length_b Unit-cell length b in angstroms. 62.4 em_2d_crystal_entity.length_c Thickness of 2D crystal 62.4 P 1 P 2 P 1 2 P 1 21 C 1 2 P 2 2 2 P 2 2 21 P 2 21 21 C 2 2 2 P 4 P 4 2 2 P 4 21 2 P 3 P 3 1 2 P 3 2 1 P 6 P 6 2 2 There are 17 plane groups classified as oblique, rectangular, square, and hexagonal. To describe the symmetry of 2D crystals of biological molecules, plane groups are expanded to equivalent noncentrosymmetric space groups. The 2D crystal plane corresponds to the 'ab' plane of the space group. Enumerated space group descriptions include the plane group number in parentheses, the H-M plane group symbol, and the plane group class. em_2d_crystal_entity.id PRIMARY KEY em_2d_crystal_entity.image_processing_id Pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. 0 em_3d_crystal_entity Data items in the EM_SYMMETRY_3DX category record 3D crystal symmetry parameters utilized in 3DEM reconstruction averaging. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 em_3d_crystal_entityCategory This property indicates that datablock has a category holder em_3d_crystal_entityCategory. em_3d_crystal_entityCategory This property indicates that em_3d_crystal_entityCategory. has a category em_3d_crystal_entity. em_3d_crystal_entityItem Abstract datatype property for em_3d_crystal_entity items. reference_to_em_3d_crystal_entity cross-reference to em_3d_crystal_entity. referenced_by_em_3d_crystal_entity cross-reference from em_3d_crystal_entity. em_3d_crystal_entity.angle_alpha Unit-cell angle alpha in degrees. 120.0 em_3d_crystal_entity.angle_beta Unit-cell angle beta in degrees. 120.0 em_3d_crystal_entity.angle_gamma Unit-cell angle gamma in degrees. 120.0 em_3d_crystal_entity.length_a Unit-cell length a in angstroms. 62.4 em_3d_crystal_entity.length_b Unit-cell length b in angstroms. 62.4 em_3d_crystal_entity.length_c Unit-cell length c in angstroms. 62.4 em_3d_crystal_entity.space_group_name Space group name. P 1 P 21 21 2 I 4 H 3 em_3d_crystal_entity.space_group_num Space group number. 22 em_3d_crystal_entity.id PRIMARY KEY em_3d_crystal_entity.image_processing_id Pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. 0 em_3d_fitting Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_3d_fittingCategory> <VRPTx:em_3d_fitting entry_id="1DYL" id="1"> <VRPTx:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS.</VRPTx:details> <VRPTx:method>AUTOMATIC</VRPTx:method> <VRPTx:overall_b_value xsi:nil="true" /> <VRPTx:ref_protocol>RIGID BODY REFINEMENT</VRPTx:ref_protocol> <VRPTx:ref_space>REAL</VRPTx:ref_space> <VRPTx:target_criteria>R-FACTOR</VRPTx:target_criteria> </VRPTx:em_3d_fitting> </VRPTx:em_3d_fittingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_3d_fittingCategory This property indicates that datablock has a category holder em_3d_fittingCategory. em_3d_fittingCategory This property indicates that em_3d_fittingCategory. has a category em_3d_fitting. em_3d_fittingItem Abstract datatype property for em_3d_fitting items. reference_to_em_3d_fitting cross-reference to em_3d_fitting. referenced_by_em_3d_fitting cross-reference from em_3d_fitting. em_3d_fitting.details Any additional details regarding fitting of atomic coordinates into the 3DEM volume, including data and considerations from other methods used in computation of the model. Initial local fitting was done using Chimera and then NMFF was used for flexible fitting. em_3d_fitting.method The method used to fit atomic coordinates into the 3dem reconstructed map. em_3d_fitting.overall_b_value The overall B (temperature factor) value for the 3d-em volume. 200 RIGID BODY FIT FLEXIBLE FIT BACKBONE TRACE AB INITIO MODEL OTHER The refinement protocol used. REAL RECIPROCAL A flag to indicate whether fitting was carried out in real or reciprocal refinement space. em_3d_fitting.target_criteria The measure used to assess quality of fit of the atomic coordinates in the 3DEM map volume. Cross-correlation coefficient em_3d_fitting.entry_id This data item is a pointer to _entry_id in the ENTRY category. em_3d_fitting.id The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed map volume. 0 em_3d_fitting_list Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_3d_fitting_listCategory> <VRPTx:em_3d_fitting_list _3d_fitting_id="l" id="1"> <VRPTx:pdb_chain_id xsi:nil="true" /> <VRPTx:pdb_entry_id>1VCQ</VRPTx:pdb_entry_id> </VRPTx:em_3d_fitting_list> </VRPTx:em_3d_fitting_listCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_3d_fitting_listCategory This property indicates that datablock has a category holder em_3d_fitting_listCategory. em_3d_fitting_listCategory This property indicates that em_3d_fitting_listCategory. has a category em_3d_fitting_list. em_3d_fitting_listItem Abstract datatype property for em_3d_fitting_list items. reference_to_em_3d_fitting_list cross-reference to em_3d_fitting_list. referenced_by_em_3d_fitting_list cross-reference from em_3d_fitting_list. em_3d_fitting_list.accession_code This item identifies an accession code of the resource where the initial model is used em_3d_fitting_list.details Details about the model used in fitting. The initial model consisted of the complete biological assembly for PDB entry 2GTL. em_3d_fitting_list.initial_refinement_model_id The value of attribute initial_refinement_model_id in category em_3d_fitting itentifies the id in the _pdbx_initial_refinement_model em_3d_fitting_list.pdb_chain_id The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank. The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank. em_3d_fitting_list.pdb_chain_residue_range Residue range for the identified chain. 5-545 em_3d_fitting_list.pdb_entry_id The PDB code for the entry used in fitting. 1EHZ PDB AlphaFold RoseTTAFold ModelArchive SwissModel Modeller ITasser Other This item identifies the resource of initial model used for refinement in silico model experimental model integrative model other This item describes the type of the initial model was generated em_3d_fitting_list._3d_fitting_id The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer to attribute id in category em_3d_fitting in the 3d_fitting category em_3d_fitting_list.id PRIMARY KEY 0 em_3d_reconstruction Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_3d_reconstructionCategory> <VRPTx:em_3d_reconstruction id="1"> <VRPTx:actual_pixel_size>2.52</VRPTx:actual_pixel_size> <VRPTx:details xsi:nil="true" /> <VRPTx:entry_id>1DYL</VRPTx:entry_id> <VRPTx:method>CROSS-COMMON LINES</VRPTx:method> <VRPTx:nominal_pixel_size>2.64</VRPTx:nominal_pixel_size> <VRPTx:resolution>9</VRPTx:resolution> <VRPTx:resolution_method xsi:nil="true" /> </VRPTx:em_3d_reconstruction> </VRPTx:em_3d_reconstructionCategory> 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_3d_reconstructionCategory This property indicates that datablock has a category holder em_3d_reconstructionCategory. em_3d_reconstructionCategory This property indicates that em_3d_reconstructionCategory. has a category em_3d_reconstruction. em_3d_reconstructionItem Abstract datatype property for em_3d_reconstruction items. reference_to_em_3d_reconstruction cross-reference to em_3d_reconstruction. referenced_by_em_3d_reconstruction cross-reference from em_3d_reconstruction. em_3d_reconstruction.actual_pixel_size The actual pixel size of the projection set of images in Angstroms. 2.8 5.76 em_3d_reconstruction.algorithm The reconstruction algorithm/technique used to generate the map. em_3d_reconstruction.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_3d_reconstruction.details Any additional details used in the 3d reconstruction. a modified version of SPIDER program was used for the reconstruction em_3d_reconstruction.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_3d_reconstruction.euler_angles_details Euler angles details em_3d_reconstruction.magnification_calibration The magnification calibration method for the 3d reconstruction. TMV images em_3d_reconstruction.method The algorithm method used for the 3d-reconstruction. cross-common lines polar Fourier transform (PFT) em_3d_reconstruction.nominal_pixel_size The nominal pixel size of the projection set of images in Angstroms. 3.11 6.78 em_3d_reconstruction.num_class_averages The number of classes used in the final 3d reconstruction 300 em_3d_reconstruction.num_particles The number of 2D projections or 3D subtomograms used in the 3d reconstruction 300 HALF-MAPS REFINED AGAINST SAME DATA HALF-MAPS REFINED INDEPENDENTLY HALF-MAPS REFINED WITH FREQUENCY RANGE OMITTED HALF-MAPS REFINED INDEPENDENTLY WITH FREQUENCY RANGE OMITTED OTHER Indicates details on how the half-map used for resolution determination (usually by FSC) have been generated. em_3d_reconstruction.resolution The final resolution (in angstroms) of the 3D reconstruction. 8.9 10.0 em_3d_reconstruction.resolution_method The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off POINT HELICAL 2D CRYSTAL 3D CRYSTAL The type of symmetry applied to the reconstruction em_3d_reconstruction.id PRIMARY KEY em_3d_reconstruction.image_processing_id Foreign key to the EM_IMAGE_PROCESSING category 0 em_admin Administration-related data items Example 1 <VRPTx:em_adminCategory> <VRPTx:em_admin entry_id="D_100005"> <VRPTx:current_status>REL</VRPTx:current_status> <VRPTx:deposition_date>2008-12-01</VRPTx:deposition_date> <VRPTx:details xsi:nil="true" /> <VRPTx:last_update>2011-05-22</VRPTx:last_update> <VRPTx:map_release_date>2009-12-01</VRPTx:map_release_date> </VRPTx:em_admin> </VRPTx:em_adminCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 em_adminCategory This property indicates that datablock has a category holder em_adminCategory. em_adminCategory This property indicates that em_adminCategory. has a category em_admin. em_adminItem Abstract datatype property for em_admin items. reference_to_em_admin cross-reference to em_admin. referenced_by_em_admin cross-reference from em_admin. YES NO Indicates whether the authors have declared that this is a composite map deposition PROC WAIT AUTH REUP REPL AUXU AUXS AUCO REFI POLC HPUB HOLD HOLD8W REL WDRN OBS This data item indicates the current status of the EMDB entry. em_admin.deposition_date date of the entry deposition PDBE RCSB PDBJ PDBC entry deposition site em_admin.details EMDB administration details em_admin.last_update date of last update to the file em_admin.map_release_date date of map release for this entry RCSB PDBE PDBJ PDBC The site where the file was deposited. RCSB PDBE PDBJ PDBC em_admin.title Title for the EMDB entry. em_admin.entry_id An identifier for EM map (a.k.a. EMDB ID). 0 em_buffer Data items in the BUFFER category record details of the sample buffer. 0 1 0 1 0 1 1 1 em_bufferCategory This property indicates that datablock has a category holder em_bufferCategory. em_bufferCategory This property indicates that em_bufferCategory. has a category em_buffer. em_bufferItem Abstract datatype property for em_buffer items. reference_to_em_buffer cross-reference to em_buffer. referenced_by_em_buffer cross-reference from em_buffer. em_buffer.details Additional details about the buffer. 20mM NaCl, 10mM Tris-HCL,1mM MgCl2,1mM EDTA em_buffer.name The name of the buffer. Polymix buffer em_buffer.pH The pH of the sample buffer. 5.5 em_buffer.id PRIMARY KEY em_buffer.specimen_id Pointer to attribute id in category em_specimen 0 em_buffer_component Buffer category 0 1 0 1 0 1 0 1 1 1 em_buffer_componentCategory This property indicates that datablock has a category holder em_buffer_componentCategory. em_buffer_componentCategory This property indicates that em_buffer_componentCategory. has a category em_buffer_component. em_buffer_componentItem Abstract datatype property for em_buffer_component items. reference_to_em_buffer_component cross-reference to em_buffer_component. referenced_by_em_buffer_component cross-reference from em_buffer_component. em_buffer_component.concentration The concentration of the sample (arbitrary units). 1.35 em_buffer_component.concentration_units Units for the sample concentration value. mg/mL em_buffer_component.formula Formula for buffer component. NaCl em_buffer_component.name Name of the buffer component. sodium chloride em_buffer_component.buffer_id Foreign key to the entry category. em_buffer_component.id PRIMARY KEY 0 em_crystal_formation Description of growth of a 2D, 3D, or helical crystal array. 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 em_crystal_formationCategory This property indicates that datablock has a category holder em_crystal_formationCategory. em_crystal_formationCategory This property indicates that em_crystal_formationCategory. has a category em_crystal_formation. em_crystal_formationItem Abstract datatype property for em_crystal_formation items. reference_to_em_crystal_formation cross-reference to em_crystal_formation. referenced_by_em_crystal_formation cross-reference from em_crystal_formation. em_crystal_formation.atmosphere The type of atmosphere in which crystals were grown Crystallization was performed in an environmental chamber with constant nitrogen gas flow. em_crystal_formation.details Description of growth of a 2D, 3D, or helical crystal array. Lysozyme (200 mg/ml) was mixed 1 to 1 with precipitant solution (3.5M sodium chloride, 15% PEG5000, 50 mM sodium acetate pH 4.5). Microcrystals were grown by the hanging drop method. em_crystal_formation.instrument Instrument used to prepare the crystalline array Langmuir trough Gryphon LCP em_crystal_formation.lipid_mixture Description of the lipid mixture used for crystallization monoolein and monopalmitolein were mixed 1:1 em_crystal_formation.lipid_protein_ratio The molar ratio of lipid to protein in the crystallized sample 5.0 em_crystal_formation.specimen_id Foreign key relationship to the em_specimen category em_crystal_formation.temperature The value of the temperature in kelvin used for growing the crystals. 298 em_crystal_formation.time Time period for array crystallization, in time unit indicated (min, hr, day, month, year) 50 MINUTE HOUR DAY MONTH YEAR Time unit for array crystallization em_crystal_formation.id PRIMARY KEY 0 em_ctf_correction Description of the Contrast Transfer Function (CTF) correction Example 1 - <VRPTx:em_ctf_correctionCategory> <VRPTx:em_ctf_correction id="1"> <VRPTx:em_image_processing_id>1</VRPTx:em_image_processing_id> <VRPTx:type>PHASE FLIPPING ONLY</VRPTx:type> </VRPTx:em_ctf_correction> </VRPTx:em_ctf_correctionCategory> 0 1 0 1 0 1 1 em_ctf_correctionCategory This property indicates that datablock has a category holder em_ctf_correctionCategory. em_ctf_correctionCategory This property indicates that em_ctf_correctionCategory. has a category em_ctf_correction. em_ctf_correctionItem Abstract datatype property for em_ctf_correction items. reference_to_em_ctf_correction cross-reference to em_ctf_correction. referenced_by_em_ctf_correction cross-reference from em_ctf_correction. em_ctf_correction.details Any additional details about CTF correction CTF amplitude correction was performed following 3D reconstruction em_ctf_correction.em_image_processing_id Foreign key to the EM_IMAGE_PROCESSING category em_ctf_correction.type Type of CTF correction applied em_ctf_correction.id PRIMARY KEY 0 em_diffraction Microscopy parameters relevant only for crystallography Example 1 - <VRPTx:em_diffractionCategory> <VRPTx:em_diffraction id="1"> <VRPTx:camera_length>800</VRPTx:camera_length> <VRPTx:imaging_id>1</VRPTx:imaging_id> </VRPTx:em_diffraction> <VRPTx:em_diffraction id="2"> <VRPTx:camera_length>750</VRPTx:camera_length> <VRPTx:imaging_id>2</VRPTx:imaging_id> </VRPTx:em_diffraction> </VRPTx:em_diffractionCategory> 1 1 1 1 0 1 1 em_diffractionCategory This property indicates that datablock has a category holder em_diffractionCategory. em_diffractionCategory This property indicates that em_diffractionCategory. has a category em_diffraction. em_diffractionItem Abstract datatype property for em_diffraction items. reference_to_em_diffraction cross-reference to em_diffraction. referenced_by_em_diffraction cross-reference from em_diffraction. em_diffraction.camera_length The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. 800 em_diffraction.imaging_id Foreign key to the EM_IMAGING category em_diffraction.tilt_angle_list Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment. 20,40,50,55 em_diffraction.id PRIMARY KEY 0 em_diffraction_shell Statistical parameters for electron diffraction measurements within a resolution shell Example 1 - <VRPTx:em_diffraction_shellCategory> <VRPTx:em_diffraction_shell id="1"> <VRPTx:fourier_space_coverage>93.0</VRPTx:fourier_space_coverage> <VRPTx:high_resolution>7.5</VRPTx:high_resolution> <VRPTx:low_resolution>45</VRPTx:low_resolution> <VRPTx:multiplicity>2.3</VRPTx:multiplicity> <VRPTx:num_structure_factors>327</VRPTx:num_structure_factors> <VRPTx:phase_residual>13.5</VRPTx:phase_residual> </VRPTx:em_diffraction_shell> </VRPTx:em_diffraction_shellCategory> 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 em_diffraction_shellCategory This property indicates that datablock has a category holder em_diffraction_shellCategory. em_diffraction_shellCategory This property indicates that em_diffraction_shellCategory. has a category em_diffraction_shell. em_diffraction_shellItem Abstract datatype property for em_diffraction_shell items. reference_to_em_diffraction_shell cross-reference to em_diffraction_shell. referenced_by_em_diffraction_shell cross-reference from em_diffraction_shell. em_diffraction_shell.em_diffraction_stats_id Pointer to EM CRYSTALLOGRAPHY STATS em_diffraction_shell.fourier_space_coverage Completeness of the structure factor data within this resolution shell, in percent 93.2 em_diffraction_shell.high_resolution High resolution limit for this shell (angstroms) 3.0 em_diffraction_shell.low_resolution Low resolution limit for this shell (angstroms) 5.5 em_diffraction_shell.multiplicity Multiplicity (average number of measurements) for the structure factors in this resolution shell 2.5 em_diffraction_shell.num_structure_factors Number of measured structure factors in this resolution shell 244 em_diffraction_shell.phase_residual Phase residual for this resolution shell, in degrees 13.5 em_diffraction_shell.id PRIMARY KEY 0 em_diffraction_stats Statistical parameters for electron diffraction measurements Example 1 - <VRPTx:em_diffraction_statsCategory> <VRPTx:em_diffraction_stats id="1"> <VRPTx:fourier_space_coverage>92</VRPTx:fourier_space_coverage> <VRPTx:high_resolution>7.2</VRPTx:high_resolution> <VRPTx:num_intensities_measured>1524</VRPTx:num_intensities_measured> <VRPTx:num_structure_factors>325</VRPTx:num_structure_factors> <VRPTx:overall_phase_error>18.6</VRPTx:overall_phase_error> <VRPTx:overall_phase_residual>9.5</VRPTx:overall_phase_residual> <VRPTx:phase_error_rejection_criteria>None</VRPTx:phase_error_rejection_criteria> <VRPTx:r_merge>19.5</VRPTx:r_merge> <VRPTx:r_sym>23.2</VRPTx:r_sym> </VRPTx:em_diffraction_stats> </VRPTx:em_diffraction_statsCategory> 0 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 0 1 1 em_diffraction_statsCategory This property indicates that datablock has a category holder em_diffraction_statsCategory. em_diffraction_statsCategory This property indicates that em_diffraction_statsCategory. has a category em_diffraction_stats. em_diffraction_statsItem Abstract datatype property for em_diffraction_stats items. reference_to_em_diffraction_stats cross-reference to em_diffraction_stats. referenced_by_em_diffraction_stats cross-reference from em_diffraction_stats. em_diffraction_stats.details Any addition details about the structure factor measurements Phases were obtained from micrograph images of the 2D crystals em_diffraction_stats.fourier_space_coverage Completeness of the structure factor data within the defined space group at the reported resolution (percent). 89.3 em_diffraction_stats.high_resolution High resolution limit of the structure factor data, in angstroms 7.5 em_diffraction_stats.image_processing_id Pointer to attribute id in category em_image_processing em_diffraction_stats.num_intensities_measured Total number of diffraction intensities measured (before averaging) 1590 em_diffraction_stats.num_structure_factors Number of structure factors obtained (merged amplitudes + phases) 325 em_diffraction_stats.overall_phase_error Overall phase error in degrees 17.5 em_diffraction_stats.overall_phase_residual Overall phase residual in degrees 17.5 em_diffraction_stats.phase_error_rejection_criteria Criteria used to reject phases Structure factors with phase errors higher than 20 degrees were omitted from refinement em_diffraction_stats.r_merge Rmerge value (percent) 19.8 em_diffraction_stats.r_sym Rsym value (percent) 24.4 em_diffraction_stats.id PRIMARY KEY 0 em_embedding Sugar embedding category 0 1 1 1 1 1 1 em_embeddingCategory This property indicates that datablock has a category holder em_embeddingCategory. em_embeddingCategory This property indicates that em_embeddingCategory. has a category em_embedding. em_embeddingItem Abstract datatype property for em_embedding items. reference_to_em_embedding cross-reference to em_embedding. referenced_by_em_embedding cross-reference from em_embedding. em_embedding.details Staining procedure used in the specimen preparation. The crystal suspension was injected into the lens of a drop of buffer containing 1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume of 1% glucose was then added and the solution thoroughly but gently mixed. The grid was then blotted, air dried, and frozen in LN2. em_embedding.material The embedding material. tannin and glucose em_embedding.specimen_id Foreign key relationship to the EM SPECIMEN category em_embedding.id PRIMARY KEY 0 em_entity_assembly Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. Example 1 - based on PDB entry 1C2W <VRPTx:em_entity_assemblyCategory> <VRPTx:em_entity_assembly id="1"> <VRPTx:name>50S Ribosomal Subunit</VRPTx:name> <VRPTx:parent_id>0</VRPTx:parent_id> <VRPTx:type>RIBOSOME</VRPTx:type> </VRPTx:em_entity_assembly> </VRPTx:em_entity_assemblyCategory> Example 2 - based on PDB entry 3IY7 <VRPTx:em_entity_assemblyCategory> <VRPTx:em_entity_assembly id="1"> <VRPTx:name>Fab fragment from MAb F interacting with feline panleukopenia virus (FPV)</VRPTx:name> <VRPTx:parent_id>0</VRPTx:parent_id> <VRPTx:type>COMPLEX</VRPTx:type> </VRPTx:em_entity_assembly> <VRPTx:em_entity_assembly id="2"> <VRPTx:name>feline panleukopenia virus</VRPTx:name> <VRPTx:parent_id>1</VRPTx:parent_id> <VRPTx:synonym>FPV</VRPTx:synonym> <VRPTx:type>VIRUS</VRPTx:type> </VRPTx:em_entity_assembly> <VRPTx:em_entity_assembly id="3"> <VRPTx:name>Fab fragment from Mab F</VRPTx:name> <VRPTx:parent_id>1</VRPTx:parent_id> <VRPTx:synonym>Fab</VRPTx:synonym> <VRPTx:type>COMPLEX</VRPTx:type> </VRPTx:em_entity_assembly> </VRPTx:em_entity_assemblyCategory> 0 1 0 1 0 1 0 1 1 1 0 1 0 1 1 1 0 1 0 1 0 1 1 em_entity_assemblyCategory This property indicates that datablock has a category holder em_entity_assemblyCategory. em_entity_assemblyCategory This property indicates that em_entity_assemblyCategory. has a category em_entity_assembly. em_entity_assemblyItem Abstract datatype property for em_entity_assembly items. reference_to_em_entity_assembly cross-reference to em_entity_assembly. referenced_by_em_entity_assembly cross-reference from em_entity_assembly. YES NO An indication if an assembly is contains a chimeric polymer em_entity_assembly.details Additional details about the sample or sample subcomponent. Fab fragment generated by proteolytic cleavage of LA2 IgG antibody. em_entity_assembly.entity_id_list Macromolecules associated with this component, if defined as comma separated list of entity ids (integers). 1,2,3,4 YES NO mutant flag em_entity_assembly.name The name of the sample or sample subcomponent. Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB 80S Ribosome bound to emetine messenger RNA initiation factor 2 GroEL antibody Fab fragment em_entity_assembly.number_of_copies number of copies em_entity_assembly.oligomeric_details Oligomeric details em_entity_assembly.parent_id The parent of this assembly. This data item is an internal category pointer to attribute id. in category em_entity_assembly By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero). NATURAL RECOMBINANT MULTIPLE SOURCES SYNTHETIC The type of source (e.g., natural source) for the component (sample or sample subcomponent) em_entity_assembly.synonym Alternative name of the component. FADV-1 em_entity_assembly.type The general type of the sample or sample subcomponent. em_entity_assembly.id PRIMARY KEY 0 em_entity_assembly_molwt Data items in this category record details about the molecular weight of an assembly component of the sample. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_entity_assembly_molwtCategory> <VRPTx:em_entity_assembly_molwt id="1"> <VRPTx:entity_assembly_id>1</VRPTx:entity_assembly_id> <VRPTx:units>MEGADALTONS</VRPTx:units> <VRPTx:value>30.5</VRPTx:value> </VRPTx:em_entity_assembly_molwt> </VRPTx:em_entity_assembly_molwtCategory> 1 1 0 1 0 1 0 1 1 em_entity_assembly_molwtCategory This property indicates that datablock has a category holder em_entity_assembly_molwtCategory. em_entity_assembly_molwtCategory This property indicates that em_entity_assembly_molwtCategory. has a category em_entity_assembly_molwt. em_entity_assembly_molwtItem Abstract datatype property for em_entity_assembly_molwt items. reference_to_em_entity_assembly_molwt cross-reference to em_entity_assembly_molwt. referenced_by_em_entity_assembly_molwt cross-reference from em_entity_assembly_molwt. em_entity_assembly_molwt.entity_assembly_id A reference to em_entity_assembly.id which uniquely identifies one sample or sample subcomponent of the imaged specimen. YES NO Identifies whether the given molecular weight was derived experimentally. MEGADALTONS KILODALTONS/NANOMETER Molecular weight units. em_entity_assembly_molwt.value The molecular weight of the sample or sample subcomponent 0.53 em_entity_assembly_molwt.id PRIMARY KEY 0 em_entity_assembly_naturalsource Data items in this category record taxonomic details about the natural source for EM assemblies and assembly components. Example 1 - <VRPTx:em_entity_assembly_naturalsourceCategory> <VRPTx:em_entity_assembly_naturalsource id="1"> <VRPTx:cellular_location xsi:nil="true" /> <VRPTx:entity_assembly_id>8333</VRPTx:entity_assembly_id> <VRPTx:ncbi_tax_id>Escherichia coli</VRPTx:ncbi_tax_id> <VRPTx:organ xsi:nil="true" /> <VRPTx:organelle>cytoplasm</VRPTx:organelle> <VRPTx:organism>K12</VRPTx:organism> <VRPTx:strain xsi:nil="true" /> <VRPTx:tissue xsi:nil="true" /> </VRPTx:em_entity_assembly_naturalsource> </VRPTx:em_entity_assembly_naturalsourceCategory> 0 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 0 1 0 1 1 em_entity_assembly_naturalsourceCategory This property indicates that datablock has a category holder em_entity_assembly_naturalsourceCategory. em_entity_assembly_naturalsourceCategory This property indicates that em_entity_assembly_naturalsourceCategory. has a category em_entity_assembly_naturalsource. em_entity_assembly_naturalsourceItem Abstract datatype property for em_entity_assembly_naturalsource items. reference_to_em_entity_assembly_naturalsource cross-reference to em_entity_assembly_naturalsource. referenced_by_em_entity_assembly_naturalsource cross-reference from em_entity_assembly_naturalsource. em_entity_assembly_naturalsource.cell The cell type from which the component was obtained. CHO HELA 3T3 em_entity_assembly_naturalsource.cellular_location The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane em_entity_assembly_naturalsource.details Additional details describing this natural source. em_entity_assembly_naturalsource.entity_assembly_id Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category. em_entity_assembly_naturalsource.ncbi_tax_id The NCBI taxonomy id for the natural organism source of the component. 10804 9606 em_entity_assembly_naturalsource.organ The organ of the organism from which the component was obtained. heart em_entity_assembly_naturalsource.organelle The organelle from which the component was obtained. Golgi Mitochondrion Cytoskeleton em_entity_assembly_naturalsource.organism The scientific name of the source organism for the component Homo sapiens Gallus gallus em_entity_assembly_naturalsource.strain The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly_naturalsource.tissue The tissue of the natural organism from which the component was obtained. Cartilage Liver Eye lens em_entity_assembly_naturalsource.id PRIMARY KEY 0 em_entity_assembly_recombinant Data items in this category record details about recombinant expression of the assembly or assembly component. Example 1 - <VRPTx:em_entity_assembly_recombinantCategory> <VRPTx:em_entity_assembly_recombinant id="1"> <VRPTx:entity_assembly_id>1</VRPTx:entity_assembly_id> <VRPTx:organism>Escherichia coli</VRPTx:organism> <VRPTx:plasmid>pET17c</VRPTx:plasmid> </VRPTx:em_entity_assembly_recombinant> </VRPTx:em_entity_assembly_recombinantCategory> 0 1 1 1 1 1 1 1 0 1 0 1 1 em_entity_assembly_recombinantCategory This property indicates that datablock has a category holder em_entity_assembly_recombinantCategory. em_entity_assembly_recombinantCategory This property indicates that em_entity_assembly_recombinantCategory. has a category em_entity_assembly_recombinant. em_entity_assembly_recombinantItem Abstract datatype property for em_entity_assembly_recombinant items. reference_to_em_entity_assembly_recombinant cross-reference to em_entity_assembly_recombinant. referenced_by_em_entity_assembly_recombinant cross-reference from em_entity_assembly_recombinant. em_entity_assembly_recombinant.cell The cell of the host organism from which the expressed component was obtained, if relevant. Potato root em_entity_assembly_recombinant.entity_assembly_id Pointer to the expressed component described in the EM ENTITY ASSEMBLY category. em_entity_assembly_recombinant.ncbi_tax_id The NCBI taxonomy id of the expression host used to produce the component. em_entity_assembly_recombinant.organism Expression system host organism used to produce the component. escherichia coli saccharomyces cerevisiae em_entity_assembly_recombinant.plasmid The plasmid used to produce the component in the expression system. pBR322 pMB9 em_entity_assembly_recombinant.strain The strain of the host organism from which the expresed component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly_recombinant.id PRIMARY KEY 0 em_entity_assembly_synthetic Data items in this category record taxonomic details about the synthetic source for EM assemblies and assembly components. Example 1 <VRPTx:em_entity_assembly_syntheticCategory> <VRPTx:em_entity_assembly_synthetic entity_assembly_id="1" id="1"> <VRPTx:cellular_location xsi:nil="true" /> <VRPTx:ncbi_tax_id>8333</VRPTx:ncbi_tax_id> <VRPTx:organ xsi:nil="true" /> <VRPTx:organelle xsi:nil="true" /> <VRPTx:organism>Escherichia coli</VRPTx:organism> <VRPTx:strain>K12</VRPTx:strain> <VRPTx:tissue xsi:nil="true" /> </VRPTx:em_entity_assembly_synthetic> </VRPTx:em_entity_assembly_syntheticCategory> 0 1 0 1 1 1 0 1 0 1 1 1 0 1 0 1 1 1 em_entity_assembly_syntheticCategory This property indicates that datablock has a category holder em_entity_assembly_syntheticCategory. em_entity_assembly_syntheticCategory This property indicates that em_entity_assembly_syntheticCategory. has a category em_entity_assembly_synthetic. em_entity_assembly_syntheticItem Abstract datatype property for em_entity_assembly_synthetic items. reference_to_em_entity_assembly_synthetic cross-reference to em_entity_assembly_synthetic. referenced_by_em_entity_assembly_synthetic cross-reference from em_entity_assembly_synthetic. em_entity_assembly_synthetic.cell The cell type from which the component was obtained. CHO HELA 3T3 em_entity_assembly_synthetic.cellular_location The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane em_entity_assembly_synthetic.ncbi_tax_id The NCBI taxonomy id for the synthetic organism source of the component. 10804 9606 em_entity_assembly_synthetic.organ The organ of the organism from which the component was obtained. heart em_entity_assembly_synthetic.organelle The organelle from which the component was obtained. Golgi Mitochondrion Cytoskeleton em_entity_assembly_synthetic.organism The scientific name of the source organism for the component Homo sapiens Gallus gallus em_entity_assembly_synthetic.strain The strain of the synthetic organism from which the component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly_synthetic.tissue The tissue of the synthetic organism from which the component was obtained. Cartilage Liver Eye lens em_entity_assembly_synthetic.entity_assembly_id Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category. em_entity_assembly_synthetic.id PRIMARY KEY 0 em_experiment Data items in the EM_EXPERIMENT category provide high-level classification of the EM experiment. Example 1 - based on PDB entry 1EG0 <VRPTx:em_experimentCategory> <VRPTx:em_experiment entry_id="1EG0"> <VRPTx:aggregation_state>PARTICLE</VRPTx:aggregation_state> <VRPTx:reconstruction_method>SINGLE PARTICLE</VRPTx:reconstruction_method> </VRPTx:em_experiment> </VRPTx:em_experimentCategory> 1 1 1 1 1 1 1 1 1 em_experimentCategory This property indicates that datablock has a category holder em_experimentCategory. em_experimentCategory This property indicates that em_experimentCategory. has a category em_experiment. em_experimentItem Abstract datatype property for em_experiment items. reference_to_em_experiment cross-reference to em_experiment. referenced_by_em_experiment cross-reference from em_experiment. 2D ARRAY 3D ARRAY HELICAL ARRAY FILAMENT PARTICLE TISSUE CELL The aggregation/assembly state of the imaged specimen. em_experiment.entity_assembly_id Foreign key to the EM_ENTITY_ASSEMBLY category em_experiment.id PRIMARY KEY SINGLE PARTICLE HELICAL CRYSTALLOGRAPHY SUBTOMOGRAM AVERAGING TOMOGRAPHY The reconstruction method used in the EM experiment. em_experiment.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 em_helical_entity Data items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component. 0 1 0 1 1 1 0 1 1 1 em_helical_entityCategory This property indicates that datablock has a category holder em_helical_entityCategory. em_helical_entityCategory This property indicates that em_helical_entityCategory. has a category em_helical_entity. em_helical_entityItem Abstract datatype property for em_helical_entity items. reference_to_em_helical_entity cross-reference to em_helical_entity. referenced_by_em_helical_entity cross-reference from em_helical_entity. em_helical_entity.angular_rotation_per_subunit The angular rotation per helical subunit in degrees. Negative values indicate left-handed helices; positive values indicate right handed helices. -34.616000 em_helical_entity.axial_rise_per_subunit The axial rise per subunit in the helical assembly. 17.400000 em_helical_entity.axial_symmetry Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1. C1 D2 C7 em_helical_entity.details Any other details regarding the helical assembly Dihedral symmetry em_helical_entity.id PRIMARY KEY em_helical_entity.image_processing_id This data item is a pointer to attribute id in category em_image_processing. 0 em_image_processing Data items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure. Example 1 - <VRPTx:em_image_processingCategory> <VRPTx:em_image_processing id="1" image_recording_id="1"> <VRPTx:details>The selected images were high-pass filtered and normalized</VRPTx:details> </VRPTx:em_image_processing> </VRPTx:em_image_processingCategory> 0 1 1 1 em_image_processingCategory This property indicates that datablock has a category holder em_image_processingCategory. em_image_processingCategory This property indicates that em_image_processingCategory. has a category em_image_processing. em_image_processingItem Abstract datatype property for em_image_processing items. reference_to_em_image_processing cross-reference to em_image_processing. referenced_by_em_image_processing cross-reference from em_image_processing. em_image_processing.details Method details. The selected images were high-pass filtered and normalized em_image_processing.id PRIMARY KEY em_image_processing.image_recording_id Foreign key to the EM_IMAGE_RECORDING 0 em_image_recording Data items in the EM_IMAGE_RECORDING category record details of the image recording (either film/microdensitometer or electronic detector) and parameters for image digitization. Example 1 - images collected on film <VRPTx:em_image_recordingCategory> <VRPTx:em_image_recording id="1" imaging_id="1"> <VRPTx:avg_electron_dose_per_image>0.9</VRPTx:avg_electron_dose_per_image> <VRPTx:film_or_detector_model>GENERIC FILM</VRPTx:film_or_detector_model> <VRPTx:num_diffraction_images>48</VRPTx:num_diffraction_images> </VRPTx:em_image_recording> </VRPTx:em_image_recordingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_image_recordingCategory This property indicates that datablock has a category holder em_image_recordingCategory. em_image_recordingCategory This property indicates that em_image_recordingCategory. has a category em_image_recording. em_image_recordingItem Abstract datatype property for em_image_recording items. reference_to_em_image_recording cross-reference to em_image_recording. referenced_by_em_image_recording cross-reference from em_image_recording. em_image_recording.average_exposure_time The average exposure time for each image. 2.0 em_image_recording.avg_electron_dose_per_image The electron dose received by the specimen per image (electrons per square angstrom). 30.0 em_image_recording.avg_electron_dose_per_subtomogram The average total electron dose received by the specimen for each subtomogram (electrons per square angstrom). em_image_recording.details Any additional details about image recording. Images were collected in movie-mode at 17 frames per second COUNTING INTEGRATING SUPER-RESOLUTION OTHER The detector mode used during image recording. em_image_recording.film_or_detector_model The detector type used for recording images. Usually film , CCD camera or direct electron detector. em_image_recording.num_diffraction_images The number of diffraction images collected. em_image_recording.num_grids_imaged Number of grids in the microscopy session em_image_recording.num_real_images The number of micrograph images collected. em_image_recording.id PRIMARY KEY em_image_recording.imaging_id This data item the id of the microscopy settings used in the imaging. 0 em_image_scans Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_image_scansCategory> <VRPTx:em_image_scans id="2"> <VRPTx:details xsi:nil="true" /> <VRPTx:entry_id>1DYL</VRPTx:entry_id> <VRPTx:number_digital_images>48</VRPTx:number_digital_images> <VRPTx:od_range xsi:nil="true" /> <VRPTx:quant_bit_size xsi:nil="true" /> <VRPTx:sampling_size xsi:nil="true" /> <VRPTx:scanner_model xsi:nil="true" /> </VRPTx:em_image_scans> </VRPTx:em_image_scansCategory> 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_image_scansCategory This property indicates that datablock has a category holder em_image_scansCategory. em_image_scansCategory This property indicates that em_image_scansCategory. has a category em_image_scans. em_image_scansItem Abstract datatype property for em_image_scans items. reference_to_em_image_scans cross-reference to em_image_scans. referenced_by_em_image_scans cross-reference from em_image_scans. em_image_scans.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_image_scans.details Any additional details about image recording. em_image_scans.dimension_height Height of scanned image, in pixels em_image_scans.dimension_width Width of scanned image, in pixels em_image_scans.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_image_scans.frames_per_image Total number of time-slice (movie) frames taken per image. 10 em_image_scans.number_digital_images The number of real images. em_image_scans.od_range The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light gray and OD=3 is opaque. 1.4 em_image_scans.quant_bit_size The number of bits per pixel. 8 em_image_scans.sampling_size The sampling step size (microns) set on the scanner. ZEISS SCAI EMIL 10 OPTRONICS PERKIN ELMER TEMSCAN EIKONIX IEEE 488 NIKON COOLSCAN NIKON SUPER COOLSCAN 9000 IMAGE SCIENCE PATCHWORK DENSITOMETER PRIMESCAN OTHER The scanner model. em_image_scans.used_frames_per_image Range of time-slice (movie) frames used for the reconstruction. 2-10 em_image_scans.id The value of attribute id in category em_image_scans must uniquely identify the images scanned. em_image_scans.image_recording_id Foreign key linked to _em_image_recording 0 em_imaging Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_imagingCategory> <VRPTx:em_imaging entry_id="1DYL" id="1"> <VRPTx:accelerating_voltage>200</VRPTx:accelerating_voltage> <VRPTx:calibrated_magnification xsi:nil="true" /> <VRPTx:date>1998-15-06</VRPTx:date> <VRPTx:details xsi:nil="true" /> <VRPTx:detector_distance xsi:nil="true" /> <VRPTx:electron_source>FEG</VRPTx:electron_source> <VRPTx:illumination_mode>bright field</VRPTx:illumination_mode> <VRPTx:microscope_model>FEI/PHILIPS CM200 FEG</VRPTx:microscope_model> <VRPTx:mode>low dose</VRPTx:mode> <VRPTx:nominal_cs>2.0</VRPTx:nominal_cs> <VRPTx:nominal_defocus_max>7600</VRPTx:nominal_defocus_max> <VRPTx:nominal_defocus_min>975</VRPTx:nominal_defocus_min> <VRPTx:nominal_magnification>50000</VRPTx:nominal_magnification> <VRPTx:recording_temperature_maximum xsi:nil="true" /> <VRPTx:recording_temperature_minimum xsi:nil="true" /> <VRPTx:specimen_holder_model>gatan 626-0300</VRPTx:specimen_holder_model> <VRPTx:specimen_holder_type>cryotransfer</VRPTx:specimen_holder_type> <VRPTx:temperature>95</VRPTx:temperature> <VRPTx:tilt_angle_max>0</VRPTx:tilt_angle_max> <VRPTx:tilt_angle_min>0</VRPTx:tilt_angle_min> </VRPTx:em_imaging> </VRPTx:em_imagingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 1 em_imagingCategory This property indicates that datablock has a category holder em_imagingCategory. em_imagingCategory This property indicates that em_imagingCategory. has a category em_imaging. em_imagingItem Abstract datatype property for em_imaging items. reference_to_em_imaging cross-reference to em_imaging. referenced_by_em_imaging cross-reference from em_imaging. em_imaging.accelerating_voltage A value of accelerating voltage (in kV) used for imaging. 300 NONE BASIC ZEMLIN TABLEAU COMA FREE OTHER The type of procedure used to align the microscope electron beam. em_imaging.astigmatism Astigmatism em_imaging.c2_aperture_diameter The open diameter of the c2 condenser lens, in microns. 100 em_imaging.calibrated_defocus_max The maximum calibrated defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 5000 em_imaging.calibrated_defocus_min The minimum calibrated defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 1200 em_imaging.calibrated_magnification The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. 61200 em_imaging.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. NITROGEN HELIUM Cryogen type used to maintain the specimen stage temperature during imaging in the microscope. em_imaging.date Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. 2001-05-08 em_imaging.details Any additional imaging details. Preliminary grid screening was performed manually. em_imaging.detector_distance The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. em_imaging.electron_beam_tilt_params Electron beam tilt params em_imaging.electron_source The source of electrons. The electron gun. FLOOD BEAM SPOT SCAN OTHER The mode of illumination. FEI MORGAGNI FEI POLARA 300 FEI TALOS ARCTICA FEI TECNAI 10 FEI TECNAI 12 FEI TECNAI 20 FEI TECNAI F20 FEI TECNAI F30 FEI TECNAI ARCTICA FEI TECNAI SPHERA FEI TECNAI SPIRIT FEI TITAN FEI TITAN KRIOS FEI/PHILIPS CM10 FEI/PHILIPS CM12 FEI/PHILIPS CM120T FEI/PHILIPS CM200FEG FEI/PHILIPS CM200FEG/SOPHIE FEI/PHILIPS CM200FEG/ST FEI/PHILIPS CM200FEG/UT FEI/PHILIPS CM200T FEI/PHILIPS CM300FEG/HE FEI/PHILIPS CM300FEG/ST FEI/PHILIPS CM300FEG/T FEI/PHILIPS EM400 FEI/PHILIPS EM420 HITACHI EF2000 HITACHI EF3000 HITACHI H7600 HITACHI HF2000 HITACHI HF3000 HITACHI H3000 UHVEM HITACHI H-9500SD JEOL 100B JEOL 100CX JEOL 1010 JEOL 1000EES JEOL 1200 JEOL 1200EX JEOL 1200EXII JEOL 1230 JEOL 1400 JEOL 1400/HR + YPS FEG JEOL 2000EX JEOL 2000EXII JEOL 2010 JEOL 2010F JEOL 2010HT JEOL 2010HC JEOL 2010UHR JEOL 2011 JEOL 2100 JEOL 2100F JEOL 2200FS JEOL 2200FSC JEOL 3000SFF JEOL 3100FEF JEOL 3100FFC JEOL 3200FS JEOL 3200FSC JEOL KYOTO-3000SFF JEOL 4000 JEOL 4000EX JEOL CRYO ARM 200 JEOL CRYO ARM 300 SIEMENS SULEIKA TFS GLACIOS TFS KRIOS TFS TALOS TFS TALOS F200C TFS TALOS L120C TFS TUNDRA ZEISS LEO912 ZEISS LIBRA120PLUS The name of the model of microscope. 4D-STEM BRIGHT FIELD DARK FIELD DIFFRACTION OTHER The mode of imaging. em_imaging.nominal_cs The spherical aberration coefficient (Cs) in millimeters, of the objective lens. 2.0 em_imaging.nominal_defocus_max The maximum defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 5000 em_imaging.nominal_defocus_min The minimum defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 1200 em_imaging.nominal_magnification The magnification indicated by the microscope readout. 60000 em_imaging.recording_temperature_maximum The specimen temperature maximum (kelvin) for the duration of imaging. 70 em_imaging.recording_temperature_minimum The specimen temperature minimum (kelvin) for the duration of imaging. em_imaging.residual_tilt Residual tilt of the electron beam (in miliradians) FEI TITAN KRIOS AUTOGRID HOLDER FISCHIONE 2550 FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER GATAN HELIUM GATAN LIQUID NITROGEN GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER HOME BUILD JEOL JEOL CRYOSPECPORTER JEOL 3200FSC CRYOHOLDER PHILIPS ROTATION HOLDER SIDE ENTRY, EUCENTRIC OTHER The name of the model of specimen holder used during imaging. em_imaging.specimen_holder_type The type of specimen holder used during imaging. cryo em_imaging.specimen_id Foreign key to the EM_SPECIMEN category em_imaging.temperature The mean specimen stage temperature (kelvin) during imaging in the microscope. 70 em_imaging.tilt_angle_max The maximum angle at which the specimen was tilted to obtain recorded images. 70 em_imaging.tilt_angle_min The minimum angle at which the specimen was tilted to obtain recorded images. -70 em_imaging.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_imaging.id PRIMARY KEY 0 em_imaging_optics Description of a few specialist optics apparatus Example 1 - <VRPTx:em_imaging_opticsCategory> <VRPTx:em_imaging_optics id="1" imaging_id="1"> <VRPTx:chr_aberration_corrector>CEOS manufactured Cc corrector</VRPTx:chr_aberration_corrector> <VRPTx:energyfilter_lower>0</VRPTx:energyfilter_lower> <VRPTx:energyfilter_name>FEI</VRPTx:energyfilter_name> <VRPTx:energyfilter_upper>15</VRPTx:energyfilter_upper> </VRPTx:em_imaging_optics> </VRPTx:em_imaging_opticsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_imaging_opticsCategory This property indicates that datablock has a category holder em_imaging_opticsCategory. em_imaging_opticsCategory This property indicates that em_imaging_opticsCategory. has a category em_imaging_optics. em_imaging_opticsItem Abstract datatype property for em_imaging_optics items. reference_to_em_imaging_optics cross-reference to em_imaging_optics. referenced_by_em_imaging_optics cross-reference from em_imaging_optics. em_imaging_optics.chr_aberration_corrector Chromatic aberration corrector information CEOS manufactured Cc corrector em_imaging_optics.details Details on the use of the phase plate Phase plate evolution varied between different microscopes used to collect data but positions were shifted once phase evolution progressed past 120 degrees. em_imaging_optics.energyfilter_lower The energy filter range lower value in electron volts (eV) set by spectrometer. 0 em_imaging_optics.energyfilter_name The type of energy filter spectrometer GIF 200 em_imaging_optics.energyfilter_slit_width The energy filter range slit width in electron volts (eV). 35 em_imaging_optics.energyfilter_upper The energy filter range upper value in electron volts (eV) set by spectrometer. 15 em_imaging_optics.phase_plate Phase plate information ZERNIKE PHASE PLATE em_imaging_optics.sph_aberration_corrector Spherical aberration corrector information Microscope was modified with a Cs corrector with two hexapole elements. em_imaging_optics.id PRIMARY KEY em_imaging_optics.imaging_id Foreign key to the EM IMAGING category 0 em_particle_selection Data items in this category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_particle_selectionCategory> <VRPTx:em_particle_selection id="1" image_processing_id="1"> <VRPTx:details xsi:nil="true" /> <VRPTx:method>INTERACTIVE</VRPTx:method> <VRPTx:num_particles_selected>5267</VRPTx:num_particles_selected> </VRPTx:em_particle_selection> </VRPTx:em_particle_selectionCategory> 0 1 0 1 0 1 0 1 1 1 em_particle_selectionCategory This property indicates that datablock has a category holder em_particle_selectionCategory. em_particle_selectionCategory This property indicates that em_particle_selectionCategory. has a category em_particle_selection. em_particle_selectionItem Abstract datatype property for em_particle_selection items. reference_to_em_particle_selection cross-reference to em_particle_selection. referenced_by_em_particle_selection cross-reference from em_particle_selection. em_particle_selection.details Additional detail such as description of filters used, if selection was manual or automated, and/or template details. negative monitor contrast facilitated particle picking em_particle_selection.method The method used for selecting particles particles picked interactively from monitor em_particle_selection.num_particles_selected The number of particles selected from the projection set of images. 840 em_particle_selection.reference_model Description of reference model used for particle selection em_particle_selection.id PRIMARY KEY em_particle_selection.image_processing_id The value of attribute image_processing_id in category em_particle_selection points to the EM_IMAGE_PROCESSING category. 0 em_single_particle_entity Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type. Example 1 - <VRPTx:em_single_particle_entityCategory> <VRPTx:em_single_particle_entity id="1" image_processing_id="1"> <VRPTx:point_symmetry>I</VRPTx:point_symmetry> </VRPTx:em_single_particle_entity> </VRPTx:em_single_particle_entityCategory> 1 1 0 1 1 1 em_single_particle_entityCategory This property indicates that datablock has a category holder em_single_particle_entityCategory. em_single_particle_entityCategory This property indicates that em_single_particle_entityCategory. has a category em_single_particle_entity. em_single_particle_entityItem Abstract datatype property for em_single_particle_entity items. reference_to_em_single_particle_entity cross-reference to em_single_particle_entity. referenced_by_em_single_particle_entity cross-reference from em_single_particle_entity. em_single_particle_entity.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_single_particle_entity.point_symmetry Point symmetry symbol, either Cn, Dn, T, O, or I em_single_particle_entity.id PRIMARY KEY em_single_particle_entity.image_processing_id Pointer to attribute id in category em_image_processing. 0 em_software Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. Example 1 - <VRPTx:em_softwareCategory> <VRPTx:em_software id="1"> <VRPTx:category>IMAGE ACQUISITION</VRPTx:category> <VRPTx:details xsi:nil="true" /> <VRPTx:name>Leginon</VRPTx:name> <VRPTx:version>1.3</VRPTx:version> </VRPTx:em_software> <VRPTx:em_software id="2"> <VRPTx:category>PARTICLE SELECTION</VRPTx:category> <VRPTx:details xsi:nil="true" /> <VRPTx:name>X3D</VRPTx:name> <VRPTx:version xsi:nil="true" /> </VRPTx:em_software> <VRPTx:em_software id="3"> <VRPTx:category>BACKGROUND MASKING</VRPTx:category> <VRPTx:details xsi:nil="true" /> <VRPTx:name>bsoft</VRPTx:name> <VRPTx:version>1.1</VRPTx:version> </VRPTx:em_software> <VRPTx:em_software id="4"> <VRPTx:category>RECONSTRUCTION</VRPTx:category> <VRPTx:details>em3dr2 -low 20</VRPTx:details> <VRPTx:name>EM2DR2</VRPTx:name> <VRPTx:version>3.2</VRPTx:version> </VRPTx:em_software> <VRPTx:em_software id="5"> <VRPTx:category>EULER ASSIGNMENT</VRPTx:category> <VRPTx:details xsi:nil="true" /> <VRPTx:name>erandom</VRPTx:name> <VRPTx:version xsi:nil="true" /> </VRPTx:em_software> <VRPTx:em_software id="6"> <VRPTx:category>CTF CORRECTION</VRPTx:category> <VRPTx:details xsi:nil="true" /> <VRPTx:name>bctf</VRPTx:name> <VRPTx:version xsi:nil="true" /> </VRPTx:em_software> <VRPTx:em_software id="7"> <VRPTx:category>MODEL FITTING</VRPTx:category> <VRPTx:details xsi:nil="true" /> <VRPTx:name>chimera</VRPTx:name> <VRPTx:version>1.6</VRPTx:version> </VRPTx:em_software> </VRPTx:em_softwareCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 em_softwareCategory This property indicates that datablock has a category holder em_softwareCategory. em_softwareCategory This property indicates that em_softwareCategory. has a category em_software. em_softwareItem Abstract datatype property for em_software items. reference_to_em_software cross-reference to em_software. referenced_by_em_software cross-reference from em_software. IMAGE ACQUISITION PARTICLE SELECTION VOLUME SELECTION CLASSIFICATION MASKING RECONSTRUCTION INITIAL EULER ASSIGNMENT FINAL EULER ASSIGNMENT CTF CORRECTION LAYERLINE INDEXING DIFFRACTION INDEXING MODEL FITTING MODEL REFINEMENT SERIES ALIGNMENT MOLECULAR REPLACEMENT LATTICE DISTORTION CORRECTION SYMMETRY DETERMINATION CRYSTALLOGRAPHY MERGING EWALD SPHERE CORRECTION OTHER The purpose of the software. em_software.details Details about the software used. EMAN2 e2boxer.py was used to automatically select particle images. em_software.fitting_id Pointer to attribute id in category em_3d_fitting in the EM_3D_FITTING category. em_software.image_processing_id Pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. em_software.imaging_id Pointer to attribute id in category em_imaging in the EM_IMAGING category. em_software.name The name of the software package used, e.g., RELION. Depositors are strongly encouraged to provide a value in this field. EMAN Imagic Spider Bsoft UCSF-Chimera em_software.version The version of the software. 9.03 2.1 em_software.id PRIMARY KEY 0 em_specimen Data items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy. Example 1 - based on PDB 2FL8 <VRPTx:em_specimenCategory> <VRPTx:em_specimen experiment_id="1" id="1"> <VRPTx:embedding_applied>NO</VRPTx:embedding_applied> <VRPTx:shadowing_applied>NO</VRPTx:shadowing_applied> <VRPTx:staining_applied>NO</VRPTx:staining_applied> <VRPTx:vitrification_applied>YES</VRPTx:vitrification_applied> </VRPTx:em_specimen> </VRPTx:em_specimenCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 em_specimenCategory This property indicates that datablock has a category holder em_specimenCategory. em_specimenCategory This property indicates that em_specimenCategory. has a category em_specimen. em_specimenItem Abstract datatype property for em_specimen items. reference_to_em_specimen cross-reference to em_specimen. referenced_by_em_specimen cross-reference from em_specimen. em_specimen.concentration The concentration (in milligrams per milliliter, mg/ml) of the complex in the sample. 1.35 em_specimen.details A description of any additional details of the specimen preparation. This sample was monodisperse. Au was deposited at a 30 degree angle to 15 nm thickness. Colloidal gold particles were deposited by dipping into dilute solution. The specimen was frozen at high pressure using the bal-tec hpm 010 instrument. The embedded sample was sectioned at 100 K to 50 nm final thickness. YES NO 'YES' indicates that the specimen has been embedded. YES NO 'YES' indicates that the specimen has been shadowed. YES NO 'YES' indicates that the specimen has been stained. YES NO 'YES' indicates that the specimen was vitrified by cryopreservation. em_specimen.experiment_id Pointer to attribute id in category em_experiment. em_specimen.id PRIMARY KEY 0 em_staining Staining category Example 1 - <VRPTx:em_stainingCategory> <VRPTx:em_staining id="1"> <VRPTx:material>Uranyl Acetate</VRPTx:material> <VRPTx:specimen_id>1</VRPTx:specimen_id> <VRPTx:type>NEGATIVE</VRPTx:type> </VRPTx:em_staining> </VRPTx:em_stainingCategory> 0 1 1 1 1 1 1 1 1 em_stainingCategory This property indicates that datablock has a category holder em_stainingCategory. em_stainingCategory This property indicates that em_stainingCategory. has a category em_staining. em_stainingItem Abstract datatype property for em_staining items. reference_to_em_staining cross-reference to em_staining. referenced_by_em_staining cross-reference from em_staining. em_staining.details Staining procedure used in the specimen preparation. Negatively stained EM specimens were prepared using a carbon-sandwich technique and uranyl-formate stain. em_staining.material The staining material. Uranyl Acetate em_staining.specimen_id Foreign key relationship to the EM SPECIMEN category NEGATIVE POSITIVE NONE Type of staining. em_staining.id PRIMARY KEY 0 em_virus_entity Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_virus_entityCategory> <VRPTx:em_virus_entity entity_assembly_id="1" id="1"> <VRPTx:empty>NO</VRPTx:empty> <VRPTx:enveloped>YES</VRPTx:enveloped> <VRPTx:virus_host_category>VERTERBRATES</VRPTx:virus_host_category> <VRPTx:virus_isolate>STRAIN</VRPTx:virus_isolate> <VRPTx:virus_type>VIRUS</VRPTx:virus_type> </VRPTx:em_virus_entity> </VRPTx:em_virus_entityCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_virus_entityCategory This property indicates that datablock has a category holder em_virus_entityCategory. em_virus_entityCategory This property indicates that em_virus_entityCategory. has a category em_virus_entity. em_virus_entityItem Abstract datatype property for em_virus_entity items. reference_to_em_virus_entity cross-reference to em_virus_entity. referenced_by_em_virus_entity cross-reference from em_virus_entity. em_virus_entity.details Additional details about this virus entity YES NO Flag to indicate if the virus is empty or not. YES NO Flag to indicate if the virus is enveloped or not. em_virus_entity.virus_host_category The host category description for the virus. ALGAE ARCHAEA BACTERIA(EUBACTERIA) FUNGI INVERTEBRATES PLANTAE (HIGHER PLANTS) PROTOZOA VERTEBRATES STRAIN SEROTYPE SEROCOMPLEX SUBSPECIES SPECIES OTHER The isolate from which the virus was obtained. VIRION SATELLITE PRION VIROID VIRUS-LIKE PARTICLE The type of virus. em_virus_entity.entity_assembly_id This data item is a pointer to attribute id in category em_virus_entity in the ENTITY_ASSEMBLY category. em_virus_entity.id PRIMARY KEY 0 em_virus_natural_host Data items in this category record details of a virus entity. 0 1 0 1 0 1 1 1 em_virus_natural_hostCategory This property indicates that datablock has a category holder em_virus_natural_hostCategory. em_virus_natural_hostCategory This property indicates that em_virus_natural_hostCategory. has a category em_virus_natural_host. em_virus_natural_hostItem Abstract datatype property for em_virus_natural_host items. reference_to_em_virus_natural_host cross-reference to em_virus_natural_host. referenced_by_em_virus_natural_host cross-reference from em_virus_natural_host. em_virus_natural_host.ncbi_tax_id The NCBI taxonomy id for the natural host organism of the virus 9606 9031 em_virus_natural_host.organism The host organism from which the virus was isolated. Homo sapiens Gallus gallus em_virus_natural_host.strain The strain of the host organism from which the virus was obtained, if relevant. DH5a BMH 71-18 em_virus_natural_host.entity_assembly_id Pointer to attribute id in category em_entity_assembly. em_virus_natural_host.id PRIMARY KEY 0 em_virus_shell Data items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number. Example 1 - Bluetongue Virus <VRPTx:em_virus_shellCategory> <VRPTx:em_virus_shell entity_assembly_id="1" id="1"> <VRPTx:diameter>348</VRPTx:diameter> <VRPTx:name>VP7 layer</VRPTx:name> <VRPTx:triangulation>13</VRPTx:triangulation> </VRPTx:em_virus_shell> <VRPTx:em_virus_shell entity_assembly_id="1" id="2"> <VRPTx:diameter>348</VRPTx:diameter> <VRPTx:name>VP3 layer</VRPTx:name> <VRPTx:triangulation>2</VRPTx:triangulation> </VRPTx:em_virus_shell> </VRPTx:em_virus_shellCategory> 0 1 0 1 0 1 1 1 em_virus_shellCategory This property indicates that datablock has a category holder em_virus_shellCategory. em_virus_shellCategory This property indicates that em_virus_shellCategory. has a category em_virus_shell. em_virus_shellItem Abstract datatype property for em_virus_shell items. reference_to_em_virus_shell cross-reference to em_virus_shell. referenced_by_em_virus_shell cross-reference from em_virus_shell. em_virus_shell.diameter The value of the diameter (in angstroms) for this virus shell. 524.0 em_virus_shell.name The name for this virus shell. em_virus_shell.triangulation The triangulation number, T, describes the organization of subunits within an icosahedron. T is defined as T= h^2 + h*k + k^2, where h and k are positive integers that define the position of the five-fold vertex on the original hexagonal net. 27 em_virus_shell.entity_assembly_id The value of attribute entity_assembly_id in category em_virus_shell is a pointer to attribute id in category em_entity_assembly category. em_virus_shell.id PRIMARY KEY 0 em_virus_synthetic Data items in this category record details of a synthetic virus entity. 0 1 0 1 0 1 1 1 em_virus_syntheticCategory This property indicates that datablock has a category holder em_virus_syntheticCategory. em_virus_syntheticCategory This property indicates that em_virus_syntheticCategory. has a category em_virus_synthetic. em_virus_syntheticItem Abstract datatype property for em_virus_synthetic items. reference_to_em_virus_synthetic cross-reference to em_virus_synthetic. referenced_by_em_virus_synthetic cross-reference from em_virus_synthetic. em_virus_synthetic.ncbi_tax_id The NCBI taxonomy ID of the host species from which the virus was isolated 10804 9606 em_virus_synthetic.organism The host organism from which the virus was isolated. Homo sapiens Gallus gallus em_virus_synthetic.strain The strain of the host organism from which the virus was obtained, if relevant. DH5a BMH 71-18 em_virus_synthetic.entity_assembly_id Pointer to attribute id in category em_entity_assembly. em_virus_synthetic.id PRIMARY KEY 0 em_vitrification Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_vitrificationCategory> <VRPTx:em_vitrification id="1"> <VRPTx:cryogen_name>ETHANE</VRPTx:cryogen_name> <VRPTx:details> SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.</VRPTx:details> <VRPTx:entry_id>1DYL</VRPTx:entry_id> <VRPTx:humidity>90</VRPTx:humidity> <VRPTx:instrument xsi:nil="true" /> <VRPTx:method>PLUNGE VITRIFICATION</VRPTx:method> <VRPTx:temp>95</VRPTx:temp> <VRPTx:time_resolved_state xsi:nil="true" /> </VRPTx:em_vitrification> </VRPTx:em_vitrificationCategory> 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 em_vitrificationCategory This property indicates that datablock has a category holder em_vitrificationCategory. em_vitrificationCategory This property indicates that em_vitrificationCategory. has a category em_vitrification. em_vitrificationItem Abstract datatype property for em_vitrification items. reference_to_em_vitrification cross-reference to em_vitrification. referenced_by_em_vitrification cross-reference from em_vitrification. em_vitrification.chamber_temperature The temperature (in kelvin) of the sample just prior to vitrification. 298 em_vitrification.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. HELIUM NITROGEN PROPANE ETHANE ETHANE-PROPANE METHANE FREON 22 FREON 12 OTHER This is the name of the cryogen. em_vitrification.details Any additional details relating to vitrification. Vitrification carried out in argon atmosphere. em_vitrification.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_vitrification.humidity Relative humidity (%) of air surrounding the specimen just prior to vitrification. 90 CRYOSOL VITROJET EMS-002 RAPID IMMERSION FREEZER FEI VITROBOT MARK I FEI VITROBOT MARK II FEI VITROBOT MARK III FEI VITROBOT MARK IV GATAN CRYOPLUNGE 3 HOMEMADE PLUNGER LEICA PLUNGER LEICA EM GP LEICA EM CPC LEICA KF80 REICHERT-JUNG PLUNGER SPOTITON SPT LABTECH CHAMELEON ZEISS PLUNGE FREEZER CRYOBOX The type of instrument used in the vitrification process. em_vitrification.method The procedure for vitrification. plunge freezing em_vitrification.temp The vitrification temperature (in kelvin), e.g., temperature of the plunge instrument cryogen bath. 90 em_vitrification.time_resolved_state The length of time after an event effecting the sample that vitrification was induced and a description of the event. plunge 30 msec after spraying with effector em_vitrification.id PRIMARY KEY em_vitrification.specimen_id This data item is a pointer to attribute id in category em_specimen 0 em_volume_selection Volume selection in image processing Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <VRPTx:em_volume_selectionCategory> <VRPTx:em_volume_selection id="1" image_processing_id="1"> <VRPTx:details xsi:nil="true" /> <VRPTx:method>INTERACTIVE</VRPTx:method> <VRPTx:num_volumes_extracted>5267</VRPTx:num_volumes_extracted> </VRPTx:em_volume_selection> </VRPTx:em_volume_selectionCategory> 0 1 0 1 1 1 1 1 0 1 1 1 em_volume_selectionCategory This property indicates that datablock has a category holder em_volume_selectionCategory. em_volume_selectionCategory This property indicates that em_volume_selectionCategory. has a category em_volume_selection. em_volume_selectionItem Abstract datatype property for em_volume_selection items. reference_to_em_volume_selection cross-reference to em_volume_selection. referenced_by_em_volume_selection cross-reference from em_volume_selection. em_volume_selection.details Any additional details used for selecting volumes. negative monitor contrast facilitated volume picking em_volume_selection.method The method used for selecting volumes. volumes picked interactively em_volume_selection.num_tomograms The number of tomograms used in the extraction/selection 20 em_volume_selection.num_volumes_extracted The number of volumes selected from the projection set of images. 840 em_volume_selection.reference_model Description of reference model used for volume selection em_volume_selection.id PRIMARY KEY em_volume_selection.image_processing_id The value of attribute image_processing_id in category em_volume_selection points to the EM_IMAGE_PROCESSING category. 0 entity Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:entityCategory> <VRPTx:entity id="1"> <VRPTx:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</VRPTx:details> <VRPTx:formula_weight>10916</VRPTx:formula_weight> <VRPTx:type>polymer</VRPTx:type> </VRPTx:entity> <VRPTx:entity id="2"> <VRPTx:details xsi:nil="true" /> <VRPTx:formula_weight>762</VRPTx:formula_weight> <VRPTx:type>non-polymer</VRPTx:type> </VRPTx:entity> <VRPTx:entity id="3"> <VRPTx:details xsi:nil="true" /> <VRPTx:formula_weight>18</VRPTx:formula_weight> <VRPTx:type>water</VRPTx:type> </VRPTx:entity> </VRPTx:entityCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entityCategory This property indicates that datablock has a category holder entityCategory. entityCategory This property indicates that entityCategory. has a category entity. entityItem Abstract datatype property for entity items. reference_to_entity cross-reference to entity. referenced_by_entity cross-reference from entity. entity.details A description of special aspects of the entity. entity.formula_weight Formula mass in daltons of the entity. entity.pdbx_description A description of the entity. Corresponds to the compound name in the PDB format. DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3') PROFLAVINE PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1)) entity.pdbx_ec Enzyme Commission (EC) number(s) 2.7.7.7 entity.pdbx_formula_weight_exptl Experimentally determined formula mass in daltons of the entity MASS SPEC Method used to determine attribute pdbx_formula_weight_exptl in category entity. MASS SPEC entity.pdbx_fragment Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN entity.pdbx_modification Description(s) of any chemical or post-translational modifications entity.pdbx_mutation Details about any entity mutation(s). Y31H DEL(298-323) entity.pdbx_number_of_molecules A place holder for the number of molecules of the entity in the entry. 1 2 3 entity.pdbx_parent_entity_id An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source. 1 2 3 nat man syn The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. polymer non-polymer macrolide water branched Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. entity.id The value of attribute id in category entity must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. 0 entity_name_com Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:entity_name_comCategory> <VRPTx:entity_name_com entity_id="1"> <VRPTx:name>HIV-1 protease monomer</VRPTx:name> </VRPTx:entity_name_com> <VRPTx:entity_name_com entity_id="1"> <VRPTx:name>HIV-1 PR monomer</VRPTx:name> </VRPTx:entity_name_com> <VRPTx:entity_name_com entity_id="2"> <VRPTx:name>acetyl-pepstatin</VRPTx:name> </VRPTx:entity_name_com> <VRPTx:entity_name_com entity_id="2"> <VRPTx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</VRPTx:name> </VRPTx:entity_name_com> <VRPTx:entity_name_com entity_id="3"> <VRPTx:name>water</VRPTx:name> </VRPTx:entity_name_com> </VRPTx:entity_name_comCategory> 0 1 0 1 1 entity_name_comCategory This property indicates that datablock has a category holder entity_name_comCategory. entity_name_comCategory This property indicates that entity_name_comCategory. has a category entity_name_com. entity_name_comItem Abstract datatype property for entity_name_com items. reference_to_entity_name_com cross-reference to entity_name_com. referenced_by_entity_name_com cross-reference from entity_name_com. entity_name_com.name A common name for the entity. HIV protease monomer hemoglobin alpha chain 2-fluoro-1,4-dichloro benzene arbutin UNIPROT AUTHOR Provides the provenance of the name in the attribute name in category entity_name_com field entity_name_com.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_name_sys Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:entity_name_sysCategory> <VRPTx:entity_name_sys entity_id="1"> <VRPTx:name>EC 3.4.23.16</VRPTx:name> </VRPTx:entity_name_sys> <VRPTx:entity_name_sys entity_id="2"> <VRPTx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</VRPTx:name> </VRPTx:entity_name_sys> <VRPTx:entity_name_sys entity_id="3"> <VRPTx:name>water</VRPTx:name> </VRPTx:entity_name_sys> </VRPTx:entity_name_sysCategory> 0 1 0 1 1 entity_name_sysCategory This property indicates that datablock has a category holder entity_name_sysCategory. entity_name_sysCategory This property indicates that entity_name_sysCategory. has a category entity_name_sys. entity_name_sysItem Abstract datatype property for entity_name_sys items. reference_to_entity_name_sys cross-reference to entity_name_sys. referenced_by_entity_name_sys cross-reference from entity_name_sys. entity_name_sys.name The systematic name for the entity. hydroquinone-beta-D-pyranoside EC 2.1.1.1 2-fluoro-1,4-dichlorobenzene entity_name_sys.system The system used to generate the systematic name of the entity. Chemical Abstracts conventions enzyme convention Sigma catalog entity_name_sys.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_poly Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:entity_polyCategory> <VRPTx:entity_poly entity_id="1"> <VRPTx:nstd_chirality>no</VRPTx:nstd_chirality> <VRPTx:nstd_linkage>no</VRPTx:nstd_linkage> <VRPTx:nstd_monomer>no</VRPTx:nstd_monomer> <VRPTx:type>polypeptide(L)</VRPTx:type> <VRPTx:type_details xsi:nil="true" /> </VRPTx:entity_poly> </VRPTx:entity_polyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entity_polyCategory This property indicates that datablock has a category holder entity_polyCategory. entity_polyCategory This property indicates that entity_polyCategory. has a category entity_poly. entity_polyItem Abstract datatype property for entity_poly items. reference_to_entity_poly cross-reference to entity_poly. referenced_by_entity_poly cross-reference from entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in attribute type in category entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by attribute type in category entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer that is not considered standard. entity_poly.number_of_monomers The number of monomers in the polymer. entity_poly.pdbx_seq_one_letter_code Sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymer, each residue is represented by the code of its individual type. A cyclic polymer is represented in linear sequence from the chosen start to end. A for Alanine or Adenosine-5'-monophosphate C for Cysteine or Cytidine-5'-monophosphate D for Aspartic acid E for Glutamic acid F for Phenylalanine G for Glycine or Guanosine-5'-monophosphate H for Histidine I for Isoleucine or Inosinic Acid L for Leucine K for Lysine M for Methionine N for Asparagine or Unknown ribonucleotide O for Pyrrolysine P for Proline Q for Glutamine R for Arginine S for Serine T for Threonine U for Selenocysteine or Uridine-5'-monophosphate V for Valine W for Tryptophan Y for Tyrosine (DA) for 2'-deoxyadenosine-5'-monophosphate (DC) for 2'-deoxycytidine-5'-monophosphate (DG) for 2'-deoxyguanosine-5'-monophosphate (DT) for Thymidine-5'-monophosphate (MSE) for Selenomethionine (SEP) for Phosphoserine (TPO) for Phosphothreonine (PTR) for Phosphotyrosine (PCA) for Pyroglutamic acid (UNK) for Unknown amino acid (ACE) for Acetylation cap (NH2) for Amidation cap (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD entity_poly.pdbx_seq_one_letter_code_can Canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in attribute pdbx_seq_one_letter_code in category entity_poly. Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in attribute mon_nstd_parent_comp_id in category chem_comp, or by letter 'X' if parent is not specified. Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. For modifications with several parent amino acids, all corresponding parent amino acid codes will be listed (ex. chromophores). MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD entity_poly.pdbx_seq_one_letter_code_sample For cases in which the sample and model sequence differ this item contains the sample chemical sequence expressed as string of one-letter amino acid codes. Modified may be include as 'X' or with their 3-letter codes in parentheses. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other entity_poly.pdbx_strand_id The PDB strand/chain id(s) corresponding to this polymer entity. A B A,B,C entity_poly.pdbx_target_identifier For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database. 356560 polypeptide(D) polypeptide(L) polydeoxyribonucleotide polyribonucleotide polydeoxyribonucleotide/polyribonucleotide hybrid cyclic-pseudo-peptide peptide nucleic acid other The type of the polymer. entity_poly.type_details A description of special aspects of the polymer type. monomer Ala 16 is a D-amino acid the oligomer contains alternating RNA and DNA units entity_poly.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_poly_seq Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:entity_poly_seqCategory> <VRPTx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></VRPTx:entity_poly_seq> <VRPTx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></VRPTx:entity_poly_seq> </VRPTx:entity_poly_seqCategory> 0 1 1 1 1 entity_poly_seqCategory This property indicates that datablock has a category holder entity_poly_seqCategory. entity_poly_seqCategory This property indicates that entity_poly_seqCategory. has a category entity_poly_seq. entity_poly_seqItem Abstract datatype property for entity_poly_seq items. reference_to_entity_poly_seq cross-reference to entity_poly_seq. referenced_by_entity_poly_seq cross-reference from entity_poly_seq. no n yes y A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. entity_poly_seq.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. entity_poly_seq.mon_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. entity_poly_seq.num The value of attribute num in category entity_poly_seq must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. 0 entry There is only one item in the ENTRY category, attribute id in category entry. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:entryCategory> <VRPTx:entry id="5HVP"></VRPTx:entry> </VRPTx:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:entryCategory> <VRPTx:entry id="TOZ"></VRPTx:entry> </VRPTx:entryCategory> 1 entryCategory This property indicates that datablock has a category holder entryCategory. entryCategory This property indicates that entryCategory. has a category entry. entryItem Abstract datatype property for entry items. reference_to_entry cross-reference to entry. referenced_by_entry cross-reference from entry. entry.id The value of attribute id in category entry identifies the data block. Note that this item need not be a number; it can be any unique identifier. 0 entry_link Data items in the ENTRY_LINK category record the relationships between the current data block identified by attribute id in category entry and other data blocks within the current file which may be referenced in the current data block. Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <VRPTx:entry_linkCategory> <VRPTx:entry_link entry_id="KSE_TEXT" id="KSE_COM"> <VRPTx:details>experimental data common to ref./mod. structures</VRPTx:details> </VRPTx:entry_link> <VRPTx:entry_link entry_id="KSE_TEXT" id="KSE_REF"> <VRPTx:details>reference structure</VRPTx:details> </VRPTx:entry_link> <VRPTx:entry_link entry_id="KSE_TEXT" id="KSE_MOD"> <VRPTx:details>modulated structure</VRPTx:details> </VRPTx:entry_link> </VRPTx:entry_linkCategory> 0 1 1 1 entry_linkCategory This property indicates that datablock has a category holder entry_linkCategory. entry_linkCategory This property indicates that entry_linkCategory. has a category entry_link. entry_linkItem Abstract datatype property for entry_link items. reference_to_entry_link cross-reference to entry_link. referenced_by_entry_link cross-reference from entry_link. entry_link.details A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. entry_link.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. entry_link.id The value of attribute id in category entry_link identifies a data block related to the current data block. 0 exptl Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <VRPTx:exptlCategory> <VRPTx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction"> <VRPTx:absorpt_coefficient_mu>1.22</VRPTx:absorpt_coefficient_mu> <VRPTx:absorpt_correction_T_max>0.896</VRPTx:absorpt_correction_T_max> <VRPTx:absorpt_correction_T_min>0.802</VRPTx:absorpt_correction_T_min> <VRPTx:absorpt_correction_type>integration</VRPTx:absorpt_correction_type> <VRPTx:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</VRPTx:absorpt_process_details> <VRPTx:crystals_number>1</VRPTx:crystals_number> <VRPTx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</VRPTx:details> <VRPTx:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</VRPTx:method_details> </VRPTx:exptl> </VRPTx:exptlCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 exptlCategory This property indicates that datablock has a category holder exptlCategory. exptlCategory This property indicates that exptlCategory. has a category exptl. exptlItem Abstract datatype property for exptl items. reference_to_exptl cross-reference to exptl. referenced_by_exptl cross-reference from exptl. exptl.absorpt_coefficient_mu The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. exptl.absorpt_correction_T_max The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. exptl.absorpt_correction_T_min The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. analytical cylinder empirical gaussian integration multi-scan none numerical psi-scan refdelf sphere The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. exptl.absorpt_process_details Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. Tompa analytical exptl.crystals_number The total number of crystals used in the measurement of intensities. exptl.details Any special information about the experimental work prior to the intensity measurement. See also attribute preparation in category exptl_crystal. exptl.method_details A description of special aspects of the experimental method. 29 structures minimized average structure exptl.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION INFRARED SPECTROSCOPY EPR FLUORESCENCE TRANSFER THEORETICAL MODEL The method used in the experiment. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION 0 ndb_struct_conf_na Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry. 0 1 1 1 ndb_struct_conf_naCategory This property indicates that datablock has a category holder ndb_struct_conf_naCategory. ndb_struct_conf_naCategory This property indicates that ndb_struct_conf_naCategory. has a category ndb_struct_conf_na. ndb_struct_conf_naItem Abstract datatype property for ndb_struct_conf_na items. reference_to_ndb_struct_conf_na cross-reference to ndb_struct_conf_na. referenced_by_ndb_struct_conf_na cross-reference from ndb_struct_conf_na. ndb_struct_conf_na.feature_count This data item counts the number of occurences of this feature in this entry. ndb_struct_conf_na.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. double helix a-form double helix b-form double helix z-form double helix other right-handed double helix triple helix quadruple helix parallel strands internal loop bulge loop tetraloop hairpin loop two-way junction three-way junction four-way junction mismatched base pair This data item identifies a secondary structure feature of this entry. 0 ndb_struct_na_base_pair Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions. <VRPTx:ndb_struct_na_base_pairCategory> <VRPTx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="1" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="8" j_symmetry="7_555" model_number="1"> <VRPTx:buckle>-5.523</VRPTx:buckle> <VRPTx:opening>-3.291</VRPTx:opening> <VRPTx:propeller>-6.752</VRPTx:propeller> <VRPTx:shear>-0.396</VRPTx:shear> <VRPTx:stagger>-0.018</VRPTx:stagger> <VRPTx:stretch>-0.156</VRPTx:stretch> </VRPTx:ndb_struct_na_base_pair> <VRPTx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="2" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="7" j_symmetry="7_555" model_number="1"> <VRPTx:buckle>-4.727</VRPTx:buckle> <VRPTx:opening>2.311</VRPTx:opening> <VRPTx:propeller>-9.765</VRPTx:propeller> <VRPTx:shear>-0.094</VRPTx:shear> <VRPTx:stagger>-0.334</VRPTx:stagger> <VRPTx:stretch>-0.220</VRPTx:stretch> </VRPTx:ndb_struct_na_base_pair> <VRPTx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="3" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="6" j_symmetry="7_555" model_number="1"> <VRPTx:buckle>-6.454</VRPTx:buckle> <VRPTx:opening>-1.181</VRPTx:opening> <VRPTx:propeller>-12.575</VRPTx:propeller> <VRPTx:shear>-0.285</VRPTx:shear> <VRPTx:stagger>0.008</VRPTx:stagger> <VRPTx:stretch>-0.239</VRPTx:stretch> </VRPTx:ndb_struct_na_base_pair> </VRPTx:ndb_struct_na_base_pairCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 ndb_struct_na_base_pairCategory This property indicates that datablock has a category holder ndb_struct_na_base_pairCategory. ndb_struct_na_base_pairCategory This property indicates that ndb_struct_na_base_pairCategory. has a category ndb_struct_na_base_pair. ndb_struct_na_base_pairItem Abstract datatype property for ndb_struct_na_base_pair items. reference_to_ndb_struct_na_base_pair cross-reference to ndb_struct_na_base_pair. referenced_by_ndb_struct_na_base_pair cross-reference from ndb_struct_na_base_pair. ndb_struct_na_base_pair.buckle The value of the base pair buckle parameter. ndb_struct_na_base_pair.hbond_type_12 Base pair classification of Westhoff and Leontis. ndb_struct_na_base_pair.hbond_type_28 Base pair classification of Saenger cWW tWW cWH cHW tWH tHW cWS cSW tWS tSW cHH tHH cHS cSH tHS tSH cSS tSS Base pair classification of Leontis and Westhof. The Leontis-Westhof classification system annotates basepairs according to the interacting edge used by each base (Watson-Crick, Hoogsteen, or Sugar), and glycosidic bond orientation (cis, trans). For six of twelve classes, the correct Leontis-Westhof notation depends upon the order (i,j) of the identified nucleotides. Leontis NB and Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512. https://doi.org/10.1017/s1355838201002515 Replacement for category item attribute hbond_type_12 in category ndb_struct_na_base_pair. The older item encodes the 12 classes by a numerical index, without identifying the interacting edges used by each base in nucleotides i,j. ndb_struct_na_base_pair.i_PDB_ins_code Describes the PDB insertion code of the i-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_auth_asym_id Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_auth_seq_id Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_PDB_ins_code Describes the PDB insertion code of the j-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_auth_asym_id Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_auth_seq_id Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.opening The value of the base pair opening parameter. ndb_struct_na_base_pair.pair_name Text label for this base pair. ndb_struct_na_base_pair.pair_number Sequential number of pair in the pair sequence. ndb_struct_na_base_pair.propeller The value of the base pair propeller parameter. ndb_struct_na_base_pair.shear The value of the base pair shear parameter. ndb_struct_na_base_pair.stagger The value of the base pair stagger parameter. ndb_struct_na_base_pair.stretch The value of the base pair stretch parameter. ndb_struct_na_base_pair.i_label_asym_id Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_label_comp_id Describes the component id of the i-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_label_seq_id Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_symmetry Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the base pair. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair.j_label_asym_id Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_label_comp_id Describes the component id of the j-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_label_seq_id Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_symmetry Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the base pair. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair.model_number Describes the model number of the base pair. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. 0 ndb_struct_na_base_pair_step Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions. <VRPTx:ndb_struct_na_base_pair_stepCategory> <VRPTx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="1" i_label_seq_id_2="2" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="8" j_label_seq_id_2="7" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1"> <VRPTx:rise>3.339</VRPTx:rise> <VRPTx:roll>9.755</VRPTx:roll> <VRPTx:shift>0.369</VRPTx:shift> <VRPTx:slide>-1.414</VRPTx:slide> <VRPTx:tilt>3.056</VRPTx:tilt> <VRPTx:twist>33.530</VRPTx:twist> </VRPTx:ndb_struct_na_base_pair_step> <VRPTx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="2" i_label_seq_id_2="3" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="7" j_label_seq_id_2="6" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1"> <VRPTx:rise>3.371</VRPTx:rise> <VRPTx:roll>6.725</VRPTx:roll> <VRPTx:shift>0.176</VRPTx:shift> <VRPTx:slide>-1.672</VRPTx:slide> <VRPTx:tilt>-1.176</VRPTx:tilt> <VRPTx:twist>30.004</VRPTx:twist> </VRPTx:ndb_struct_na_base_pair_step> </VRPTx:ndb_struct_na_base_pair_stepCategory> 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ndb_struct_na_base_pair_stepCategory This property indicates that datablock has a category holder ndb_struct_na_base_pair_stepCategory. ndb_struct_na_base_pair_stepCategory This property indicates that ndb_struct_na_base_pair_stepCategory. has a category ndb_struct_na_base_pair_step. ndb_struct_na_base_pair_stepItem Abstract datatype property for ndb_struct_na_base_pair_step items. reference_to_ndb_struct_na_base_pair_step cross-reference to ndb_struct_na_base_pair_step. referenced_by_ndb_struct_na_base_pair_step cross-reference from ndb_struct_na_base_pair_step. ndb_struct_na_base_pair_step.helical_rise The value of the base pair step helical rise parameter. ndb_struct_na_base_pair_step.helical_twist The value of the base pair step helical twist parameter. ndb_struct_na_base_pair_step.i_PDB_ins_code_1 Describes the PDB insertion code of the i-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_PDB_ins_code_2 Describes the PDB insertion code of the i-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_asym_id_1 Describes the author's asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_asym_id_2 Describes the author's asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_seq_id_1 Describes the author's sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_seq_id_2 Describes the author's sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.inclination The value of the base pair step inclination parameter. ndb_struct_na_base_pair_step.j_PDB_ins_code_1 Describes the PDB insertion code of the j-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_PDB_ins_code_2 Describes the PDB insertion code of the j-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_asym_id_1 Describes the author's asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_asym_id_2 Describes the author's asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_seq_id_1 Describes the author's sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_seq_id_2 Describes the author's sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.rise The value of the base pair step rise parameter. ndb_struct_na_base_pair_step.roll The value of the base pair step roll parameter. ndb_struct_na_base_pair_step.shift The value of the base pair step shift parameter. ndb_struct_na_base_pair_step.slide The value of the base pair step slide parameter. ndb_struct_na_base_pair_step.step_name The text name of this step. ndb_struct_na_base_pair_step.step_number The sequence number of this step in the step sequence. ndb_struct_na_base_pair_step.tilt The value of the base pair step tilt parameter. ndb_struct_na_base_pair_step.tip The value of the base pair step twist parameter. ndb_struct_na_base_pair_step.twist The value of the base pair step twist parameter. ndb_struct_na_base_pair_step.x_displacement The value of the base pair step X displacement parameter. ndb_struct_na_base_pair_step.y_displacement The value of the base pair step Y displacement parameter. ndb_struct_na_base_pair_step.i_label_asym_id_1 Describes the asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_asym_id_2 Describes the asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_comp_id_1 Describes the component id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_comp_id_2 Describes the component id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_seq_id_1 Describes the sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_seq_id_2 Describes the sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_symmetry_1 Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the first base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.i_symmetry_2 Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the second base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.j_label_asym_id_1 Describes the asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_asym_id_2 Describes the asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_comp_id_1 Describes the component id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_comp_id_2 Describes the component id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_seq_id_1 Describes the sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_seq_id_2 Describes the sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_symmetry_1 Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the first base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.j_symmetry_2 Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the second base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.model_number Describes the model number of the base pair step. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. 0 pdbx_audit_author Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <VRPTx:pdbx_audit_authorCategory> <VRPTx:pdbx_audit_author ordinal="1"> <VRPTx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</VRPTx:address> <VRPTx:name>Fitzgerald, Paula M.D.</VRPTx:name> </VRPTx:pdbx_audit_author> <VRPTx:pdbx_audit_author ordinal="2"> <VRPTx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</VRPTx:address> <VRPTx:name>McKeever, Brian M.</VRPTx:name> </VRPTx:pdbx_audit_author> <VRPTx:pdbx_audit_author ordinal="3"> <VRPTx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</VRPTx:address> <VRPTx:name>Van Middlesworth, J.F.</VRPTx:name> </VRPTx:pdbx_audit_author> <VRPTx:pdbx_audit_author ordinal="4"> <VRPTx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</VRPTx:address> <VRPTx:name>Springer, James P.</VRPTx:name> </VRPTx:pdbx_audit_author> </VRPTx:pdbx_audit_authorCategory> 0 1 1 1 1 pdbx_audit_authorCategory This property indicates that datablock has a category holder pdbx_audit_authorCategory. pdbx_audit_authorCategory This property indicates that pdbx_audit_authorCategory. has a category pdbx_audit_author. pdbx_audit_authorItem Abstract datatype property for pdbx_audit_author items. reference_to_pdbx_audit_author cross-reference to pdbx_audit_author. referenced_by_pdbx_audit_author cross-reference from pdbx_audit_author. pdbx_audit_author.address The address of an author of this data block. If there are multiple authors, attribute address in category pdbx_audit_author is looped with attribute name in category pdbx_audit_author. Department Institute Street City and postcode COUNTRY pdbx_audit_author.name The name of an author of this data block. If there are multiple authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A pdbx_audit_author.ordinal A unique sequential integer identifier for each author. 1 2 3 0 pdbx_audit_revision_category Data items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <VRPTx:pdbx_audit_revision_categoryCategory> <VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <VRPTx:category>audit_author</VRPTx:category> </VRPTx:pdbx_audit_revision_category> <VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="2" revision_ordinal="1"> <VRPTx:category>citation</VRPTx:category> </VRPTx:pdbx_audit_revision_category> <VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="3" revision_ordinal="1"> <VRPTx:category>citation_author</VRPTx:category> </VRPTx:pdbx_audit_revision_category> <VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="4" revision_ordinal="2"> <VRPTx:category>citation</VRPTx:category> </VRPTx:pdbx_audit_revision_category> </VRPTx:pdbx_audit_revision_categoryCategory> 1 1 1 1 1 pdbx_audit_revision_categoryCategory This property indicates that datablock has a category holder pdbx_audit_revision_categoryCategory. pdbx_audit_revision_categoryCategory This property indicates that pdbx_audit_revision_categoryCategory. has a category pdbx_audit_revision_category. pdbx_audit_revision_categoryItem Abstract datatype property for pdbx_audit_revision_category items. reference_to_pdbx_audit_revision_category cross-reference to pdbx_audit_revision_category. referenced_by_pdbx_audit_revision_category cross-reference from pdbx_audit_revision_category. pdbx_audit_revision_category.category The category updated in the pdbx_audit_revision_category record. audit_author citation Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_category.ordinal A unique identifier for the pdbx_audit_revision_category record. 1 pdbx_audit_revision_category.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_revision_details Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records. Example 1 - <VRPTx:pdbx_audit_revision_detailsCategory> <VRPTx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <VRPTx:provider>repository</VRPTx:provider> <VRPTx:type>Initial release</VRPTx:type> </VRPTx:pdbx_audit_revision_details> <VRPTx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="2" revision_ordinal="7"> <VRPTx:description>Remodeling of inhibitor</VRPTx:description> <VRPTx:provider>author</VRPTx:provider> <VRPTx:type>Coordinate replacement</VRPTx:type> </VRPTx:pdbx_audit_revision_details> </VRPTx:pdbx_audit_revision_detailsCategory> 0 1 0 1 0 1 0 1 1 1 1 pdbx_audit_revision_detailsCategory This property indicates that datablock has a category holder pdbx_audit_revision_detailsCategory. pdbx_audit_revision_detailsCategory This property indicates that pdbx_audit_revision_detailsCategory. has a category pdbx_audit_revision_details. pdbx_audit_revision_detailsItem Abstract datatype property for pdbx_audit_revision_details items. reference_to_pdbx_audit_revision_details cross-reference to pdbx_audit_revision_details. referenced_by_pdbx_audit_revision_details cross-reference from pdbx_audit_revision_details. pdbx_audit_revision_details.description Additional details describing the revision. pdbx_audit_revision_details.details Further details describing the revision. repository author The provider of the revision. repository Initial release Coordinate replacement Obsolete Remediation A type classification of the revision Initial release Structure model NMR restraints NMR shifts Structure factors The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_details.ordinal A unique identifier for the pdbx_audit_revision_details record. 1 pdbx_audit_revision_details.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_revision_group Data items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 - <VRPTx:pdbx_audit_revision_groupCategory> <VRPTx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="1" revision_ordinal="2"> <VRPTx:group>citation</VRPTx:group> </VRPTx:pdbx_audit_revision_group> <VRPTx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="2" revision_ordinal="3"> <VRPTx:group>sample</VRPTx:group> </VRPTx:pdbx_audit_revision_group> </VRPTx:pdbx_audit_revision_groupCategory> 1 1 1 1 1 pdbx_audit_revision_groupCategory This property indicates that datablock has a category holder pdbx_audit_revision_groupCategory. pdbx_audit_revision_groupCategory This property indicates that pdbx_audit_revision_groupCategory. has a category pdbx_audit_revision_group. pdbx_audit_revision_groupItem Abstract datatype property for pdbx_audit_revision_group items. reference_to_pdbx_audit_revision_group cross-reference to pdbx_audit_revision_group. referenced_by_pdbx_audit_revision_group cross-reference from pdbx_audit_revision_group. Advisory Atomic model Author supporting evidence Data collection Data processing Database references Derived calculations Experimental data Experimental preparation Initial release Non-polymer description Other Polymer sequence Refinement description Structure summary Source and taxonomy Version format compliance The collection of categories updated with this revision. citation Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_group.ordinal A unique identifier for the pdbx_audit_revision_group record. 1 pdbx_audit_revision_group.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_revision_history Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry. Example 1 - <VRPTx:pdbx_audit_revision_historyCategory> <VRPTx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="1"> <VRPTx:major_revision>1</VRPTx:major_revision> <VRPTx:minor_revision>0</VRPTx:minor_revision> <VRPTx:revision_date>2017-03-01</VRPTx:revision_date> </VRPTx:pdbx_audit_revision_history> <VRPTx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="2"> <VRPTx:major_revision>1</VRPTx:major_revision> <VRPTx:minor_revision>1</VRPTx:minor_revision> <VRPTx:revision_date>2017-03-08</VRPTx:revision_date> </VRPTx:pdbx_audit_revision_history> </VRPTx:pdbx_audit_revision_historyCategory> 1 1 1 1 1 1 1 1 pdbx_audit_revision_historyCategory This property indicates that datablock has a category holder pdbx_audit_revision_historyCategory. pdbx_audit_revision_historyCategory This property indicates that pdbx_audit_revision_historyCategory. has a category pdbx_audit_revision_history. pdbx_audit_revision_historyItem Abstract datatype property for pdbx_audit_revision_history items. reference_to_pdbx_audit_revision_history cross-reference to pdbx_audit_revision_history. referenced_by_pdbx_audit_revision_history cross-reference from pdbx_audit_revision_history. pdbx_audit_revision_history.major_revision The major version number of deposition release. 1 pdbx_audit_revision_history.minor_revision The minor version number of deposition release. 1 pdbx_audit_revision_history.revision_date The release date of the revision 2017-03-08 Structure model NMR restraints NMR shifts Structure factors The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_history.ordinal A unique identifier for the pdbx_audit_revision_history record. 1 0 pdbx_audit_revision_item Data items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <VRPTx:pdbx_audit_revision_itemCategory> <VRPTx:pdbx_audit_revision_item data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <VRPTx:item>_atom_site.type_symbol</VRPTx:item> </VRPTx:pdbx_audit_revision_item> </VRPTx:pdbx_audit_revision_itemCategory> 1 1 1 1 1 pdbx_audit_revision_itemCategory This property indicates that datablock has a category holder pdbx_audit_revision_itemCategory. pdbx_audit_revision_itemCategory This property indicates that pdbx_audit_revision_itemCategory. has a category pdbx_audit_revision_item. pdbx_audit_revision_itemItem Abstract datatype property for pdbx_audit_revision_item items. reference_to_pdbx_audit_revision_item cross-reference to pdbx_audit_revision_item. referenced_by_pdbx_audit_revision_item cross-reference from pdbx_audit_revision_item. pdbx_audit_revision_item.item A high level explanation the author has provided for submitting a revision. _atom_site.type_symbol Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_item.ordinal A unique identifier for the pdbx_audit_revision_item record. 1 pdbx_audit_revision_item.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_bond_distance_limits This category provides a table of upper and lower distance limits used as criteria in determining covalent bonds. The table is organized by atom type pairs. Example 1 - Abbreviated bond distance limit table <VRPTx:pdbx_bond_distance_limitsCategory> <VRPTx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Ag"> <VRPTx:lower_limit>1.85</VRPTx:lower_limit> <VRPTx:upper_limit>2.70</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Ag"> <VRPTx:lower_limit>1.85</VRPTx:lower_limit> <VRPTx:upper_limit>2.70</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Ag"> <VRPTx:lower_limit>2.00</VRPTx:lower_limit> <VRPTx:upper_limit>3.00</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="Al" atom_type_2="H"> <VRPTx:lower_limit>1.35</VRPTx:lower_limit> <VRPTx:upper_limit>1.65</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="As" atom_type_2="H"> <VRPTx:lower_limit>1.20</VRPTx:lower_limit> <VRPTx:upper_limit>1.60</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Au"> <VRPTx:lower_limit>1.80</VRPTx:lower_limit> <VRPTx:upper_limit>2.80</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Au"> <VRPTx:lower_limit>1.80</VRPTx:lower_limit> <VRPTx:upper_limit>2.80</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Au"> <VRPTx:lower_limit>1.80</VRPTx:lower_limit> <VRPTx:upper_limit>3.00</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="B" atom_type_2="B"> <VRPTx:lower_limit>1.45</VRPTx:lower_limit> <VRPTx:upper_limit>1.95</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="C" atom_type_2="B"> <VRPTx:lower_limit>1.20</VRPTx:lower_limit> <VRPTx:upper_limit>1.85</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> <VRPTx:pdbx_bond_distance_limits atom_type_1="F" atom_type_2="B"> <VRPTx:lower_limit>1.20</VRPTx:lower_limit> <VRPTx:upper_limit>1.75</VRPTx:upper_limit> </VRPTx:pdbx_bond_distance_limits> </VRPTx:pdbx_bond_distance_limitsCategory> 1 1 1 1 1 1 pdbx_bond_distance_limitsCategory This property indicates that datablock has a category holder pdbx_bond_distance_limitsCategory. pdbx_bond_distance_limitsCategory This property indicates that pdbx_bond_distance_limitsCategory. has a category pdbx_bond_distance_limits. pdbx_bond_distance_limitsItem Abstract datatype property for pdbx_bond_distance_limits items. reference_to_pdbx_bond_distance_limits cross-reference to pdbx_bond_distance_limits. referenced_by_pdbx_bond_distance_limits cross-reference from pdbx_bond_distance_limits. pdbx_bond_distance_limits.lower_limit The lower bond distance limit. pdbx_bond_distance_limits.upper_limit The upper bond distance limit. pdbx_bond_distance_limits.atom_type_1 The first atom type defining the bond C N P pdbx_bond_distance_limits.atom_type_2 The first atom type defining the bond C N P 0 pdbx_branch_scheme The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities. Example 1 - <VRPTx:pdbx_branch_schemeCategory> <VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="NAG" num="1"> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_mon_id>NAG</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>1592</VRPTx:auth_seq_num> <VRPTx:hetero>n</VRPTx:hetero> <VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id> <VRPTx:pdb_mon_id>NAG</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>1</VRPTx:pdb_seq_num> </VRPTx:pdbx_branch_scheme> <VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="GAL" num="2"> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_mon_id>GAL</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>1591</VRPTx:auth_seq_num> <VRPTx:hetero>n</VRPTx:hetero> <VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id> <VRPTx:pdb_mon_id>GAL</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>2</VRPTx:pdb_seq_num> </VRPTx:pdbx_branch_scheme> <VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="3"> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_mon_id>FUC</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>1590</VRPTx:auth_seq_num> <VRPTx:hetero>n</VRPTx:hetero> <VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id> <VRPTx:pdb_mon_id>FUC</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>3</VRPTx:pdb_seq_num> </VRPTx:pdbx_branch_scheme> <VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="4"> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_mon_id>FUC</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>1593</VRPTx:auth_seq_num> <VRPTx:hetero>n</VRPTx:hetero> <VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id> <VRPTx:pdb_mon_id>FUC</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>4</VRPTx:pdb_seq_num> </VRPTx:pdbx_branch_scheme> </VRPTx:pdbx_branch_schemeCategory> 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 pdbx_branch_schemeCategory This property indicates that datablock has a category holder pdbx_branch_schemeCategory. pdbx_branch_schemeCategory This property indicates that pdbx_branch_schemeCategory. has a category pdbx_branch_scheme. pdbx_branch_schemeItem Abstract datatype property for pdbx_branch_scheme items. reference_to_pdbx_branch_scheme cross-reference to pdbx_branch_scheme. referenced_by_pdbx_branch_scheme cross-reference from pdbx_branch_scheme. pdbx_branch_scheme.auth_asym_id This data item is a pointer to attribute pdbx_auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.auth_mon_id This data item is a pointer to attribute pdbx_auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.auth_seq_num This data item is a pointer to attribute pdbx_auth_seq_id in category atom_site in the ATOM_SITE category. no n yes y A flag to indicate whether this monomer in the entity is heterogeneous in sequence. pdbx_branch_scheme.pdb_asym_id This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.pdb_ins_code This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.pdb_mon_id This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.pdb_seq_num This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 pdbx_branch_scheme.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. pdbx_branch_scheme.mon_id This data item is a pointer to attribute label_comp_id in category atom_site in the PDBX_ENTITY_BRANCH_LIST category. pdbx_branch_scheme.num This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. 0 pdbx_coordinate_model The details of the composition of the coordinate model. Example 1 - <VRPTx:pdbx_coordinate_modelCategory> <VRPTx:pdbx_coordinate_model asym_id="A"> <VRPTx:type>CA ATOMS ONLY</VRPTx:type> </VRPTx:pdbx_coordinate_model> <VRPTx:pdbx_coordinate_model asym_id="B"> <VRPTx:type>CA ATOMS ONLY</VRPTx:type> </VRPTx:pdbx_coordinate_model> <VRPTx:pdbx_coordinate_model asym_id="X"> <VRPTx:type>P ATOMS ONLY</VRPTx:type> </VRPTx:pdbx_coordinate_model> <VRPTx:pdbx_coordinate_model asym_id="Y"> <VRPTx:type>P ATOMS ONLY</VRPTx:type> </VRPTx:pdbx_coordinate_model> </VRPTx:pdbx_coordinate_modelCategory> 1 1 1 pdbx_coordinate_modelCategory This property indicates that datablock has a category holder pdbx_coordinate_modelCategory. pdbx_coordinate_modelCategory This property indicates that pdbx_coordinate_modelCategory. has a category pdbx_coordinate_model. pdbx_coordinate_modelItem Abstract datatype property for pdbx_coordinate_model items. reference_to_pdbx_coordinate_model cross-reference to pdbx_coordinate_model. referenced_by_pdbx_coordinate_model cross-reference from pdbx_coordinate_model. CA ATOMS ONLY P ATOMS ONLY A classification of the composition of the coordinate model. CA ATOMS ONLY P ATOMS ONLY pdbx_coordinate_model.asym_id A reference to attribute id in category struct_asym. 1 A 0 pdbx_database_related Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry. <VRPTx:pdbx_database_relatedCategory> <VRPTx:pdbx_database_related content_type="native structure" db_id="1ABC" db_name="PDB"></VRPTx:pdbx_database_related> </VRPTx:pdbx_database_relatedCategory> 0 1 1 1 1 pdbx_database_relatedCategory This property indicates that datablock has a category holder pdbx_database_relatedCategory. pdbx_database_relatedCategory This property indicates that pdbx_database_relatedCategory. has a category pdbx_database_related. pdbx_database_relatedItem Abstract datatype property for pdbx_database_related items. reference_to_pdbx_database_related cross-reference to pdbx_database_related. referenced_by_pdbx_database_related cross-reference from pdbx_database_related. pdbx_database_related.details A description of the related entry. 1ABC contains the same protein complexed with Netropsin. minimized average structure representative structure ensemble derivative structure native structure associated EM volume other EM volume focused EM volume consensus EM volume associated NMR restraints associated structure factors associated SAS data protein target sequence and/or protocol data split re-refinement complete structure unspecified other The identifying content type of the related entry. minimized average structure representative structure ensemble derivative structure native structure associated EM volume other EM volume associated NMR restraints associated structure factors associated SAS data protein target sequence and/or protocol data split re-refinement complete structure unspecified other pdbx_database_related.db_id The identifying code in the related database. 1ABC BDL001 BIOISIS BMCD BMRB EMDB NDB PDB PDB-Dev SASBDB TargetDB TargetTrack The name of the database containing the related entry. PDB - Protein Databank NDB - Nucleic Acid Database BMRB - BioMagResBank EMDB - Electron Microscopy Database BMCD - Biological Macromolecule Crystallization Database TargetTrack - Target Registration and Protocol Database SASBDB - Small Angle Scattering Biological Data Bank 0 pdbx_database_status These are internal RCSB records to keep track of data processing and status of the entry. <VRPTx:pdbx_database_statusCategory> <VRPTx:pdbx_database_status entry_id="1ABC"> <VRPTx:deposit_site>RCSB</VRPTx:deposit_site> <VRPTx:process_site>RCSB</VRPTx:process_site> <VRPTx:status_code>REL</VRPTx:status_code> </VRPTx:pdbx_database_status> </VRPTx:pdbx_database_statusCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_database_statusCategory This property indicates that datablock has a category holder pdbx_database_statusCategory. pdbx_database_statusCategory This property indicates that pdbx_database_statusCategory. has a category pdbx_database_status. pdbx_database_statusItem Abstract datatype property for pdbx_database_status items. reference_to_pdbx_database_status cross-reference to pdbx_database_status. referenced_by_pdbx_database_status cross-reference from pdbx_database_status. Y N This code indicates whether the entry belongs to Structural Genomics Project. Y NDB RCSB PDBE PDBJ BMRB BNL PDBC The site where the file was deposited. NDB RCSB PDBE PDBJ BMRB BNL PDBC CAPRI CASP CASD-NMR FoldIt GPCR Dock D3R RNA-Puzzles The methods development category in which this entry has been placed. CASP CASD-NMR Y N A flag indicating that the entry is compatible with the PDB format. A value of 'N' indicates that the no PDB format data file is corresponding to this entry is available in the PDB archive. Y NDB RCSB PDBE PDBJ BNL PDBC The site where the file was deposited. NDB RCSB PDBE PDBJ BNL PDBC pdbx_database_status.recvd_initial_deposition_date The date of initial deposition. (The first message for deposition has been received.) 1983-02-21 PROC WAIT REL HOLD HPUB REFI OBS WDRN AUTH POLC REPL AUCO TRSF RMVD DEL REV UPD BIB Code for status of file. REL HPUB PROC WAIT AUTH POLC REPL AUCO REL HOLD HPUB OBS RMVD WDRN Code for status of chemical shift data file. PROC = Processing in progress WAIT = Awaiting author approval REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted WDRN = Entry has been withdrawn by depositor PROC WAIT REL HOLD HPUB OBS WDRN AUTH POLC REPL AUCO RMVD Code for status of NMR constraints file. PROC = To be processed REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted WDRN = Entry has been withdrawn by depositor WAIT = Awaiting author approval PROC WAIT AUCO AUTH POLC REPL REL HOLD HPUB OBS RMVD WDRN Code for status of unified NMR data file. PROC = Processing in progress WAIT = Awaiting author approval REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted WDRN = Entry has been withdrawn by depositor PROC WAIT REL HOLD HPUB OBS WDRN AUTH POLC REPL RMVD Code for status of structure factor file. PROC = To be processed REL = Released HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted WDRN = Entry has been withdrawn by depositor WAIT = Awaiting author approval pdbx_database_status.validation_created_date The date of wwPDB validation information created. 2017-02-12 pdbx_database_status.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_dcc_density Data items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...). 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_dcc_densityCategory This property indicates that datablock has a category holder pdbx_dcc_densityCategory. pdbx_dcc_densityCategory This property indicates that pdbx_dcc_densityCategory. has a category pdbx_dcc_density. pdbx_dcc_densityItem Abstract datatype property for pdbx_dcc_density items. reference_to_pdbx_dcc_density cross-reference to pdbx_dcc_density. referenced_by_pdbx_dcc_density cross-reference from pdbx_dcc_density. pdbx_dcc_density.B_babinet One of the scale factors (B0) used in the bulk solvent correction (from REFMAC). Babinet bulk solvent model: KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2)) Simple solvent model: KB = K0*exp(-B0*s^2) (i.e. K1=0) See also '_pdbx_dcc_density.B_solvent', '_pdbx_dcc_density.K_solvent'. pdbx_dcc_density.B_solvent One of the scale factors (B1) used in the bulk solvent correction (from REFMAC). Babinet bulk solvent model: KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2)) Simple solvent model: KB = K0*exp(-B0*s^2) (i.e. K1=0) See also '_pdbx_dcc_density.B_babinet', '_pdbx_dcc_density.K_babinet'. pdbx_dcc_density.B_wilson The estimated B factor from the structure factor file by the Wilson plot (from Xtriage). pdbx_dcc_density.B_wilson_scale The scale factor for calculating the B factor by the Wilson plot (from Xtriage). pdbx_dcc_density.Biso_max The maximum isotropic B factor reported in the model file. pdbx_dcc_density.Biso_mean The occupancy weighted mean isotropic B factor reported in the model file. pdbx_dcc_density.Biso_min The minimum isotropic B factor reported in the model file. pdbx_dcc_density.Bmean-Bwilson The difference between the isotropic B factor and the Bfators from Wilson plot. pdbx_dcc_density.Cruickshank_dpi_xyz The DPI on the model determined by REFMAC. pdbx_dcc_density.DCC_version The version of the DCC program. pdbx_dcc_density.I_over_sigI_diff The difference of the <I/SigmaI> in the last two points of the plot of <I/SigmaI> vs resolution (expected to be negative). pdbx_dcc_density.I_over_sigI_mean The overall mean value of <I/SigmaI> for the reflections. pdbx_dcc_density.I_over_sigI_resh The <I/SigmaI> at the highest resolution bin calculated by Xtriage. pdbx_dcc_density.K_babinet One of the scale factors (K0) used in the bulk solvent correction (from REFMAC). Babinet bulk solvent model: KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2)) Simple solvent model: KB = K0*exp(-B0*s^2) (i.e. K1=0) See also '_pdbx_dcc_density.B_solvent', '_pdbx_dcc_density.K_solvent'. pdbx_dcc_density.K_solvent One of the scale factors (K1) used in the bulk solvent correction (from REFMAC). Babinet bulk solvent model: KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2)) Simple solvent model: KB = K0*exp(-B0*s^2) (i.e. K1=0) See also '_pdbx_dcc_density.B_babinet', '_pdbx_dcc_density.K_babinet'. pdbx_dcc_density.Matthew_coeff The Matthew coefficient. pdbx_dcc_density.Padilla-Yeates_L2_mean Value of <L^2> calculated by Xtriage using acentric reflections. (untwinned: 0.333; perfect twin: 0.200). pdbx_dcc_density.Padilla-Yeates_L2_mean_pointless Value of <L^2> calculated by Pointless using acentric reflections. (untwinned: 0.333; perfect twin: 0.200). pdbx_dcc_density.Padilla-Yeates_L_mean Value of <|L|> calculated by Xtriage using acentric reflections. (untwinned: 0.500; perfect twin: 0.375). pdbx_dcc_density.R_value_R_free The Rfree reported in the model file. pdbx_dcc_density.R_value_R_work The Rwork reported in the model file. pdbx_dcc_density.Rfree-Rwork The difference between reported Rfree and reported Rwork. pdbx_dcc_density.TLS_refinement_reported Whether TLS was used in refinement. Y for yes, and N for no. pdbx_dcc_density.Z-score Z-scores are computed (by Xtriage) on the basis of a Bernoulli model assuming independence of weak reflections with respect to anisotropy. pdbx_dcc_density.Z_score_L_test Multivariate Z score for the L-test calculated by Xtriage using acentric reflections. It is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. pdbx_dcc_density.aniso_B11 The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. pdbx_dcc_density.aniso_B12 The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. pdbx_dcc_density.aniso_B13 The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. pdbx_dcc_density.aniso_B22 The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. pdbx_dcc_density.aniso_B23 The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. pdbx_dcc_density.aniso_B33 The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. pdbx_dcc_density.anisotropy The anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) calculated by Xtriage. pdbx_dcc_density.correlation_overall The overall electron density correlation coefficient. pdbx_dcc_density.dpi_free_R The DPI calculated based on the free set, determined by REFMAC. pdbx_dcc_density.error Details of any error or warning messages. pdbx_dcc_density.fom The mean figure of merit after refinement. pdbx_dcc_density.free_set_count The number of unique reflections for calculating Rfree (testing set) reported in the model file. pdbx_dcc_density.ice_ring Boolean whether ice ring exists (Y) or not (N) as determined by Xtriage. pdbx_dcc_density.iso_B_value_type The type of B factors (partial or full) for the residue. pdbx_dcc_density.ls_d_res_high The highest resolution limit reported in the model file. pdbx_dcc_density.ls_d_res_high_sf The highest resolution limit calculated from the structure factor file. pdbx_dcc_density.ls_d_res_low The lowest resolution limit reported in the model file. pdbx_dcc_density.ls_d_res_low_sf The lowest resolution limit calculated from the structure factor file. pdbx_dcc_density.ls_number_reflns_R_free The number of reflections that satisfy the resolution limits established by _pdbx_dcc_density.ls_d_res_high and _pdbx_dcc_density.ls_d_res_low , and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. pdbx_dcc_density.ls_percent_reflns_R_free The number of reflections that satisfy the resolution limits established by _pdbx_dcc_density.ls_d_res_high and _pdbx_dcc_density.ls_d_res_low , and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. pdbx_dcc_density.ls_percent_reflns_obs The number of reflections that satisfy the resolution limits established by attribute ls_d_res_high in category pdbx_dcc_density and attribute ls_d_res_low in category pdbx_dcc_density, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. pdbx_dcc_density.mFo-DFc-3sigma_negative The number of electron density negative peaks less than 3 sigma. pdbx_dcc_density.mFo-DFc-3sigma_positive The number of electron density positive peaks larger than 3 sigma. pdbx_dcc_density.mFo-DFc-6sigma_negative The number of electron density negative peaks less than 6 sigma. pdbx_dcc_density.mFo-DFc-6sigma_positive The number of electron density positive peaks larger than 6 sigma. pdbx_dcc_density.mean_E2_1_abs Value of <|E^2 - 1|> calculated by Xtriage using acentric reflections.(untwinned: 0.736; perfect twin 0.541). pdbx_dcc_density.mean_F_square_over_mean_F2 Value of <F>^2/<F^2> calculated by Xtriage using acentric reflections.(untwinned: 0.785; perfect twin 0.885). pdbx_dcc_density.mean_I2_over_mean_I_square Value of <I^2>/<I>^2 calculated by Xtriage using acentric reflections.(untwinned: 2.000; perfect twin 1.500). pdbx_dcc_density.mtrix_number Number of matrix for the NCS groups used in refinement. pdbx_dcc_density.ncs_group_number Number of NCS groups used in refinement. pdbx_dcc_density.occupancy_max The maximum occupancy reported in the model file. pdbx_dcc_density.occupancy_mean The averaged occupancy reported in the model file. pdbx_dcc_density.occupancy_min The minimum occupancy reported in the model file. pdbx_dcc_density.partial_B_value_correction_attempted Whether attempt to convert the partial to full B factors before validation. pdbx_dcc_density.partial_B_value_correction_success Whether the conversion of partial B to full B factor is successful (Y) or not (N). pdbx_dcc_density.pdbtype The keywords of the structure (taken from attribute pdbx_keywords) in category struct_keywords. pdbx_dcc_density.prob_peak_value The probability to tell the existence of translational pseudo symmetry. p_values smaller than 0.05 (1e-3) might indicate weak (strong) translational pseudo symmetry (by Xtriage). pdbx_dcc_density.real_space_R_overall The overall real space R factor. pdbx_dcc_density.reflection_status_archived Whether the status is of reflection is archived (Y) or not (N). pdbx_dcc_density.reflection_status_used Whether the status of the reflection is used (Y) or not (N). pdbx_dcc_density.reflns_number_obs The number of reflections classified as observed by Xtriage. This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. pdbx_dcc_density.reflns_outlier_acentric The number of acentric reflections classified as outliers on the basis of Wilson statistics (by Xtriage). If pseudo translational symmetry exists, a large number of 'outliers' will be present. pdbx_dcc_density.reflns_outlier_centric The number of centric reflections classified as outliers by Xtriage. pdbx_dcc_density.reflns_twin Boolean (Y/N) whether the twin is reported. pdbx_dcc_density.solvent_content The solvent content. pdbx_dcc_density.space_group_name_H-M Hermann-Mauguin space-group symbol reported in the model file. pdbx_dcc_density.space_group_pointless Hermann-Mauguin space-group symbol calculated by the POINTLESS program using the structure factor file. pdbx_dcc_density.tls_group_number Number of TLS groups used in refinement. pdbx_dcc_density.translational_pseudo_symmetry Boolean whether translational pseudo symmetry exist (Y) or not (N) as determined by Xtriage. pdbx_dcc_density.twin_Rfactor The Rfactor calculated by Xtriage using the twin operator related data. (Smaller values indicate twins). pdbx_dcc_density.twin_by_xtriage Boolean (Y/N) whether twin is detected by Xtriage. pdbx_dcc_density.twin_fraction Twin fractions determined by REFMAC. pdbx_dcc_density.twin_fraction_xtriage The twin fraction determined by Xtriage. pdbx_dcc_density.twin_operator Twin operators determined by REFMAC. pdbx_dcc_density.twin_operator_xtriage A list of the twin operators determined by Xtriage. pdbx_dcc_density.twin_type Type of twin (merohedral,Pseudo-merohedral or non-merohedral) determined by Xtriage. pdbx_dcc_density.unit_cell The unit cell parameters (a b c alpha beta gamma) separated by a space. pdbx_dcc_density.wavelength The wavelength reported from the model file. pdbx_dcc_density.working_set_count The number of unique reflections for refinement (working set) reported in the model file. pdbx_dcc_density.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_dcc_density_corr Data items in the category record calculated metrics from various programs (such as phenix, refmac, cns, sfcheck). 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_dcc_density_corrCategory This property indicates that datablock has a category holder pdbx_dcc_density_corrCategory. pdbx_dcc_density_corrCategory This property indicates that pdbx_dcc_density_corrCategory. has a category pdbx_dcc_density_corr. pdbx_dcc_density_corrItem Abstract datatype property for pdbx_dcc_density_corr items. reference_to_pdbx_dcc_density_corr cross-reference to pdbx_dcc_density_corr. referenced_by_pdbx_dcc_density_corr cross-reference from pdbx_dcc_density_corr. pdbx_dcc_density_corr.correlation The overall real space density correlation coefficient. pdbx_dcc_density_corr.correlation_coeff_Fo_to_Fc The correlations between the observed and calculated structure factors. pdbx_dcc_density_corr.details Any additional details of the calculations. pdbx_dcc_density_corr.ls_R_factor_R_all The calculated Rfactor using all the data. pdbx_dcc_density_corr.ls_R_factor_R_free The calculated Rfree using the test set data. pdbx_dcc_density_corr.ls_R_factor_R_work The calculated Rfactor using the working set data. pdbx_dcc_density_corr.ls_d_res_high The highest resolution limit in calculating the metrics in this category. pdbx_dcc_density_corr.ls_d_res_low The lowest resolution limit in calculating the metrics in this category. pdbx_dcc_density_corr.ls_number_reflns_R_free The number of reflections for the test set only. pdbx_dcc_density_corr.ls_number_reflns_obs The number of unique reflections (work+test sets). pdbx_dcc_density_corr.ls_percent_reflns_R_free The number of reflections that satisfy the resolution limits established by _pdbx_dcc_density_corr.ls_d_res_high and _pdbx_dcc_density_corr.ls_d_res_low , and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. pdbx_dcc_density_corr.ls_percent_reflns_obs The percentage of unique reflections (work+test sets). pdbx_dcc_density_corr.program The program used to calculate the metrics in this category. pdbx_dcc_density_corr.real_space_R The overall real space R factor. pdbx_dcc_density_corr.ordinal The ordered number in the output list. 0 pdbx_dcc_entity_geometry Data items in the category record the deviations about geometry (such as bond length, angle, dihedral, chirality, planarity) of each entity. 0 1 1 1 0 1 1 1 0 1 0 1 1 1 pdbx_dcc_entity_geometryCategory This property indicates that datablock has a category holder pdbx_dcc_entity_geometryCategory. pdbx_dcc_entity_geometryCategory This property indicates that pdbx_dcc_entity_geometryCategory. has a category pdbx_dcc_entity_geometry. pdbx_dcc_entity_geometryItem Abstract datatype property for pdbx_dcc_entity_geometry items. reference_to_pdbx_dcc_entity_geometry cross-reference to pdbx_dcc_entity_geometry. referenced_by_pdbx_dcc_entity_geometry cross-reference from pdbx_dcc_entity_geometry. pdbx_dcc_entity_geometry.angle_overall_rmsz The overall root mean square deviation for the Z-score of bond angles in comparison to consensus geometries. The values are computed by MolProbity (dangle) with reference to parameters; Engh and Huber (2001) and Parkinson et al. (1996). pdbx_dcc_entity_geometry.auth_asym_id Pointer to attribute auth_asym_id in category atom_site. pdbx_dcc_entity_geometry.bond_overall_rmsz The overall root mean square deviation for the Z-score of bond lengths in comparison to standard geometries. The values are computed by MolProbity (dangle) with reference to parameters; Engh and Huber (2001) and Parkinson et al. (1996). pdbx_dcc_entity_geometry.entity_id Pointer to attribute label_entity_id in category atom_site. pdbx_dcc_entity_geometry.number_angles The number of bond angles in the entity used in calculation of '_pdbx_dcc_entity_geometry.angle_overall_rmsz'. pdbx_dcc_entity_geometry.number_bonds The number of bond lengths in the entity used in calculation of '_pdbx_dcc_entity_geometry.bond_overall_rmsz'. pdbx_dcc_entity_geometry.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_dcc_entity_geometry.label_asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 0 pdbx_dcc_geometry Data items in the category record the overall deviations about geometry (such as bond length, angle, dihedral, chirality, planarity). These data are calculated with the phenix module model_vs_data. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_dcc_geometryCategory This property indicates that datablock has a category holder pdbx_dcc_geometryCategory. pdbx_dcc_geometryCategory This property indicates that pdbx_dcc_geometryCategory. has a category pdbx_dcc_geometry. pdbx_dcc_geometryItem Abstract datatype property for pdbx_dcc_geometry items. reference_to_pdbx_dcc_geometry cross-reference to pdbx_dcc_geometry. referenced_by_pdbx_dcc_geometry cross-reference from pdbx_dcc_geometry. pdbx_dcc_geometry.RNA_suiteness_score RNA suiteness score is the conformer matching score of RNA backbone (suite) in comparison to the consensus conformation. Higher score (closer to 1.0) indicates good agreement with the consensus conformation. Ref: Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM, RNA Ontology Consortium. "RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." RNA (2008), 14(3), 465-481 pdbx_dcc_geometry.Ramachandran_allowed_number Number of allowed residues in Ramachandran plot. pdbx_dcc_geometry.Ramachandran_allowed_percent Percentage of allowed residues in Ramachandran plot. pdbx_dcc_geometry.Ramachandran_favored_number Number of favored residues in Ramachandran plot. pdbx_dcc_geometry.Ramachandran_favored_percent Percentage of favored residues in Ramachandran plot. pdbx_dcc_geometry.Ramachandran_outlier_number Number of outliers in Ramachandran plot. pdbx_dcc_geometry.Ramachandran_outlier_percent Percentage of outliers in Ramachandran plot. pdbx_dcc_geometry.Ramachandran_outlier_percent_nmr_well_formed Percentage of outliers in Ramachandran plot within polypeptide chain segments structurally well formed in the ensemble representation of NMR structure. See also the definition of attribute Ramachandran_outlier_percent_nmr_well_formed in category pdbx_dcc_geometry. pdbx_dcc_geometry.all_atom_clashscore All atom score is determined by steric overlaps >0.4A per 1000 atoms. pdbx_dcc_geometry.all_atom_clashscore_nmr_well_formed All atom score is determined by steric overlaps >0.4A per 1000 atoms within polypeptide chain segments structurally well formed in the ensemble representation of NMR structure. See also the definition of attribute all_atom_clashscore_nmr_well_formed in category pdbx_dcc_geometry. pdbx_dcc_geometry.angle_ligand_max The maximum root mean square deviation for bond angles (ligand only). pdbx_dcc_geometry.angle_ligand_rms The overall root mean square deviation for bond angles (ligand only). pdbx_dcc_geometry.angle_overall_max The maximum root mean square deviation for bond angles (all atoms). pdbx_dcc_geometry.angle_overall_rms The overall root mean square deviation for bond angles (all atoms). pdbx_dcc_geometry.angle_overall_rmsz The overall root mean square deviation for the Z-score of bond angles in comparison to consensus geometries. The values are computed by MolProbity (dangle) with reference to parameters; Engh and Huber (2001) and Parkinson et al. (1996). pdbx_dcc_geometry.bond_ligand_max The maximum root mean square deviation for bond lengths (ligand only). pdbx_dcc_geometry.bond_ligand_rms The overall root mean square deviation for bond lengths (ligand only). pdbx_dcc_geometry.bond_overall_max The maximum root mean square deviation for bond lengths (all atoms). pdbx_dcc_geometry.bond_overall_rms The overall root mean square deviation for bond lengths (all atoms). pdbx_dcc_geometry.bond_overall_rmsz The overall root mean square deviation for the Z-score of bond lengths in comparison to standard geometries. The values are computed by MolProbity (dangle) with reference to parameters; Engh and Huber (2001) and Parkinson et al. (1996). pdbx_dcc_geometry.cbeta_deviations Number of Cbeta deviations >0.25A. pdbx_dcc_geometry.chirality_overall_max The maximum root mean square deviation for chirality (all atoms). pdbx_dcc_geometry.chirality_overall_rms The overall root mean square deviation for chirality (all atoms). pdbx_dcc_geometry.dihedral_overall_max The maximum root mean square deviation for dihedrals (all atoms). pdbx_dcc_geometry.dihedral_overall_rms The overall root mean square deviation for dihedrals (all atoms). pdbx_dcc_geometry.non-bonded_rms The overall on-bonded distance (all atoms). pdbx_dcc_geometry.number_angles The number of bond angles in the entry used in calculation of '_pdbx_dcc_geometry.angle_overall_rmsz'. pdbx_dcc_geometry.number_bonds The number of bond lengths in the entry used in calculation of '_pdbx_dcc_geometry.bond_overall_rmsz'. pdbx_dcc_geometry.overall_score The overall score for the geometry (the smaller the better). pdbx_dcc_geometry.planarity_overall_max The maximum root mean square deviation for planarity (all atoms). pdbx_dcc_geometry.planarity_overall_rms The overall root mean square deviation for planarity (all atoms). pdbx_dcc_geometry.rotamer_outliers_number Number of rotamer outliers. pdbx_dcc_geometry.rotamer_outliers_percent Percentage of rotamer outliers. pdbx_dcc_geometry.rotamer_outliers_percent_nmr_well_formed Percentage of rotamer outliers within polypeptide chain segments structurally well formed in the ensemble representation of NMR structure. See also the definition of attribute rotamer_outliers_percent_nmr_well_formed in category pdbx_dcc_geometry. pdbx_dcc_geometry.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_dcc_map Data items in the category record residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Z scores for each residue, the main/side chains. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_dcc_mapCategory This property indicates that datablock has a category holder pdbx_dcc_mapCategory. pdbx_dcc_mapCategory This property indicates that pdbx_dcc_mapCategory. has a category pdbx_dcc_map. pdbx_dcc_mapItem Abstract datatype property for pdbx_dcc_map items. reference_to_pdbx_dcc_map cross-reference to pdbx_dcc_map. referenced_by_pdbx_dcc_map cross-reference from pdbx_dcc_map. pdbx_dcc_map.Biso_mean The occupancy weighted average isotropic B factors for the residue. It is defined as (SUM B*Q)/(SUM Q), where B is the isotropic B factor for each atom and Q is the occupancy. pdbx_dcc_map.Biso_mean_main_chain The occupancy weighted average isotropic B factors for the main chain atoms. pdbx_dcc_map.Biso_mean_phosphate_group The occupancy weighted average isotropic B factors for the phosphate atoms. pdbx_dcc_map.Biso_mean_side_chain The occupancy weighted average isotropic B factors for the side chain atoms. pdbx_dcc_map.EDIA_mean The averaged EDIA score (aggregates the electron density support for individual atom) for the residue. A residue with an EDIAm below 0.8 suggests that its constituent atoms display increasing inconsistency with the electron density, and should be visually inspected. pdbx_dcc_map.LLDF It is the Ligand Local Density Function defined as the (<RsR>_local - RsR_Ligand)/sigma_RsR, where <RsR>_local is the mean RSR of polymer residues in 5 angstrom (including the crystallographic symmetry) surrounding the ligand, and sigma_RsR is sigma value calculated from the surrounding residues. pdbx_dcc_map.LLDFZ Z-score of the Ligand Local Density Function (LLDF) defined as the (<RsR>_local - RsR_Ligand)/sigma_RsR, where <RsR>_local is the mean RSR of polymer residues in 5 angstrom (including the crystallographic symmetry) surrounding the ligand, and sigma_RsR is sigma value calculated from the surrounding residues. Y N A flag indicating that this ligand has RSRZ outliers where Real-Space Rfactor (RSR) exceeds 0.5 or the Z-score of Local Ligand Density Function (LLDFZ) is greater than 2. See also the definition of attribute LLDFZ in category pdbx_dcc_map. N pdbx_dcc_map.LLDF_name A comma separated unique integers to indicate a set of Local Ligand Density Function (LLDF) calculation. the Ligand Local Density Function is defined as the (<RsR>_local - RsR_Ligand)/sigma_RsR, where <RsR>_local is the mean RSR of polymer residues in 5 angstrom (including the crystallographic symmetry) surrounding the ligand, and sigma_RsR is sigma value calculated from the surrounding residues. 1 1,2 pdbx_dcc_map.LLDF_number_residues_total Total number of polymer residues included in the Ligand Local Density Function (LLDF) calculation. See also the definition of attribute LLDF in category pdbx_dcc_map. pdbx_dcc_map.LLDF_sigma The standard deviation of RSR values of polymer residues in 5 angstrom (including the crystallographic symmetry) surrounding the ligand. Refer to definition of 'sigma_RsR' in attribute LLDF in category pdbx_dcc_map. pdbx_dcc_map.OPIA Overall Percentage of well-resolved Interconnected Atoms score indicates the percentage of atoms within a residue where the EDIA score exceeds 0.8. A value below 50% suggests less than half of the atoms in the residue lack good electron density support and should be visually inspected. pdbx_dcc_map.PDB_ins_code A component of the identifier for the component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site ATOM_SITE category. pdbx_dcc_map.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_dcc_map.RSCC The Real Space electron density Correlation Coefficient for the residue. It is defined as RSCC=(<xy>-<x><y>)/[sqrt(<x**2>-<x>**2)*sqrt(<y**2>-<y>**2)] where x is the observed density from the (2mFo-DFc) map and y is the calculated density from the Fc map pdbx_dcc_map.RSCC_main_chain The Real Space electron density Correlation Coefficient for the main chain atoms. pdbx_dcc_map.RSCC_phosphate_group The Real Space electron density Correlation Coefficient for the phosphate atoms. pdbx_dcc_map.RSCC_side_chain The Real Space electron density Correlation Coefficient for the side chain atoms. pdbx_dcc_map.RSR The Real space Rfactor (RSR) for the residue. It is defined as RSR=sum(|x-y|/x+y|) which is the summation over all grid points around the residue, where x is the observed density from the (2mFo-DFc) map and y is the calculated density from the Fc map. pdbx_dcc_map.RSRZ Z score of the Real Space Rfactor (RSRZ) for the residue. It is defined as (RSR-<RSR>)/sigma_RSR, where <RSR> and sigma_RSR are for the whole map, RSR is for the residue. pdbx_dcc_map.RSRZ_main_chain Z score of the Real Space Rfactor (RSRZ) for the main chain atoms. pdbx_dcc_map.RSRZ_phosphate_group Z score of the Real Space Rfactor (RSRZ) for the phosphate atoms. pdbx_dcc_map.RSRZ_side_chain Z score of the Real Space Rfactor (RSRZ) for the side chain atoms. pdbx_dcc_map.RSR_main_chain The Real space Rfactor (RSR) for the main chain atoms. pdbx_dcc_map.RSR_phosphate_group The Real space Rfactor (RSR) for the phosphate atoms. pdbx_dcc_map.RSR_side_chain The Real space Rfactor (RSR) for the side chain atoms. pdbx_dcc_map.RSZD The real space difference density Z score (defined as Delta_rho/sigma(Delta_rho)) from Tickle (2012). It is related to the model accuracy. RSZD>3, significant extra positive density around the residue; RSZD<-3, significant extra negative density around the residue. pdbx_dcc_map.RSZD_main_chain The same as attribute RSZD in category pdbx_dcc_map, use for the main chain atoms. pdbx_dcc_map.RSZD_phosphate_group The same as attribute RSZD in category pdbx_dcc_map, use for the phosphate atoms of nucleic acids. pdbx_dcc_map.RSZD_side_chain The same as attribute RSZD in category pdbx_dcc_map, use for the side chain atoms. pdbx_dcc_map.RSZO The real space observed density Z score (defined as <rho_obs>/sigma(Delta_rho)) from Tickle (2012). It is related to the model precision (B factors). Small or large value means weak or strong density for the residue. pdbx_dcc_map.RSZO_Zscore The Z score of RSZO (or the Z score of <rho_obs>/sigma(Delta_rho)). pdbx_dcc_map.RSZO_main_chain The same as attribute RSZO in category pdbx_dcc_map, use for the main chain atoms. pdbx_dcc_map.RSZO_phosphate_group The same as attribute RSZO in category pdbx_dcc_map, use for the phosphate atoms of nucleic acids. pdbx_dcc_map.RSZO_side_chain The same as attribute RSZO in category pdbx_dcc_map, use for the side chain atoms. pdbx_dcc_map.auth_asym_id The author provided chain id. pdbx_dcc_map.auth_comp_id The author provided compound ID (residue name). pdbx_dcc_map.auth_seq_id The author provided residue number. pdbx_dcc_map.density_connectivity Defined in sfcheck. It is the product of the (2Fobs-Fcal) electron density values for the backbone atoms N, CA and C, and in the case of RNA/DNA, for P, O5', C5', C3', O3'. Low values of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing. pdbx_dcc_map.density_index_main_chain Defined in sfcheck. It is the mean density of the main chain atoms divided by the mean density of the map. pdbx_dcc_map.density_index_side_chain Defined in sfcheck. It is the mean density of the side chain atoms divided by the mean density of the map. pdbx_dcc_map.label_alt_id Author provided alternate location identifier. pdbx_dcc_map.occupancy_mean The averaged occupancy for the residue. pdbx_dcc_map.occupancy_mean_main_chain The averaged occupancy for the main chain atoms. pdbx_dcc_map.occupancy_mean_phosphate_group The averaged occupancy for the phosphate atoms. pdbx_dcc_map.occupancy_mean_side_chain The averaged occupancy for the side chain atoms. pdbx_dcc_map.quality_indicator The value indicates any problems with this group of atoms. If given as 'd', it means there is problem of local model accuracy. If given as 'w', it means weak density (there is problem of local model precision). If given as 'dw', both then problems exist. pdbx_dcc_map.shift Defined in sfcheck (displacement/sigma_of_displacement). Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. pdbx_dcc_map.shift_main_chain The same as attribute density_shift in category pdbx_dcc_map, but it is for main chain. pdbx_dcc_map.shift_side_chain The same as attribute density_shift in category pdbx_dcc_map, but it is for side chain. pdbx_dcc_map.wRSRZ_main_chain Z score of weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms. pdbx_dcc_map.wRSRZ_phosphate_group Z score of weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms. pdbx_dcc_map.wRSRZ_side_chain Z score of weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms. pdbx_dcc_map.wRSR_main_chain The weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms. pdbx_dcc_map.wRSR_phosphate_group The weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms. pdbx_dcc_map.wRSR_side_chain The weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms. pdbx_dcc_map.weighted_RSR The weighted Real Space Rfactor (defined as RSR/RSCC) for the residue. pdbx_dcc_map.weighted_RSRZ Z score of weighted Real Space Rfactor for the residue. It is defined as (wRSR-<wRSR>)/sigma_wRSR, where <wRSR> and sigma_wRSR are for the whole map, wRSR is for the residue. pdbx_dcc_map.id The ordered number of residue in the output list. 0 pdbx_dcc_map_overall Data items in the category record statistics of each entry for residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Z scores. 0 1 1 pdbx_dcc_map_overallCategory This property indicates that datablock has a category holder pdbx_dcc_map_overallCategory. pdbx_dcc_map_overallCategory This property indicates that pdbx_dcc_map_overallCategory. has a category pdbx_dcc_map_overall. pdbx_dcc_map_overallItem Abstract datatype property for pdbx_dcc_map_overall items. reference_to_pdbx_dcc_map_overall cross-reference to pdbx_dcc_map_overall. referenced_by_pdbx_dcc_map_overall cross-reference from pdbx_dcc_map_overall. pdbx_dcc_map_overall.RSRZ_outliers_percent Percentage of residues that are RSRZ outliers where the Z-score of Real Space Rfactor (RSRZ) is greater than 2. See also: https://wwpdb.org/validation/2016/XrayValidationReportHelp#fit_model_data pdbx_dcc_map_overall.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_dcc_mapman Data items in the category record details from the output of mapman used by the DCC program. 0 1 1 pdbx_dcc_mapmanCategory This property indicates that datablock has a category holder pdbx_dcc_mapmanCategory. pdbx_dcc_mapmanCategory This property indicates that pdbx_dcc_mapmanCategory. has a category pdbx_dcc_mapman. pdbx_dcc_mapmanItem Abstract datatype property for pdbx_dcc_mapman items. reference_to_pdbx_dcc_mapman cross-reference to pdbx_dcc_mapman. referenced_by_pdbx_dcc_mapman cross-reference from pdbx_dcc_mapman. pdbx_dcc_mapman.details The details of the use of mapman by the DCC program. pdbx_dcc_mapman.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_dcc_mon_geometry Data items in the category record the deviations about geometry (such as bond length, angle, dihedral, chirality, planarity) of each monomer. 0 1 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 pdbx_dcc_mon_geometryCategory This property indicates that datablock has a category holder pdbx_dcc_mon_geometryCategory. pdbx_dcc_mon_geometryCategory This property indicates that pdbx_dcc_mon_geometryCategory. has a category pdbx_dcc_mon_geometry. pdbx_dcc_mon_geometryItem Abstract datatype property for pdbx_dcc_mon_geometry items. reference_to_pdbx_dcc_mon_geometry cross-reference to pdbx_dcc_mon_geometry. referenced_by_pdbx_dcc_mon_geometry cross-reference from pdbx_dcc_mon_geometry. Y N A flag indicating that this ligand classified as outlier conformation of the monomer (Y) or not (N). If this value is 'Y', More than 40% of bonds, angles, torsions, and rings were classified as outlier. The values are computed by Mogul. See also the definition of attribute LLDFZ in category pdbx_dcc_mon_geometry. N pdbx_dcc_mon_geometry.PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site. pdbx_dcc_mon_geometry.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_dcc_mon_geometry.angle_overall_rmsz The overall root mean square deviation for the Z-score of bond angles in comparison to similar bond angles in CSD small molecule crystal structure. The values are computed by Mogul. pdbx_dcc_mon_geometry.auth_asym_id Pointer to attribute auth_asym_id in category atom_site. pdbx_dcc_mon_geometry.auth_comp_id Pointer to attribute auth_comp_id in category atom_site. pdbx_dcc_mon_geometry.auth_seq_id Pointer to attribute auth_seq_id in category atom_site. pdbx_dcc_mon_geometry.bond_overall_rmsz The overall root mean square deviation for the Z-score of bond lengths in comparison to similar bond lengths in CSD small molecule crystal structure. The values are computed by Mogul. pdbx_dcc_mon_geometry.label_alt_id Pointer to attribute label_alt_id in category atom_site. pdbx_dcc_mon_geometry.number_angles The number of bond angles in the residue used in calculation of '_pdbx_dcc_mon_geometry.angle_overall_rmsz'. pdbx_dcc_mon_geometry.number_bonds The number of bond lengths in the residue used in calculation of '_pdbx_dcc_mon_geometry.bond_overall_rmsz'. pdbx_dcc_mon_geometry.id The ordered number of residue in the output list. 0 pdbx_dcc_rscc_mapman Data items in this category record residual map properties such as correlation, real space Rfactors and the Z score calculated from refmac and mapman. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_dcc_rscc_mapmanCategory This property indicates that datablock has a category holder pdbx_dcc_rscc_mapmanCategory. pdbx_dcc_rscc_mapmanCategory This property indicates that pdbx_dcc_rscc_mapmanCategory. has a category pdbx_dcc_rscc_mapman. pdbx_dcc_rscc_mapmanItem Abstract datatype property for pdbx_dcc_rscc_mapman items. reference_to_pdbx_dcc_rscc_mapman cross-reference to pdbx_dcc_rscc_mapman. referenced_by_pdbx_dcc_rscc_mapman cross-reference from pdbx_dcc_rscc_mapman. pdbx_dcc_rscc_mapman.Biso_mean The occupancy weighted average isotropic B factors for the residue. pdbx_dcc_rscc_mapman.auth_asym_id The author provided chain id. pdbx_dcc_rscc_mapman.auth_comp_id The author provided compound ID (residue name). pdbx_dcc_rscc_mapman.auth_seq_id The author provided residue number. pdbx_dcc_rscc_mapman.correlation The real space electron density correlation coefficient (RSCC) for the residue. pdbx_dcc_rscc_mapman.flag Residue with density problem will be flagged as P. pdbx_dcc_rscc_mapman.label_alt_id The author provided alternate location identifier. pdbx_dcc_rscc_mapman.label_ins_code PDB insertion code. pdbx_dcc_rscc_mapman.model_id The component model identifier for this analysis. pdbx_dcc_rscc_mapman.occupancy_mean The average occupancy for the residue. pdbx_dcc_rscc_mapman.real_space_R The Real Space Rfactor (RSR) for the residue. pdbx_dcc_rscc_mapman.real_space_Zscore The Z score of the Real Space Rfactor (RSRZ) for the residue. pdbx_dcc_rscc_mapman.weighted_real_space_R The weighted Real Space Rfactor (RSR/RSCC) for the residue. pdbx_dcc_rscc_mapman.id The ordered number in the output list. 0 pdbx_dcc_rscc_mapman_overall Data items in the category record overall map properties such as correlation, real space Rfactors and the Z score calculated from refmac and mapman. 0 1 0 1 0 1 0 1 1 pdbx_dcc_rscc_mapman_overallCategory This property indicates that datablock has a category holder pdbx_dcc_rscc_mapman_overallCategory. pdbx_dcc_rscc_mapman_overallCategory This property indicates that pdbx_dcc_rscc_mapman_overallCategory. has a category pdbx_dcc_rscc_mapman_overall. pdbx_dcc_rscc_mapman_overallItem Abstract datatype property for pdbx_dcc_rscc_mapman_overall items. reference_to_pdbx_dcc_rscc_mapman_overall cross-reference to pdbx_dcc_rscc_mapman_overall. referenced_by_pdbx_dcc_rscc_mapman_overall cross-reference from pdbx_dcc_rscc_mapman_overall. pdbx_dcc_rscc_mapman_overall.correlation The overall real space electron density correlation coefficient (RSCC) for the structure. pdbx_dcc_rscc_mapman_overall.correlation_sigma The overall standard deviation of the real space electron density correlation coefficient (RSCC) for the structure. pdbx_dcc_rscc_mapman_overall.real_space_R The overall Real Space Rfactor (RSR) for the structure. pdbx_dcc_rscc_mapman_overall.real_space_R_sigma The overall standard deviation of the Real Space Rfactor (RSR) for the structure. pdbx_dcc_rscc_mapman_overall.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_diffrn_reflns_shell Data items in the DIFFRN_REFLNS_SHELL category record details about the reflection data set within shells of resolution. Example 1 - diffraction properties with shells <VRPTx:pdbx_diffrn_reflns_shellCategory> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="5.18" d_res_low="50.00" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.029</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.154</VRPTx:chi_squared> <VRPTx:number_obs>11791</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="4.11" d_res_low="5.18" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.033</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.098</VRPTx:chi_squared> <VRPTx:number_obs>11717</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="3.59" d_res_low="4.11" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.043</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.044</VRPTx:chi_squared> <VRPTx:number_obs>11792</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="3.26" d_res_low="3.59" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.059</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.104</VRPTx:chi_squared> <VRPTx:number_obs>11718</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="3.03" d_res_low="3.26" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.087</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.160</VRPTx:chi_squared> <VRPTx:number_obs>11753</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="2.85" d_res_low="3.03" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.130</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.169</VRPTx:chi_squared> <VRPTx:number_obs>11811</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="2.71" d_res_low="2.85" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.174</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.170</VRPTx:chi_squared> <VRPTx:number_obs>11752</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> <VRPTx:pdbx_diffrn_reflns_shell d_res_high="2.59" d_res_low="2.71" diffrn_id="1"> <VRPTx:Rmerge_I_obs>0.227</VRPTx:Rmerge_I_obs> <VRPTx:chi_squared>1.165</VRPTx:chi_squared> <VRPTx:number_obs>11767</VRPTx:number_obs> <VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs> </VRPTx:pdbx_diffrn_reflns_shell> </VRPTx:pdbx_diffrn_reflns_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_diffrn_reflns_shellCategory This property indicates that datablock has a category holder pdbx_diffrn_reflns_shellCategory. pdbx_diffrn_reflns_shellCategory This property indicates that pdbx_diffrn_reflns_shellCategory. has a category pdbx_diffrn_reflns_shell. pdbx_diffrn_reflns_shellItem Abstract datatype property for pdbx_diffrn_reflns_shell items. reference_to_pdbx_diffrn_reflns_shell cross-reference to pdbx_diffrn_reflns_shell. referenced_by_pdbx_diffrn_reflns_shell cross-reference from pdbx_diffrn_reflns_shell. pdbx_diffrn_reflns_shell.Rmerge_I_obs The R factor for the reflections that satisfy the merging criteria for the resolution shell. pdbx_diffrn_reflns_shell.Rsym_value The R factor for averaging the symmetry related reflections for the resolution shell. pdbx_diffrn_reflns_shell.chi_squared The overall Chi-squared statistic for the resolution shell. pdbx_diffrn_reflns_shell.number_obs The number of observed reflections in the resolution shell. pdbx_diffrn_reflns_shell.percent_possible_obs The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by attribute d_resolution_high in category diffrn_reflns_shell and attribute d_resolution_low in category diffrn_reflns_shell and the observation limit established by attribute observed_criterion. in category diffrn_reflns pdbx_diffrn_reflns_shell.redundancy The overall redundancy for the resolution shell. pdbx_diffrn_reflns_shell.rejects The number of rejected reflections in the resolution shell pdbx_diffrn_reflns_shell.d_res_high The highest resolution for the interplanar spacings in the resolution shell. pdbx_diffrn_reflns_shell.d_res_low The lowest resolution for the interplanar spacings in the resolution shell. pdbx_diffrn_reflns_shell.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. This item distingush the different data sets 0 pdbx_distant_solvent_atoms Data items in the PDBX_DISTANT_SOLVENT_ATOMS category list the solvent atoms remote from any macromolecule. Example 1 - <VRPTx:pdbx_distant_solvent_atomsCategory> <VRPTx:pdbx_distant_solvent_atoms id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>W</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>O</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:neighbor_ligand_distance xsi:nil="true" /> <VRPTx:neighbor_macromolecule_distance>7.3</VRPTx:neighbor_macromolecule_distance> </VRPTx:pdbx_distant_solvent_atoms> <VRPTx:pdbx_distant_solvent_atoms id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>W</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>O</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>413</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:neighbor_ligand_distance xsi:nil="true" /> <VRPTx:neighbor_macromolecule_distance>8.4</VRPTx:neighbor_macromolecule_distance> </VRPTx:pdbx_distant_solvent_atoms> <VRPTx:pdbx_distant_solvent_atoms id="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>W</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>O</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>414</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:neighbor_ligand_distance xsi:nil="true" /> <VRPTx:neighbor_macromolecule_distance>7.2</VRPTx:neighbor_macromolecule_distance> </VRPTx:pdbx_distant_solvent_atoms> <VRPTx:pdbx_distant_solvent_atoms id="4"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>W</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>O</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>415</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:neighbor_ligand_distance xsi:nil="true" /> <VRPTx:neighbor_macromolecule_distance>8.3</VRPTx:neighbor_macromolecule_distance> </VRPTx:pdbx_distant_solvent_atoms> </VRPTx:pdbx_distant_solvent_atomsCategory> 0 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_distant_solvent_atomsCategory This property indicates that datablock has a category holder pdbx_distant_solvent_atomsCategory. pdbx_distant_solvent_atomsCategory This property indicates that pdbx_distant_solvent_atomsCategory. has a category pdbx_distant_solvent_atoms. pdbx_distant_solvent_atomsItem Abstract datatype property for pdbx_distant_solvent_atoms items. reference_to_pdbx_distant_solvent_atoms cross-reference to pdbx_distant_solvent_atoms. referenced_by_pdbx_distant_solvent_atoms cross-reference from pdbx_distant_solvent_atoms. pdbx_distant_solvent_atoms.PDB_ins_code Part of the identifier for the distant solvent atom. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.PDB_model_num Part of the identifier for the distant solvent atom. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.auth_asym_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.auth_atom_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.auth_comp_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.auth_seq_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.label_alt_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.label_asym_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.label_atom_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.label_comp_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.label_seq_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_distant_solvent_atoms.neighbor_ligand_distance Distance to closest neighboring ligand or solvent atom. pdbx_distant_solvent_atoms.neighbor_macromolecule_distance Distance to closest neighboring macromolecule atom. pdbx_distant_solvent_atoms.id The value of attribute id in category pdbx_distant_solvent_atoms must uniquely identify each item in the PDBX_DISTANT_SOLVENT_ATOMS list. This is an integer serial number. 0 pdbx_domain Data items in the PDBX_DOMAIN category record information about domain definitions. A domain need not correspond to a completely polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain. Example 1 - <VRPTx:pdbx_domainCategory> <VRPTx:pdbx_domain id="d1"> <VRPTx:details>Chains A, B</VRPTx:details> </VRPTx:pdbx_domain> <VRPTx:pdbx_domain id="d2"> <VRPTx:details>Asym_id D Residues 1-134</VRPTx:details> </VRPTx:pdbx_domain> </VRPTx:pdbx_domainCategory> 0 1 1 pdbx_domainCategory This property indicates that datablock has a category holder pdbx_domainCategory. pdbx_domainCategory This property indicates that pdbx_domainCategory. has a category pdbx_domain. pdbx_domainItem Abstract datatype property for pdbx_domain items. reference_to_pdbx_domain cross-reference to pdbx_domain. referenced_by_pdbx_domain cross-reference from pdbx_domain. pdbx_domain.details A description of special aspects of the structural elements that comprise a domain. The loop between residues 18 and 23. pdbx_domain.id The value of attribute id in category pdbx_domain must uniquely identify a record in the PDBX_DOMAIN list. Note that this item need not be a number; it can be any unique identifier. 0 pdbx_domain_range Data items in the PDBX_DOMAIN_RANGE category identify the beginning and ending points of polypeptide chain segments that form all or part of a domain. Example 1 - <VRPTx:pdbx_domain_rangeCategory> <VRPTx:pdbx_domain_range id="1"> <VRPTx:beg_label_alt_id>A</VRPTx:beg_label_alt_id> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>1</VRPTx:beg_label_seq_id> <VRPTx:domain_id>d1</VRPTx:domain_id> <VRPTx:end_label_alt_id>A</VRPTx:end_label_alt_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>29</VRPTx:end_label_seq_id> </VRPTx:pdbx_domain_range> <VRPTx:pdbx_domain_range id="2"> <VRPTx:beg_label_alt_id>A</VRPTx:beg_label_alt_id> <VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>31</VRPTx:beg_label_seq_id> <VRPTx:domain_id>d1</VRPTx:domain_id> <VRPTx:end_label_alt_id>A</VRPTx:end_label_alt_id> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>59</VRPTx:end_label_seq_id> </VRPTx:pdbx_domain_range> <VRPTx:pdbx_domain_range id="3"> <VRPTx:beg_label_alt_id>A</VRPTx:beg_label_alt_id> <VRPTx:beg_label_asym_id>C</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>61</VRPTx:beg_label_seq_id> <VRPTx:domain_id>d1</VRPTx:domain_id> <VRPTx:end_label_alt_id>A</VRPTx:end_label_alt_id> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>89</VRPTx:end_label_seq_id> </VRPTx:pdbx_domain_range> <VRPTx:pdbx_domain_range id="4"> <VRPTx:beg_label_alt_id>A</VRPTx:beg_label_alt_id> <VRPTx:beg_label_asym_id>D</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>91</VRPTx:beg_label_seq_id> <VRPTx:domain_id>d2</VRPTx:domain_id> <VRPTx:end_label_alt_id>A</VRPTx:end_label_alt_id> <VRPTx:end_label_asym_id>D</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>119</VRPTx:end_label_seq_id> </VRPTx:pdbx_domain_range> <VRPTx:pdbx_domain_range id="5"> <VRPTx:beg_label_alt_id>A</VRPTx:beg_label_alt_id> <VRPTx:beg_label_asym_id>E</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>121</VRPTx:beg_label_seq_id> <VRPTx:domain_id>d2</VRPTx:domain_id> <VRPTx:end_label_alt_id>A</VRPTx:end_label_alt_id> <VRPTx:end_label_asym_id>E</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>149</VRPTx:end_label_seq_id> </VRPTx:pdbx_domain_range> <VRPTx:pdbx_domain_range id="6"> <VRPTx:beg_label_alt_id>A</VRPTx:beg_label_alt_id> <VRPTx:beg_label_asym_id>F</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>151</VRPTx:beg_label_seq_id> <VRPTx:domain_id>d2</VRPTx:domain_id> <VRPTx:end_label_alt_id>A</VRPTx:end_label_alt_id> <VRPTx:end_label_asym_id>F</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>179</VRPTx:end_label_seq_id> </VRPTx:pdbx_domain_range> </VRPTx:pdbx_domain_rangeCategory> 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 pdbx_domain_rangeCategory This property indicates that datablock has a category holder pdbx_domain_rangeCategory. pdbx_domain_rangeCategory This property indicates that pdbx_domain_rangeCategory. has a category pdbx_domain_range. pdbx_domain_rangeItem Abstract datatype property for pdbx_domain_range items. reference_to_pdbx_domain_range cross-reference to pdbx_domain_range. referenced_by_pdbx_domain_range cross-reference from pdbx_domain_range. pdbx_domain_range.beg_auth_asym_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.beg_auth_comp_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.beg_auth_seq_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.beg_label_alt_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. pdbx_domain_range.beg_label_asym_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.beg_label_comp_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.beg_label_seq_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.domain_id This data item is a pointer to attribute id in category pdbx_domain in the PDBX_DOMAIN category. pdbx_domain_range.end_auth_asym_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.end_auth_comp_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.end_auth_seq_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.end_label_alt_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. pdbx_domain_range.end_label_asym_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.end_label_comp_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.end_label_seq_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_domain_range.id The value of attribute id in category pdbx_domain_range uniquely identifies a range in the PDBX_DOMAIN_RANGE category. 0 pdbx_em_atom_inclusion Data items in the category record fraction of atoms that are inside the surface at a given contour level. Ref: User guide to the wwPDB EM validation reports 9. Map-model fit 9.2 Atom inclusion Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_atom_inclusionCategory> <VRPTx:pdbx_em_atom_inclusion id="1"> <VRPTx:atom_inclusion_title>Fraction of model inside the map</VRPTx:atom_inclusion_title> <VRPTx:atom_type>all non-hydrogen atoms</VRPTx:atom_type> <VRPTx:contour_level_title>Contour level</VRPTx:contour_level_title> </VRPTx:pdbx_em_atom_inclusion> <VRPTx:pdbx_em_atom_inclusion id="2"> <VRPTx:atom_inclusion_title>Fraction of model inside the map</VRPTx:atom_inclusion_title> <VRPTx:atom_type>backbone atoms</VRPTx:atom_type> <VRPTx:contour_level_title>Contour level</VRPTx:contour_level_title> </VRPTx:pdbx_em_atom_inclusion> </VRPTx:pdbx_em_atom_inclusionCategory> 1 1 1 1 1 1 1 pdbx_em_atom_inclusionCategory This property indicates that datablock has a category holder pdbx_em_atom_inclusionCategory. pdbx_em_atom_inclusionCategory This property indicates that pdbx_em_atom_inclusionCategory. has a category pdbx_em_atom_inclusion. pdbx_em_atom_inclusionItem Abstract datatype property for pdbx_em_atom_inclusion items. reference_to_pdbx_em_atom_inclusion cross-reference to pdbx_em_atom_inclusion. referenced_by_pdbx_em_atom_inclusion cross-reference from pdbx_em_atom_inclusion. pdbx_em_atom_inclusion.atom_inclusion_title A title for the fraction of atoms inside the map of a atom inclusion plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion Fraction of model inside the map backbone atoms all non-hydrogen atoms Describe which type of atoms are used for the atom inclusion calculation. backbone atoms all non-hydrogen atoms pdbx_em_atom_inclusion.contour_level_title A title for the contour level (map value) axis of a atom inclusion plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion Contour level pdbx_em_atom_inclusion.id The value of attribute id in category pdbx_em_atom_inclusion must uniquely identify each item in the PDBX_EM_ATOM_INCLUSION list. This is an integer serial number. 0 pdbx_em_atom_inclusion_marker Data items in the category record atom inclusion plot. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_atom_inclusion_markerCategory> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="1" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.097199</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="2" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.095008</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="3" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.092817</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="4" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.090626</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="5" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.088435</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> </VRPTx:pdbx_em_atom_inclusion_markerCategory> 1 1 1 1 1 1 pdbx_em_atom_inclusion_markerCategory This property indicates that datablock has a category holder pdbx_em_atom_inclusion_markerCategory. pdbx_em_atom_inclusion_markerCategory This property indicates that pdbx_em_atom_inclusion_markerCategory. has a category pdbx_em_atom_inclusion_marker. pdbx_em_atom_inclusion_markerItem Abstract datatype property for pdbx_em_atom_inclusion_marker items. reference_to_pdbx_em_atom_inclusion_marker cross-reference to pdbx_em_atom_inclusion_marker. referenced_by_pdbx_em_atom_inclusion_marker cross-reference from pdbx_em_atom_inclusion_marker. pdbx_em_atom_inclusion_marker.atom_inclusion The fraction of specified atoms that are inside the surface at a given contour level. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion pdbx_em_atom_inclusion_marker.contour_level A certain contour level for the primary EM volume. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion pdbx_em_atom_inclusion_marker.ordinal The ordered number in the plot marker. pdbx_em_atom_inclusion_marker.plot_id Pointer to attribute id in category pdbx_em_atom_inclusion. 0 pdbx_em_density_distribution Data items in the category record map-value distribution of the primary EM volume. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.1 Map value distribution Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_density_distributionCategory> <VRPTx:pdbx_em_density_distribution id="1"> <VRPTx:map_value_title>Map-value</VRPTx:map_value_title> <VRPTx:voxel_count_scale>log10</VRPTx:voxel_count_scale> <VRPTx:voxel_count_title>Number of voxels</VRPTx:voxel_count_title> </VRPTx:pdbx_em_density_distribution> </VRPTx:pdbx_em_density_distributionCategory> 1 1 0 1 1 1 1 pdbx_em_density_distributionCategory This property indicates that datablock has a category holder pdbx_em_density_distributionCategory. pdbx_em_density_distributionCategory This property indicates that pdbx_em_density_distributionCategory. has a category pdbx_em_density_distribution. pdbx_em_density_distributionItem Abstract datatype property for pdbx_em_density_distribution items. reference_to_pdbx_em_density_distribution cross-reference to pdbx_em_density_distribution. referenced_by_pdbx_em_density_distribution cross-reference from pdbx_em_density_distribution. pdbx_em_density_distribution.map_value_title A title for the map value axis of a map-value distribution plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#map_value_distribution Map-value pdbx_em_density_distribution.voxel_count_scale A scale for the voxel count axis of a map-value distribution plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#map_value_distribution log10 pdbx_em_density_distribution.voxel_count_title A title for the voxel count axis of a map-value distribution plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#map_value_distribution Number of voxels pdbx_em_density_distribution.id The value of attribute id in category pdbx_em_density_distribution must uniquely identify each item in the PDBX_EM_DENSITY_DISTRIBUTION list. This is an integer serial number. 0 pdbx_em_density_distribution_marker Data items in the category record map-value distribution plot of the primary EM volume. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_density_distribution_markerCategory> <VRPTx:pdbx_em_density_distribution_marker ordinal="1" plot_id="1"> <VRPTx:map_value>-0.0971993208</VRPTx:map_value> <VRPTx:voxel_count>1.6812412374</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="2" plot_id="1"> <VRPTx:map_value>-0.0949910375</VRPTx:map_value> <VRPTx:voxel_count>0</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="3" plot_id="1"> <VRPTx:map_value>-0.0927827541</VRPTx:map_value> <VRPTx:voxel_count>1.3802112417</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="4" plot_id="1"> <VRPTx:map_value>-0.0905744708</VRPTx:map_value> <VRPTx:voxel_count>0</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="5" plot_id="1"> <VRPTx:map_value>-0.0883661875</VRPTx:map_value> <VRPTx:voxel_count>1.8573324964</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> </VRPTx:pdbx_em_density_distribution_markerCategory> 1 1 1 1 1 1 pdbx_em_density_distribution_markerCategory This property indicates that datablock has a category holder pdbx_em_density_distribution_markerCategory. pdbx_em_density_distribution_markerCategory This property indicates that pdbx_em_density_distribution_markerCategory. has a category pdbx_em_density_distribution_marker. pdbx_em_density_distribution_markerItem Abstract datatype property for pdbx_em_density_distribution_marker items. reference_to_pdbx_em_density_distribution_marker cross-reference to pdbx_em_density_distribution_marker. referenced_by_pdbx_em_density_distribution_marker cross-reference from pdbx_em_density_distribution_marker. pdbx_em_density_distribution_marker.map_value A certain map-value for the primary EM volume. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#map_value_estimation pdbx_em_density_distribution_marker.voxel_count The scaled number of voxels in a specific range of a given map-value. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#map_value_estimation pdbx_em_density_distribution_marker.ordinal The ordered number in the plot marker. pdbx_em_density_distribution_marker.plot_id Pointer to attribute id in category pdbx_em_density_distribution. 0 pdbx_em_fsc_curve Data items in the category record Fourier-Shell Correlation (FSC) curve. Ref: User guide to the wwPDB EM validation reports 8. FSC validation 8.1 Calculated FSC 8.2 Author provided FSC Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_curveCategory> <VRPTx:pdbx_em_fsc_curve id="1"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc</VRPTx:title> </VRPTx:pdbx_em_fsc_curve> <VRPTx:pdbx_em_fsc_curve id="2"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc</VRPTx:title> </VRPTx:pdbx_em_fsc_curve> </VRPTx:pdbx_em_fsc_curveCategory> 1 1 0 1 1 1 1 1 1 1 0 1 1 pdbx_em_fsc_curveCategory This property indicates that datablock has a category holder pdbx_em_fsc_curveCategory. pdbx_em_fsc_curveCategory This property indicates that pdbx_em_fsc_curveCategory. has a category pdbx_em_fsc_curve. pdbx_em_fsc_curveItem Abstract datatype property for pdbx_em_fsc_curve items. reference_to_pdbx_em_fsc_curve cross-reference to pdbx_em_fsc_curve. referenced_by_pdbx_em_fsc_curve cross-reference from pdbx_em_fsc_curve. pdbx_em_fsc_curve.correlation_coef_title A title for the correlation coefficient axis axis of a Fourier-Shell Correlation (FSC) curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc Correlation coefficient pdbx_em_fsc_curve.name A name for the Fourier-Shell Correlation (FSC) curve to distinguish this from others. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc calculated_fsc author_provided_fsc pdbx_em_fsc_curve.spatial_frequency_title A title for the spatial frequency axis of a Fourier-Shell Correlation (FSC) curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc Spatial frequency pdbx_em_fsc_curve.spatial_frequency_unit A unit for the spatial frequency axis of a Fourier-Shell Correlation (FSC) curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc 1/A pdbx_em_fsc_curve.title A title for the Fourier-Shell Correlation (FSC) curve to distinguish this from others. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_curve.type A short notation of the Fourier-Shell Correlation (FSC) curve that descrives how to generate the FSC curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_curve.id The value of attribute id in category pdbx_em_fsc_curve must uniquely identify each item in the PDBX_EM_FSC_CURVE list. This is an integer serial number. 0 pdbx_em_fsc_curve_marker Data items in the category record row data to plot Fourier-Shell Correlation (FSC) curve. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_curve_markerCategory> <VRPTx:pdbx_em_fsc_curve_marker ordinal="1" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="2" plot_id="1"> <VRPTx:correlation_coef>0.9999</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0046</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="3" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0091</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="4" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0137</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="5" plot_id="1"> <VRPTx:correlation_coef>0.9999</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0182</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> </VRPTx:pdbx_em_fsc_curve_markerCategory> 1 1 1 1 1 1 pdbx_em_fsc_curve_markerCategory This property indicates that datablock has a category holder pdbx_em_fsc_curve_markerCategory. pdbx_em_fsc_curve_markerCategory This property indicates that pdbx_em_fsc_curve_markerCategory. has a category pdbx_em_fsc_curve_marker. pdbx_em_fsc_curve_markerItem Abstract datatype property for pdbx_em_fsc_curve_marker items. reference_to_pdbx_em_fsc_curve_marker cross-reference to pdbx_em_fsc_curve_marker. referenced_by_pdbx_em_fsc_curve_marker cross-reference from pdbx_em_fsc_curve_marker. pdbx_em_fsc_curve_marker.correlation_coef The correlation coefficient at a spatial frequency of Fourier-Shell Correlation (FSC) curve, namely y-axis value of FSC curve. FSC is a measure of the normalized cross correlation coefficient between two 3D volumes over corresponding shells in Fourier space, i.e., as a function of spatial frequency. (sum(F~1~ conj(F~2~)) FSC~1,2~ = -------------------------------------- (sum(|F~1~|^2^) (sum(|F~2~|^2^)))^1/2^ F~1~ = complex structure factor of the first 3D volume at a spatial frequency F~2~ = complex structure factor of the second 3D volume at a spatial frequency Summation is carried over corresponding shells in Fourier space (spatial frequency). Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_curve_marker.spatial_frequency The spatial frequencies of Fourier-Shell Correlation (FSC) curve, namely x-axis value of FSC curve. (See '_pdbx_em_fsc_curve_marker.correlation_coef') Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_curve_marker.ordinal The ordered number in the plot marker. pdbx_em_fsc_curve_marker.plot_id Pointer to attribute id in category pdbx_em_fsc_curve. 0 pdbx_em_fsc_cutoff_curve Data items in the category record Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion. Ref: User guide to the wwPDB EM validation reports 8. FSC validation 8.1 Calculated FSC 8.2 Author provided FSC Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_cutoff_curveCategory> <VRPTx:pdbx_em_fsc_cutoff_curve id="1"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_one-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="2"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_0.143</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="3"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_0.5</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="4"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_0.333</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="5"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_half-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="6"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_3sigma</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="7"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_3sigma</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="8"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_one-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="9"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_0.143</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="10"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_0.5</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="11"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_0.333</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="12"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_half-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> </VRPTx:pdbx_em_fsc_cutoff_curveCategory> 1 1 0 1 1 1 1 1 0 1 1 1 0 1 1 pdbx_em_fsc_cutoff_curveCategory This property indicates that datablock has a category holder pdbx_em_fsc_cutoff_curveCategory. pdbx_em_fsc_cutoff_curveCategory This property indicates that pdbx_em_fsc_cutoff_curveCategory. has a category pdbx_em_fsc_cutoff_curve. pdbx_em_fsc_cutoff_curveItem Abstract datatype property for pdbx_em_fsc_cutoff_curve items. reference_to_pdbx_em_fsc_cutoff_curve cross-reference to pdbx_em_fsc_cutoff_curve. referenced_by_pdbx_em_fsc_cutoff_curve cross-reference from pdbx_em_fsc_cutoff_curve. pdbx_em_fsc_cutoff_curve.correlation_coef_title A title for the correlation coefficient axis axis of a Fourier-Shell Correlation (FSC) cut-off curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc Correlation coefficient pdbx_em_fsc_cutoff_curve.name A name for the Fourier-Shell Correlation (FSC) cut-off curve to distinguish this from others. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc calculated_fsc_0.143 calculated_fsc_0.333 calculated_fsc_0.5 calculated_fsc_half-bit calculated_fsc_one-bit calculated_fsc_3sigma author_provided_fsc_0.333 author_provided_fsc_0.5 author_provided_fsc_half-bit author_provided_fsc_one-bit author_provided_fsc_3sigma pdbx_em_fsc_cutoff_curve.spatial_frequency_title A title for the spatial frequency axis of a Fourier-Shell Correlation (FSC) cut-off curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc Spatial frequency pdbx_em_fsc_cutoff_curve.spatial_frequency_unit A unit for the spatial frequency axis of a Fourier-Shell Correlation (FSC) cut-off curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc 1/A pdbx_em_fsc_cutoff_curve.target_name A name of FSC curve to compare with the cut-off curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc calculated_fsc author_provided_fsc pdbx_em_fsc_cutoff_curve.title A title for the Fourier-Shell Correlation (FSC) cut-off curve to distinguish this from others. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_cutoff_curve.type A threshold of the Fourier-Shell Correlation (FSC) cut-off curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc 0.143 0.333 0.5 half-bit one-bit 3sigma pdbx_em_fsc_cutoff_curve.id The value of attribute id in category pdbx_em_fsc_cutoff_curve must uniquely identify each item in the PDBX_EM_FSC_CURVE list. This is an integer serial number. 0 pdbx_em_fsc_cutoff_curve_marker Data items in the category record row data to plot Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_cutoff_curve_markerCategory> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="1" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="2" plot_id="1"> <VRPTx:correlation_coef>0.607</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0046</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="3" plot_id="1"> <VRPTx:correlation_coef>0.5135</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0091</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="4" plot_id="1"> <VRPTx:correlation_coef>0.4674</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0137</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="5" plot_id="1"> <VRPTx:correlation_coef>0.4401</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0182</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> </VRPTx:pdbx_em_fsc_cutoff_curve_markerCategory> 1 1 0 1 1 1 pdbx_em_fsc_cutoff_curve_markerCategory This property indicates that datablock has a category holder pdbx_em_fsc_cutoff_curve_markerCategory. pdbx_em_fsc_cutoff_curve_markerCategory This property indicates that pdbx_em_fsc_cutoff_curve_markerCategory. has a category pdbx_em_fsc_cutoff_curve_marker. pdbx_em_fsc_cutoff_curve_markerItem Abstract datatype property for pdbx_em_fsc_cutoff_curve_marker items. reference_to_pdbx_em_fsc_cutoff_curve_marker cross-reference to pdbx_em_fsc_cutoff_curve_marker. referenced_by_pdbx_em_fsc_cutoff_curve_marker cross-reference from pdbx_em_fsc_cutoff_curve_marker. pdbx_em_fsc_cutoff_curve_marker.correlation_coef The correlation coefficient at a spatial frequency of Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion, namely y-axis value of FSC cut-off curve. Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_cutoff_curve_marker.spatial_frequency The spatial frequencies of Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion, namely x-axis value of FSC cut-off curve. Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. If the spatial frequency is empty, a linear cut-off line with a correlation coefficient is assumed. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#calculated_fsc https://www.wwpdb.org/validation/EMValidationReportHelp#author_provided_fsc pdbx_em_fsc_cutoff_curve_marker.ordinal The ordered number in the plot marker. pdbx_em_fsc_cutoff_curve_marker.plot_id Pointer to attribute id in category pdbx_em_fsc_cutoff_curve. 0 pdbx_em_fsc_resolution Data items in the category record estimated global resolutions from Fourier-Shell Correlation (FSC) curve using various criteria for single-particle and subtomogram averaging methods. Ref: User guide to the wwPDB EM validation reports 8. FSC validation 8.1 Resolution estimate Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_resolutionCategory> <VRPTx:pdbx_em_fsc_resolution criterion="one-bit" source="calculated_fsc"> <VRPTx:correlation_coef>0.3396</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>1</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.69</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.3715</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.143" source="calculated_fsc"> <VRPTx:correlation_coef>0.143</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>2</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.38</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4195</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.5" source="calculated_fsc"> <VRPTx:correlation_coef>0.5</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>3</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.79</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.3587</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.333" source="calculated_fsc"> <VRPTx:correlation_coef>0.333</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>4</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.65</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.3768</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="half-bit" source="calculated_fsc"> <VRPTx:correlation_coef>0.178</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>5</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.48</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4039</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="3sigma" source="calculated_fsc"> <VRPTx:correlation_coef>0.0116</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>6</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.16</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4636</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="3sigma" source="author_provided_fsc"> <VRPTx:correlation_coef>0.0108</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>7</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.01</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.498</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="one-bit" source="author_provided_fsc"> <VRPTx:correlation_coef>0.3387</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>8</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.32</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4304</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.143" source="author_provided_fsc"> <VRPTx:correlation_coef>0.143</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>9</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.15</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4648</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.5" source="author_provided_fsc"> <VRPTx:correlation_coef>0.5</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>10</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.48</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4027</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.333" source="author_provided_fsc"> <VRPTx:correlation_coef>0.333</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>11</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.32</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.431</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="half-bit" source="author_provided_fsc"> <VRPTx:correlation_coef>0.1772</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>12</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.16</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4625</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> </VRPTx:pdbx_em_fsc_resolutionCategory> 0 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 pdbx_em_fsc_resolutionCategory This property indicates that datablock has a category holder pdbx_em_fsc_resolutionCategory. pdbx_em_fsc_resolutionCategory This property indicates that pdbx_em_fsc_resolutionCategory. has a category pdbx_em_fsc_resolution. pdbx_em_fsc_resolutionItem Abstract datatype property for pdbx_em_fsc_resolution items. reference_to_pdbx_em_fsc_resolution cross-reference to pdbx_em_fsc_resolution. referenced_by_pdbx_em_fsc_resolution cross-reference from pdbx_em_fsc_resolution. pdbx_em_fsc_resolution.correlation_coef The correlation coefficient at the intersection of Fourier-Shell Correlation (FSC) curve and FSC cut-off curve (or line) that represents a given criterion. Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#resolution_estimates pdbx_em_fsc_resolution.fsc_curve_id Pointer to attribute id in category pdbx_em_fsc_curve. pdbx_em_fsc_resolution.fsc_cutoff_curve_id Pointer to attribute id in category pdbx_em_fsc_cutoff_curve. pdbx_em_fsc_resolution.resolution The spatial resolution estimated from Fourier-Shell Correlation (FSC) curve with a given criteria. The inverse value of the resolution equals to the spatial frequency at the intersection. Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#resolution_estimates pdbx_em_fsc_resolution.resolution_unit A unit for the resolution. A pdbx_em_fsc_resolution.spatial_frequency The spatial frequency at the intersection of Fourier-Shell Correlation (FSC) curve and FSC cut-off curve (or line) that represents a given criterion. The inverse value of the spatial resolution equals to the estimated resolution. Ref: Marin van Heela, Michael Schatz Fourier shell correlation threshold criteria. Journal of Structural Biology. 2005 Sep;151(3):250-262. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#resolution_estimates pdbx_em_fsc_resolution.spatial_frequency_unit A unit for the spatial frequency of Fourier-Shell Correlation (FSC) curve. 1/A pdbx_em_fsc_resolution.criterion The criterion applied to estimate resolution from a given FSC curve. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#resolution_estimates 0.143 0.333 0.5 half-bit one-bit 3sigma pdbx_em_fsc_resolution.source The source of FSC curve for resolution estimation. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#resolution_estimates calculated_fsc author_provided_fsc 0 pdbx_em_raps Data items in the category record Rotationally Averaged Power Spectrum (RAPS) for the primary EM volume (map). The RAPS provides insight into the data processing steps leading to the map, in terms of: CTF correction, Temperature factor correction, Low and/or high-pass filtering, Masking artifacts. The RAPS is only generated for cubic volumes. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.3 Rotationally averaged power spectrum Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_rapsCategory> <VRPTx:pdbx_em_raps id="1"> <VRPTx:power_scale>log10</VRPTx:power_scale> <VRPTx:power_title>Intensity</VRPTx:power_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_raps> </VRPTx:pdbx_em_rapsCategory> 0 1 1 1 1 1 1 1 1 pdbx_em_rapsCategory This property indicates that datablock has a category holder pdbx_em_rapsCategory. pdbx_em_rapsCategory This property indicates that pdbx_em_rapsCategory. has a category pdbx_em_raps. pdbx_em_rapsItem Abstract datatype property for pdbx_em_raps items. reference_to_pdbx_em_raps cross-reference to pdbx_em_raps. referenced_by_pdbx_em_raps cross-reference from pdbx_em_raps. pdbx_em_raps.power_scale A scale for the power axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps log10 pdbx_em_raps.power_title A title for the power axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps Intensity pdbx_em_raps.spatial_frequency_title A title for the spatial frequency axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps Spatial frequency pdbx_em_raps.spatial_frequency_unit A unit for the spatial frequency axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps 1/A pdbx_em_raps.id The value of attribute id in category pdbx_em_raps must uniquely identify each item in the PDBX_EM_RAPS list. This is an integer serial number. 0 pdbx_em_raps_marker Data items in the category record Rotationally Averaged Power Spectrum (RAPS) plot for the primary EM volume (map). Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_raps_markerCategory> <VRPTx:pdbx_em_raps_marker ordinal="1" plot_id="1"> <VRPTx:power>5.0361312138</VRPTx:power> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="2" plot_id="1"> <VRPTx:power>4.6874764273</VRPTx:power> <VRPTx:spatial_frequency>0.0045551653</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="3" plot_id="1"> <VRPTx:power>4.0158584907</VRPTx:power> <VRPTx:spatial_frequency>0.0091103306</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="4" plot_id="1"> <VRPTx:power>3.3080813094</VRPTx:power> <VRPTx:spatial_frequency>0.0136654959</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="5" plot_id="1"> <VRPTx:power>3.3633413357</VRPTx:power> <VRPTx:spatial_frequency>0.0182206612</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> </VRPTx:pdbx_em_raps_markerCategory> 1 1 1 1 1 1 pdbx_em_raps_markerCategory This property indicates that datablock has a category holder pdbx_em_raps_markerCategory. pdbx_em_raps_markerCategory This property indicates that pdbx_em_raps_markerCategory. has a category pdbx_em_raps_marker. pdbx_em_raps_markerItem Abstract datatype property for pdbx_em_raps_marker items. reference_to_pdbx_em_raps_marker cross-reference to pdbx_em_raps_marker. referenced_by_pdbx_em_raps_marker cross-reference from pdbx_em_raps_marker. pdbx_em_raps_marker.power The scaled power at a spatial frequency of Rotationally Averaged Power Spectrum (RAPS) plot, namely y-axis value of RAPS curve. RAPS is a measure of the distribution of power into spatial frequency (resolution) components composing the primary EM volume. sum(N~i~ |F~i~|^2^) RAPS = ------------------- sum(N~i~) N~i~ = the number of all corresponding shell in Fourier space (spatial frequency) F~i~ = complex structure factor of the primary 3D volume at a spatial frequency Summation is carried over corresponding shells in Fourier space (spatial frequency). See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps pdbx_em_raps_marker.spatial_frequency The spatial frequencies of Rotationally Averaged Power Spectrum (RAPS), namely x-axis value of RAPS curve. (See '_pdbx_em_raps_marker.power') See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps pdbx_em_raps_marker.ordinal The ordered number in the plot marker. pdbx_em_raps_marker.plot_id Pointer to attribute id in category pdbx_em_raps. 0 pdbx_em_raw_raps Data items in the category record Rotationally Averaged Power Spectrum (RAPS) for raw EM volume (map). The RAPS provides insight into the data processing steps leading to the map, in terms of: CTF correction, Temperature factor correction, Low and/or high-pass filtering, Masking artifacts. The RAPS is only generated for cubic volumes. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.3 Rotationally averaged power spectrum Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_raw_rapsCategory> <VRPTx:pdbx_em_raw_raps id="1"> <VRPTx:power_scale>log10</VRPTx:power_scale> <VRPTx:power_title>Intensity</VRPTx:power_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_raw_raps> </VRPTx:pdbx_em_raw_rapsCategory> 0 1 1 1 1 1 1 1 1 pdbx_em_raw_rapsCategory This property indicates that datablock has a category holder pdbx_em_raw_rapsCategory. pdbx_em_raw_rapsCategory This property indicates that pdbx_em_raw_rapsCategory. has a category pdbx_em_raw_raps. pdbx_em_raw_rapsItem Abstract datatype property for pdbx_em_raw_raps items. reference_to_pdbx_em_raw_raps cross-reference to pdbx_em_raw_raps. referenced_by_pdbx_em_raw_raps cross-reference from pdbx_em_raw_raps. pdbx_em_raw_raps.power_scale A scale for the power axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps log10 pdbx_em_raw_raps.power_title A title for the power axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps Intensity pdbx_em_raw_raps.spatial_frequency_title A title for the spatial frequency axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps Spatial frequency pdbx_em_raw_raps.spatial_frequency_unit A unit for the spatial frequency axis of a Rotationally Averaged Power Spectrum (RAPS) plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps 1/A pdbx_em_raw_raps.id The value of attribute id in category pdbx_em_raw_raps must uniquely identify each item in the PDBX_EM_RAW_RAPS list. This is an integer serial number. 0 pdbx_em_raw_raps_marker Data items in the category record Rotationally Averaged Power Spectrum (RAPS) plot for raw EM volume (map). Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_raw_raps_markerCategory> <VRPTx:pdbx_em_raw_raps_marker ordinal="1" plot_id="1"> <VRPTx:power>5.0361312138</VRPTx:power> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="2" plot_id="1"> <VRPTx:power>4.6874764273</VRPTx:power> <VRPTx:spatial_frequency>0.0045551653</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="3" plot_id="1"> <VRPTx:power>4.0158584907</VRPTx:power> <VRPTx:spatial_frequency>0.0091103306</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="4" plot_id="1"> <VRPTx:power>3.3080813094</VRPTx:power> <VRPTx:spatial_frequency>0.0136654959</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="5" plot_id="1"> <VRPTx:power>3.3633413357</VRPTx:power> <VRPTx:spatial_frequency>0.0182206612</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> </VRPTx:pdbx_em_raw_raps_markerCategory> 1 1 1 1 1 1 pdbx_em_raw_raps_markerCategory This property indicates that datablock has a category holder pdbx_em_raw_raps_markerCategory. pdbx_em_raw_raps_markerCategory This property indicates that pdbx_em_raw_raps_markerCategory. has a category pdbx_em_raw_raps_marker. pdbx_em_raw_raps_markerItem Abstract datatype property for pdbx_em_raw_raps_marker items. reference_to_pdbx_em_raw_raps_marker cross-reference to pdbx_em_raw_raps_marker. referenced_by_pdbx_em_raw_raps_marker cross-reference from pdbx_em_raw_raps_marker. pdbx_em_raw_raps_marker.power The scaled power at a spatial frequency of Rotationally Averaged Power Spectrum (RAPS) plot, namely y-axis value of RAPS curve. RAPS is a measure of the distribution of power into spatial frequency (resolution) components composing raw EM volume. sum(N~i~ |F~i~|^2^) RAPS = ------------------- sum(N~i~) N~i~ = the number of all corresponding shell in Fourier space (spatial frequency) F~i~ = complex structure factor of raw 3D volume at a spatial frequency Summation is carried over corresponding shells in Fourier space (spatial frequency). See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps pdbx_em_raw_raps_marker.spatial_frequency The spatial frequencies of Rotationally Averaged Power Spectrum (RAPS), namely x-axis value of RAPS curve. (See '_pdbx_em_raw_raps_marker.power') See also: https://www.wwpdb.org/validation/EMValidationReportHelp#raps pdbx_em_raw_raps_marker.ordinal The ordered number in the plot marker. pdbx_em_raw_raps_marker.plot_id Pointer to attribute id in category pdbx_em_raw_raps. 0 pdbx_em_validate_map_model Data items in the category record EM map-model validation for each residue Ref: User guide to the wwPDB EM validation reports 9. Map-Model fit 9.3 Atom inclusion by residue 0 1 1 1 0 1 0 1 1 1 1 1 1 1 0 1 1 pdbx_em_validate_map_modelCategory This property indicates that datablock has a category holder pdbx_em_validate_map_modelCategory. pdbx_em_validate_map_modelCategory This property indicates that pdbx_em_validate_map_modelCategory. has a category pdbx_em_validate_map_model. pdbx_em_validate_map_modelItem Abstract datatype property for pdbx_em_validate_map_model items. reference_to_pdbx_em_validate_map_model cross-reference to pdbx_em_validate_map_model. referenced_by_pdbx_em_validate_map_model cross-reference from pdbx_em_validate_map_model. pdbx_em_validate_map_model.PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site. pdbx_em_validate_map_model.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_em_validate_map_model.Q_score Average value of Q-scores for each residue. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#Q-score_mapped_to_coordinate_model pdbx_em_validate_map_model.atom_inclusion_all Fraction of all non-hydrogen atoms of the residue within EM volume enclosed by the recommended contour level. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion_by_contour pdbx_em_validate_map_model.auth_asym_id Pointer to attribute auth_asym_id in category atom_site. pdbx_em_validate_map_model.auth_comp_id Pointer to attribute auth_comp_id in category atom_site. pdbx_em_validate_map_model.auth_seq_id Pointer to attribute auth_seq_id in category atom_site. pdbx_em_validate_map_model.label_alt_id Pointer to attribute label_alt_id in category atom_site. pdbx_em_validate_map_model.id The ordered number of residue in the output list. 0 pdbx_em_validate_map_model_entity Data items in the category record EM map-model validation for each entity Ref: User guide to the wwPDB EM validation reports 9. Map-Model fit 9.2 Atom inclusion 1 1 0 1 0 1 1 1 1 1 pdbx_em_validate_map_model_entityCategory This property indicates that datablock has a category holder pdbx_em_validate_map_model_entityCategory. pdbx_em_validate_map_model_entityCategory This property indicates that pdbx_em_validate_map_model_entityCategory. has a category pdbx_em_validate_map_model_entity. pdbx_em_validate_map_model_entityItem Abstract datatype property for pdbx_em_validate_map_model_entity items. reference_to_pdbx_em_validate_map_model_entity cross-reference to pdbx_em_validate_map_model_entity. referenced_by_pdbx_em_validate_map_model_entity cross-reference from pdbx_em_validate_map_model_entity. pdbx_em_validate_map_model_entity.auth_asym_id Pointer to attribute auth_asym_id in category atom_site. pdbx_em_validate_map_model_entity.average_Q_score Average value of Q-scores of residues in the entity. (see attribute Q-score) in category pdbx_em_validate_map_model See also: https://www.wwpdb.org/validation/EMValidationReportHelp#Q-score_mapped_to_coordinate_model pdbx_em_validate_map_model_entity.average_atom_inclusion_all Average number of all atom inclusion of residues in the entity. (see attribute atom_inclusion_all) in category pdbx_em_validate_map_model See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion_by_contour pdbx_em_validate_map_model_entity.entity_id Pointer to attribute label_entity_id in category atom_site. pdbx_em_validate_map_model_entity.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_em_validate_map_model_entity.label_asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 0 pdbx_em_validate_map_model_overall Data items in the category record overall EM map-model validation of each entry. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.2 Volume estimate by contour -> recommended_contour_level 9. Map-Model fit 9.2 Q-score mapped to coordinate model -> Q-score 9.4 Atom inclusion -> atom_inclusion_main, atom_inclusion_all 0 1 0 1 0 1 1 1 1 pdbx_em_validate_map_model_overallCategory This property indicates that datablock has a category holder pdbx_em_validate_map_model_overallCategory. pdbx_em_validate_map_model_overallCategory This property indicates that pdbx_em_validate_map_model_overallCategory. has a category pdbx_em_validate_map_model_overall. pdbx_em_validate_map_model_overallItem Abstract datatype property for pdbx_em_validate_map_model_overall items. reference_to_pdbx_em_validate_map_model_overall cross-reference to pdbx_em_validate_map_model_overall. referenced_by_pdbx_em_validate_map_model_overall cross-reference from pdbx_em_validate_map_model_overall. pdbx_em_validate_map_model_overall.Q_score Average value of Q-scores for the whole structure. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#Q-score_mapped_to_coordinate_model pdbx_em_validate_map_model_overall.atom_inclusion_all Fraction of all non-hydrogen atoms within EM volume enclosed by the recommended contour level. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion_by_contour pdbx_em_validate_map_model_overall.atom_inclusion_main Fraction of backbone atoms within EM volume enclosed by the recommended contour level where the backbone atoms represent N, C, O, CA for amino acids, C3', C4', C5', O3', O5', P for nucleic acids and all non-hydrogen atoms of any ligand. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#atom_inclusion_by_contour pdbx_em_validate_map_model_overall.recommended_contour_level Recommended contour level of the primary map estimated by statistical analysis of the EM volume. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#map_analysis pdbx_em_validate_map_model_overall.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_em_volume_estimate Data items in the category record volume estimation of the primary EM volume. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.2 Volume estimate by contour Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_volume_estimateCategory> <VRPTx:pdbx_em_volume_estimate id="1"> <VRPTx:contour_level_title>Contour level</VRPTx:contour_level_title> <VRPTx:enclosed_volume_title>Volume</VRPTx:enclosed_volume_title> <VRPTx:enclosed_volume_unit>nm3</VRPTx:enclosed_volume_unit> </VRPTx:pdbx_em_volume_estimate> </VRPTx:pdbx_em_volume_estimateCategory> 1 1 1 1 1 1 1 pdbx_em_volume_estimateCategory This property indicates that datablock has a category holder pdbx_em_volume_estimateCategory. pdbx_em_volume_estimateCategory This property indicates that pdbx_em_volume_estimateCategory. has a category pdbx_em_volume_estimate. pdbx_em_volume_estimateItem Abstract datatype property for pdbx_em_volume_estimate items. reference_to_pdbx_em_volume_estimate cross-reference to pdbx_em_volume_estimate. referenced_by_pdbx_em_volume_estimate cross-reference from pdbx_em_volume_estimate. pdbx_em_volume_estimate.contour_level_title A title for the contour level (map value) axis of a volume estimation plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#volume_estimate Contour level pdbx_em_volume_estimate.enclosed_volume_title A title for the enclosed volume (by a contour level) axis of a volume estimation plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#volume_estimate Number of voxels pdbx_em_volume_estimate.enclosed_volume_unit A unit for the enclosed volume (by a contour level) axis of a volume estimation plot. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#volume_estimate nm3 pdbx_em_volume_estimate.id The value of attribute id in category pdbx_em_volume_estimate must uniquely identify each item in the PDBX_EM_VOLUME_ESTIMATE list. This is an integer serial number. 0 pdbx_em_volume_estimate_marker Data items in the category record volume estimation plot of the primary EM volume. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_volume_estimate_markerCategory> <VRPTx:pdbx_em_volume_estimate_marker ordinal="1" plot_id="1"> <VRPTx:contour_level>-0.0971993208</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9715137</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="2" plot_id="1"> <VRPTx:contour_level>-0.0950082897</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9583621</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="3" plot_id="1"> <VRPTx:contour_level>-0.0928172586</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9583621</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="4" plot_id="1"> <VRPTx:contour_level>-0.0906262274</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9517863</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="5" plot_id="1"> <VRPTx:contour_level>-0.0884351963</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9517863</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> </VRPTx:pdbx_em_volume_estimate_markerCategory> 1 1 1 1 1 1 pdbx_em_volume_estimate_markerCategory This property indicates that datablock has a category holder pdbx_em_volume_estimate_markerCategory. pdbx_em_volume_estimate_markerCategory This property indicates that pdbx_em_volume_estimate_markerCategory. has a category pdbx_em_volume_estimate_marker. pdbx_em_volume_estimate_markerItem Abstract datatype property for pdbx_em_volume_estimate_marker items. reference_to_pdbx_em_volume_estimate_marker cross-reference to pdbx_em_volume_estimate_marker. referenced_by_pdbx_em_volume_estimate_marker cross-reference from pdbx_em_volume_estimate_marker. pdbx_em_volume_estimate_marker.contour_level A certain contour level for the primary EM volume. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#volume_estimate pdbx_em_volume_estimate_marker.enclosed_volume The enclosed volume by a given contour level. See also: https://www.wwpdb.org/validation/EMValidationReportHelp#volume_estimate pdbx_em_volume_estimate_marker.ordinal The ordered number in the plot marker. pdbx_em_volume_estimate_marker.plot_id Pointer to attribute id in category pdbx_em_volume_estimate. 0 pdbx_entity_assembly The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities. A complex composed of one copy of entities 1 and 2. <VRPTx:pdbx_entity_assemblyCategory> <VRPTx:pdbx_entity_assembly entity_id="1" id="1"> <VRPTx:biol_id>1</VRPTx:biol_id> <VRPTx:num_copies>1</VRPTx:num_copies> </VRPTx:pdbx_entity_assembly> <VRPTx:pdbx_entity_assembly entity_id="2" id="1"> <VRPTx:biol_id>1</VRPTx:biol_id> <VRPTx:num_copies>1</VRPTx:num_copies> </VRPTx:pdbx_entity_assembly> </VRPTx:pdbx_entity_assemblyCategory> 1 1 1 1 1 1 pdbx_entity_assemblyCategory This property indicates that datablock has a category holder pdbx_entity_assemblyCategory. pdbx_entity_assemblyCategory This property indicates that pdbx_entity_assemblyCategory. has a category pdbx_entity_assembly. pdbx_entity_assemblyItem Abstract datatype property for pdbx_entity_assembly items. reference_to_pdbx_entity_assembly cross-reference to pdbx_entity_assembly. referenced_by_pdbx_entity_assembly cross-reference from pdbx_entity_assembly. pdbx_entity_assembly.biol_id An identifier for the assembly. pdbx_entity_assembly.num_copies The number of copies of this entity in the assembly. pdbx_entity_assembly.entity_id An enity identifier. A reference to attribute id in category entity. pdbx_entity_assembly.id An identifier for the assembly. 0 pdbx_entity_branch Data items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type. Example 1 - <VRPTx:pdbx_entity_branchCategory> <VRPTx:pdbx_entity_branch entity_id="2"> <VRPTx:type>oligosaccharide</VRPTx:type> </VRPTx:pdbx_entity_branch> </VRPTx:pdbx_entity_branchCategory> 1 1 1 pdbx_entity_branchCategory This property indicates that datablock has a category holder pdbx_entity_branchCategory. pdbx_entity_branchCategory This property indicates that pdbx_entity_branchCategory. has a category pdbx_entity_branch. pdbx_entity_branchItem Abstract datatype property for pdbx_entity_branch items. reference_to_pdbx_entity_branch cross-reference to pdbx_entity_branch. referenced_by_pdbx_entity_branch cross-reference from pdbx_entity_branch. oligosaccharide The type of this branched oligosaccharide. pdbx_entity_branch.entity_id The entity id for this branched entity. This data item is a pointer to attribute id in category entity 0 pdbx_entity_branch_descriptor Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide string descriptors of entity chemical structure. Example 1 - <VRPTx:pdbx_entity_branch_descriptorCategory> <VRPTx:pdbx_entity_branch_descriptor ordinal="1"> <VRPTx:descriptor>[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}</VRPTx:descriptor> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:program>PDB-CARE</VRPTx:program> <VRPTx:program_version>Beta</VRPTx:program_version> <VRPTx:type>LINUCS</VRPTx:type> </VRPTx:pdbx_entity_branch_descriptor> </VRPTx:pdbx_entity_branch_descriptorCategory> 1 1 1 1 0 1 0 1 1 1 1 pdbx_entity_branch_descriptorCategory This property indicates that datablock has a category holder pdbx_entity_branch_descriptorCategory. pdbx_entity_branch_descriptorCategory This property indicates that pdbx_entity_branch_descriptorCategory. has a category pdbx_entity_branch_descriptor. pdbx_entity_branch_descriptorItem Abstract datatype property for pdbx_entity_branch_descriptor items. reference_to_pdbx_entity_branch_descriptor cross-reference to pdbx_entity_branch_descriptor. referenced_by_pdbx_entity_branch_descriptor cross-reference from pdbx_entity_branch_descriptor. pdbx_entity_branch_descriptor.descriptor This data item contains the descriptor value for this entity. pdbx_entity_branch_descriptor.entity_id This data item is a pointer to attribute entity_id in category entity_poly in the ENTITY category. pdbx_entity_branch_descriptor.program This data item contains the name of the program or library used to compute the descriptor. PDB-CARE Other program or library OTHER GEMS pdbx_entity_branch_descriptor.program_version This data item contains the version of the program or library used to compute the descriptor. LINUCS Glycam Condensed Sequence Glycam Condensed Core Sequence WURCS This data item contains the descriptor type. pdbx_entity_branch_descriptor.ordinal Ordinal index for this category. 0 pdbx_entity_branch_link Data items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity. Example 1 - base on PDB entry 2WMG <VRPTx:pdbx_entity_branch_linkCategory> <VRPTx:pdbx_entity_branch_link link_id="1"> <VRPTx:atom_id_1>O4</VRPTx:atom_id_1> <VRPTx:atom_id_2>C1</VRPTx:atom_id_2> <VRPTx:atom_stereo_config_2>R</VRPTx:atom_stereo_config_2> <VRPTx:comp_id_1>NAG</VRPTx:comp_id_1> <VRPTx:comp_id_2>GAL</VRPTx:comp_id_2> <VRPTx:entity_branch_list_num_1>1</VRPTx:entity_branch_list_num_1> <VRPTx:entity_branch_list_num_2>2</VRPTx:entity_branch_list_num_2> <VRPTx:entity_id>2</VRPTx:entity_id> <VRPTx:leaving_atom_id_1>HO4</VRPTx:leaving_atom_id_1> <VRPTx:leaving_atom_id_2>O1</VRPTx:leaving_atom_id_2> <VRPTx:value_order>sing</VRPTx:value_order> </VRPTx:pdbx_entity_branch_link> <VRPTx:pdbx_entity_branch_link link_id="2"> <VRPTx:atom_id_1>O2</VRPTx:atom_id_1> <VRPTx:atom_id_2>C1</VRPTx:atom_id_2> <VRPTx:atom_stereo_config_2>R</VRPTx:atom_stereo_config_2> <VRPTx:comp_id_1>GAL</VRPTx:comp_id_1> <VRPTx:comp_id_2>FUC</VRPTx:comp_id_2> <VRPTx:entity_branch_list_num_1>2</VRPTx:entity_branch_list_num_1> <VRPTx:entity_branch_list_num_2>3</VRPTx:entity_branch_list_num_2> <VRPTx:entity_id>2</VRPTx:entity_id> <VRPTx:leaving_atom_id_1>HO2</VRPTx:leaving_atom_id_1> <VRPTx:leaving_atom_id_2>O1</VRPTx:leaving_atom_id_2> <VRPTx:value_order>sing</VRPTx:value_order> </VRPTx:pdbx_entity_branch_link> <VRPTx:pdbx_entity_branch_link link_id="3"> <VRPTx:atom_id_1>O3</VRPTx:atom_id_1> <VRPTx:atom_id_2>C1</VRPTx:atom_id_2> <VRPTx:atom_stereo_config_2>R</VRPTx:atom_stereo_config_2> <VRPTx:comp_id_1>NAG</VRPTx:comp_id_1> <VRPTx:comp_id_2>FUC</VRPTx:comp_id_2> <VRPTx:entity_branch_list_num_1>1</VRPTx:entity_branch_list_num_1> <VRPTx:entity_branch_list_num_2>4</VRPTx:entity_branch_list_num_2> <VRPTx:entity_id>2</VRPTx:entity_id> <VRPTx:leaving_atom_id_1>HO3</VRPTx:leaving_atom_id_1> <VRPTx:leaving_atom_id_2>O1</VRPTx:leaving_atom_id_2> <VRPTx:value_order>sing</VRPTx:value_order> </VRPTx:pdbx_entity_branch_link> </VRPTx:pdbx_entity_branch_linkCategory> 1 1 1 1 0 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_entity_branch_linkCategory This property indicates that datablock has a category holder pdbx_entity_branch_linkCategory. pdbx_entity_branch_linkCategory This property indicates that pdbx_entity_branch_linkCategory. has a category pdbx_entity_branch_link. pdbx_entity_branch_linkItem Abstract datatype property for pdbx_entity_branch_link items. reference_to_pdbx_entity_branch_link cross-reference to pdbx_entity_branch_link. referenced_by_pdbx_entity_branch_link cross-reference from pdbx_entity_branch_link. pdbx_entity_branch_link.atom_id_1 The atom identifier/name for the first atom making the linkage. pdbx_entity_branch_link.atom_id_2 The atom identifier/name for the second atom making the linkage. R S N The chiral configuration of the first atom making the linkage. R S N The chiral configuration of the second atom making the linkage. pdbx_entity_branch_link.comp_id_1 The component identifier for the first component making the linkage. This data item is a pointer to attribute comp_id in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. pdbx_entity_branch_link.comp_id_2 The component identifier for the second component making the linkage. This data item is a pointer to attribute comp_id in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. pdbx_entity_branch_link.details A description of special aspects of this linkage. pdbx_entity_branch_link.entity_branch_list_num_1 The component number for the first component making the linkage. This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. pdbx_entity_branch_link.entity_branch_list_num_2 The component number for the second component making the linkage. This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. pdbx_entity_branch_link.entity_id The entity id for this branched entity. This data item is a pointer to attribute entity_id in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. pdbx_entity_branch_link.leaving_atom_id_1 The leaving atom identifier/name bonded to the first atom making the linkage. pdbx_entity_branch_link.leaving_atom_id_2 The leaving atom identifier/name bonded to the second atom making the linkage. sing doub trip quad arom poly delo pi The bond order target for the chemical linkage. pdbx_entity_branch_link.link_id The value of attribute link_id in category pdbx_entity_branch_link uniquely identifies linkages within the branched entity. 0 pdbx_entity_branch_list Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list of monomers in a branched entity. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - <VRPTx:pdbx_entity_branch_listCategory> <VRPTx:pdbx_entity_branch_list comp_id="NAG" entity_id="2" num="1"> <VRPTx:hetero>n</VRPTx:hetero> </VRPTx:pdbx_entity_branch_list> <VRPTx:pdbx_entity_branch_list comp_id="GAL" entity_id="2" num="2"> <VRPTx:hetero>n</VRPTx:hetero> </VRPTx:pdbx_entity_branch_list> <VRPTx:pdbx_entity_branch_list comp_id="FUC" entity_id="2" num="3"> <VRPTx:hetero>n</VRPTx:hetero> </VRPTx:pdbx_entity_branch_list> <VRPTx:pdbx_entity_branch_list comp_id="FUC" entity_id="2" num="4"> <VRPTx:hetero>n</VRPTx:hetero> </VRPTx:pdbx_entity_branch_list> </VRPTx:pdbx_entity_branch_listCategory> 0 1 1 1 1 pdbx_entity_branch_listCategory This property indicates that datablock has a category holder pdbx_entity_branch_listCategory. pdbx_entity_branch_listCategory This property indicates that pdbx_entity_branch_listCategory. has a category pdbx_entity_branch_list. pdbx_entity_branch_listItem Abstract datatype property for pdbx_entity_branch_list items. reference_to_pdbx_entity_branch_list cross-reference to pdbx_entity_branch_list. referenced_by_pdbx_entity_branch_list cross-reference from pdbx_entity_branch_list. no n yes y A flag to indicate whether this monomer in the entity is heterogeneous in sequence. pdbx_entity_branch_list.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. pdbx_entity_branch_list.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. pdbx_entity_branch_list.num The value pair _pdbx_entity_branch_list.num and _pdbx_entity_branch_list.comp_id must uniquely identify a record in the PDBX_ENTITY_BRANCH_LIST list. 0 pdbx_entity_descriptor Data items in the PDBX_ENTITY_DESCRIPTOR category provide string descriptors of entity chemical structure. Example 1 - <VRPTx:pdbx_entity_descriptorCategory> <VRPTx:pdbx_entity_descriptor ordinal="1"> <VRPTx:descriptor>[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}</VRPTx:descriptor> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:program>PDB-CARE</VRPTx:program> <VRPTx:program_version>Beta</VRPTx:program_version> <VRPTx:type>LINUCS</VRPTx:type> </VRPTx:pdbx_entity_descriptor> </VRPTx:pdbx_entity_descriptorCategory> 1 1 1 1 0 1 0 1 1 1 1 pdbx_entity_descriptorCategory This property indicates that datablock has a category holder pdbx_entity_descriptorCategory. pdbx_entity_descriptorCategory This property indicates that pdbx_entity_descriptorCategory. has a category pdbx_entity_descriptor. pdbx_entity_descriptorItem Abstract datatype property for pdbx_entity_descriptor items. reference_to_pdbx_entity_descriptor cross-reference to pdbx_entity_descriptor. referenced_by_pdbx_entity_descriptor cross-reference from pdbx_entity_descriptor. pdbx_entity_descriptor.descriptor This data item contains the descriptor value for this entity. pdbx_entity_descriptor.entity_id This data item is a pointer to attribute entity_id in category entity_poly in the ENTITY category. pdbx_entity_descriptor.program This data item contains the name of the program or library used to compute the descriptor. PDB-CARE Other program or library OTHER Gems pdbx_entity_descriptor.program_version This data item contains the version of the program or library used to compute the descriptor. LINUCS Glycam Condensed Sequence Glycam Condensed Core Sequence This data item contains the descriptor type. pdbx_entity_descriptor.ordinal Ordinal index for this category. 0 pdbx_entity_nonpoly The PDBX_ENTITY_NONPOLY category provides a mapping between entity and the nonpolymer component Example 1 - based on PDB entry 3LTQ <VRPTx:pdbx_entity_nonpolyCategory> <VRPTx:pdbx_entity_nonpoly entity_id="2"> <VRPTx:comp_id>TB</VRPTx:comp_id> <VRPTx:name>TERBIUM(III) ION</VRPTx:name> </VRPTx:pdbx_entity_nonpoly> <VRPTx:pdbx_entity_nonpoly entity_id="3"> <VRPTx:comp_id>ACT</VRPTx:comp_id> <VRPTx:name>ACETATE ION</VRPTx:name> </VRPTx:pdbx_entity_nonpoly> <VRPTx:pdbx_entity_nonpoly entity_id="4"> <VRPTx:comp_id>SO4</VRPTx:comp_id> <VRPTx:name>SULFATE ION</VRPTx:name> </VRPTx:pdbx_entity_nonpoly> <VRPTx:pdbx_entity_nonpoly entity_id="5"> <VRPTx:comp_id>HOH</VRPTx:comp_id> <VRPTx:name>water</VRPTx:name> </VRPTx:pdbx_entity_nonpoly> </VRPTx:pdbx_entity_nonpolyCategory> 0 1 0 1 1 pdbx_entity_nonpolyCategory This property indicates that datablock has a category holder pdbx_entity_nonpolyCategory. pdbx_entity_nonpolyCategory This property indicates that pdbx_entity_nonpolyCategory. has a category pdbx_entity_nonpoly. pdbx_entity_nonpolyItem Abstract datatype property for pdbx_entity_nonpoly items. reference_to_pdbx_entity_nonpoly cross-reference to pdbx_entity_nonpoly. referenced_by_pdbx_entity_nonpoly cross-reference from pdbx_entity_nonpoly. pdbx_entity_nonpoly.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. pdbx_entity_nonpoly.name A name for the non-polymer entity pdbx_entity_nonpoly.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 pdbx_entity_poly_comp_link_list Data items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate the linkages between components within the polymer entity. Example 1 - <VRPTx:pdbx_entity_poly_comp_link_listCategory> <VRPTx:pdbx_entity_poly_comp_link_list link_id="1"> <VRPTx:atom_id_1 xsi:nil="true" /> <VRPTx:atom_id_2 xsi:nil="true" /> <VRPTx:atom_stereo_config_1 xsi:nil="true" /> <VRPTx:atom_stereo_config_2 xsi:nil="true" /> <VRPTx:comp_id_1 xsi:nil="true" /> <VRPTx:comp_id_2 xsi:nil="true" /> <VRPTx:entity_comp_num_1>1</VRPTx:entity_comp_num_1> <VRPTx:entity_comp_num_2>2</VRPTx:entity_comp_num_2> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:leaving_atom_id_1 xsi:nil="true" /> <VRPTx:leaving_atom_id_2 xsi:nil="true" /> <VRPTx:value_order>sing</VRPTx:value_order> </VRPTx:pdbx_entity_poly_comp_link_list> </VRPTx:pdbx_entity_poly_comp_link_listCategory> 1 1 1 1 0 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_entity_poly_comp_link_listCategory This property indicates that datablock has a category holder pdbx_entity_poly_comp_link_listCategory. pdbx_entity_poly_comp_link_listCategory This property indicates that pdbx_entity_poly_comp_link_listCategory. has a category pdbx_entity_poly_comp_link_list. pdbx_entity_poly_comp_link_listItem Abstract datatype property for pdbx_entity_poly_comp_link_list items. reference_to_pdbx_entity_poly_comp_link_list cross-reference to pdbx_entity_poly_comp_link_list. referenced_by_pdbx_entity_poly_comp_link_list cross-reference from pdbx_entity_poly_comp_link_list. pdbx_entity_poly_comp_link_list.atom_id_1 The atom identifier/name for the first atom making the linkage. pdbx_entity_poly_comp_link_list.atom_id_2 The atom identifier/name for the second atom making the linkage. R S N The chiral configuration of the first atom making the linkage. R S N The chiral configuration of the second atom making the linkage. pdbx_entity_poly_comp_link_list.comp_id_1 The component identifier for the first component making the linkage. This data item is a pointer to attribute mon_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_entity_poly_comp_link_list.comp_id_2 The component identifier for the second component making the linkage. This data item is a pointer to attribute mon_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_entity_poly_comp_link_list.details A description of special aspects of this linkage. pdbx_entity_poly_comp_link_list.entity_comp_num_1 The component number for the first component making the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_entity_poly_comp_link_list.entity_comp_num_2 The component number for the second component making the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_entity_poly_comp_link_list.entity_id The entity id for this branched entity. This data item is a pointer to attribute entity_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_entity_poly_comp_link_list.leaving_atom_id_1 The leaving atom identifier/name bonded to the first atom making the linkage. pdbx_entity_poly_comp_link_list.leaving_atom_id_2 The leaving atom identifier/name bonded to the second atom making the linkage. sing doub trip quad arom poly delo pi The bond order target for the chemical linkage. pdbx_entity_poly_comp_link_list.link_id The value of attribute link_id in category pdbx_entity_poly_comp_link_list uniquely identifies linkages within the branched entity. 0 pdbx_entry_details Data items in the PDBX_ENTRY_DETAILS category provide additional details about this entry. Example 1 - <VRPTx:pdbx_entry_detailsCategory> <VRPTx:pdbx_entry_details entry_id="1ABC"> <VRPTx:nonpolymer_details>Inhibitor VX4A in this entry adopts a highly strained conformation about C32 inorder to fit into the cleft about the active site.</VRPTx:nonpolymer_details> </VRPTx:pdbx_entry_details> </VRPTx:pdbx_entry_detailsCategory> 0 1 0 1 0 1 0 1 0 1 1 pdbx_entry_detailsCategory This property indicates that datablock has a category holder pdbx_entry_detailsCategory. pdbx_entry_detailsCategory This property indicates that pdbx_entry_detailsCategory. has a category pdbx_entry_details. pdbx_entry_detailsItem Abstract datatype property for pdbx_entry_details items. reference_to_pdbx_entry_details cross-reference to pdbx_entry_details. referenced_by_pdbx_entry_details cross-reference from pdbx_entry_details. pdbx_entry_details.compound_details Additional details about the macromolecular compounds in this entry. Y N A flag to indicate if author has indicated that there are any or no ligands that are the focus of research. Y pdbx_entry_details.nonpolymer_details Additional details about the non-polymer components in this entry. pdbx_entry_details.sequence_details Additional details about the sequence or sequence database correspondences for this entry. pdbx_entry_details.source_details Additional details about the source and taxonomy of the macromolecular components in this entry. pdbx_entry_details.entry_id This item identifies the entry. This is a reference to attribute id in category entry. 0 pdbx_helical_symmetry Data items in the PDBX_HELICAL_SYMMETRY category record details about the helical symmetry group associated with this entry. Example 1 - <VRPTx:pdbx_helical_symmetryCategory> <VRPTx:pdbx_helical_symmetry entry_id="1ABC"> <VRPTx:circular_symmetry>1</VRPTx:circular_symmetry> <VRPTx:dyad_axis>no</VRPTx:dyad_axis> <VRPTx:n_subunits_divisor>1</VRPTx:n_subunits_divisor> <VRPTx:number_of_operations>35</VRPTx:number_of_operations> <VRPTx:rise_per_n_subunits>6.10</VRPTx:rise_per_n_subunits> <VRPTx:rotation_per_n_subunits>131.84</VRPTx:rotation_per_n_subunits> </VRPTx:pdbx_helical_symmetry> </VRPTx:pdbx_helical_symmetryCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_helical_symmetryCategory This property indicates that datablock has a category holder pdbx_helical_symmetryCategory. pdbx_helical_symmetryCategory This property indicates that pdbx_helical_symmetryCategory. has a category pdbx_helical_symmetry. pdbx_helical_symmetryItem Abstract datatype property for pdbx_helical_symmetry items. reference_to_pdbx_helical_symmetry cross-reference to pdbx_helical_symmetry. referenced_by_pdbx_helical_symmetry cross-reference from pdbx_helical_symmetry. pdbx_helical_symmetry.circular_symmetry Rotational n-fold symmetry about the helical axis. no yes Two-fold symmetry perpendicular to the helical axis. pdbx_helical_symmetry.n_subunits_divisor Number of subunits used in the calculation of rise and rotation. pdbx_helical_symmetry.number_of_operations Number of operations. pdbx_helical_symmetry.rise_per_n_subunits Angular rotation (degrees) in N subunits pdbx_helical_symmetry.rotation_per_n_subunits Angular rotation (degrees) in N subunits pdbx_helical_symmetry.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_missing_nmr_star_item Items in the PDBX_MISSING_NMR_STAR_ITEM category provide information about required NMR-STAR V3 data items to parse assigned chemical shifts. 0 1 1 1 1 1 pdbx_missing_nmr_star_itemCategory This property indicates that datablock has a category holder pdbx_missing_nmr_star_itemCategory. pdbx_missing_nmr_star_itemCategory This property indicates that pdbx_missing_nmr_star_itemCategory. has a category pdbx_missing_nmr_star_item. pdbx_missing_nmr_star_itemItem Abstract datatype property for pdbx_missing_nmr_star_item items. reference_to_pdbx_missing_nmr_star_item cross-reference to pdbx_missing_nmr_star_item. referenced_by_pdbx_missing_nmr_star_item cross-reference from pdbx_missing_nmr_star_item. pdbx_missing_nmr_star_item.description The description of the missing NMR-STAR V3 data item to parse assigned chemical shifts. pdbx_missing_nmr_star_item.name The name of the missing NMR-STAR V3 data item to parse assigned chemical shifts. pdbx_missing_nmr_star_item.id The value of attribute id in category pdbx_missing_nmr_star_item must uniquely identify each item in the PDBX_MISSING_NMR_STAR_ITEM list. This is an integer serial number. pdbx_missing_nmr_star_item.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_nmr_assigned_chem_shift_list Items in the PDBX_NMR_ASSIGNED_CHEM_SHIFT_LIST category provide information about a list of reported assigned chemical shift values. 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_assigned_chem_shift_listCategory This property indicates that datablock has a category holder pdbx_nmr_assigned_chem_shift_listCategory. pdbx_nmr_assigned_chem_shift_listCategory This property indicates that pdbx_nmr_assigned_chem_shift_listCategory. has a category pdbx_nmr_assigned_chem_shift_list. pdbx_nmr_assigned_chem_shift_listItem Abstract datatype property for pdbx_nmr_assigned_chem_shift_list items. reference_to_pdbx_nmr_assigned_chem_shift_list cross-reference to pdbx_nmr_assigned_chem_shift_list. referenced_by_pdbx_nmr_assigned_chem_shift_list cross-reference from pdbx_nmr_assigned_chem_shift_list. pdbx_nmr_assigned_chem_shift_list.chem_shift_13C_err The value assigned as the error for all 13C chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.1 pdbx_nmr_assigned_chem_shift_list.chem_shift_15N_err The value assigned as the error for all 15N chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.2 pdbx_nmr_assigned_chem_shift_list.chem_shift_19F_err The value assigned as the error for all 19F chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.01 pdbx_nmr_assigned_chem_shift_list.chem_shift_1H_err The value assigned as the error for all 1H chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.01 pdbx_nmr_assigned_chem_shift_list.chem_shift_2H_err The value assigned as the error for all 2H chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.01 pdbx_nmr_assigned_chem_shift_list.chem_shift_31P_err The value assigned as the error for all 31P chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.1 pdbx_nmr_assigned_chem_shift_list.data_file_name The name of the file submitted with a deposition that contains the quantitative chemical shift data. pdbx_nmr_assigned_chem_shift_list.label A descriptive label that uniquely identifies a list of reported assigned chemical shifts. assigned chem shift set 1 Y N Whether all NMR-STAR items of assigned chemical shifts are found (Y) or not (N). pdbx_nmr_assigned_chem_shift_list.number_chem_shifts The total number of assigned chemical shifts in the assigned chemical shift list. pdbx_nmr_assigned_chem_shift_list.number_map_errors The number of assigned chemical shifts not mapped to atoms in the NMR structure. 0 pdbx_nmr_assigned_chem_shift_list.number_map_warnings The number of assigned chemical shifts ambiguously mapped to atoms in the NMR structure. 0 pdbx_nmr_assigned_chem_shift_list.number_mapped_chem_shifts The number of assigned chemical shifts successfully mapped to atoms in the NMR structure. pdbx_nmr_assigned_chem_shift_list.number_parsed_chem_shifts The number of assigned chemical shifts successfully parsed. pdbx_nmr_assigned_chem_shift_list.number_unparsed_chem_shifts The number of assigned chemical shifts not parsed. 0 pdbx_nmr_assigned_chem_shift_list.id An integer value that uniquely identifies a list of assigned chemical shifts from other sets of assigned chemical shifts in the entry. 0 pdbx_nmr_chem_shift_annotation Items in the PDBX_NMR_CHEM_SHIFT_ANNOTATION category provide information about various derived values from assigned chemical shifts. e.g. random coil index. 0 1 0 1 0 1 0 1 1 1 pdbx_nmr_chem_shift_annotationCategory This property indicates that datablock has a category holder pdbx_nmr_chem_shift_annotationCategory. pdbx_nmr_chem_shift_annotationCategory This property indicates that pdbx_nmr_chem_shift_annotationCategory. has a category pdbx_nmr_chem_shift_annotation. pdbx_nmr_chem_shift_annotationItem Abstract datatype property for pdbx_nmr_chem_shift_annotation items. reference_to_pdbx_nmr_chem_shift_annotation cross-reference to pdbx_nmr_chem_shift_annotation. referenced_by_pdbx_nmr_chem_shift_annotation cross-reference from pdbx_nmr_chem_shift_annotation. pdbx_nmr_chem_shift_annotation.auth_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_chem_shift_annotation.auth_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_chem_shift_annotation.auth_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_chem_shift_annotation.random_coil_index Assigned chemical shift value in ppm. pdbx_nmr_chem_shift_annotation.id The value of attribute id in category pdbx_nmr_chem_shift_annotation must uniquely identify each item in the PDBX_NMR_CHEM_SHIFT_ANNOTATION list. This is an integer serial number. pdbx_nmr_chem_shift_annotation.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_nmr_chem_shift_completeness Items in the PDBX_NMR_CHEM_SHIFT_COMPLETENESS category provide information about completeness of assigned chemical shifts. 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_nmr_chem_shift_completenessCategory This property indicates that datablock has a category holder pdbx_nmr_chem_shift_completenessCategory. pdbx_nmr_chem_shift_completenessCategory This property indicates that pdbx_nmr_chem_shift_completenessCategory. has a category pdbx_nmr_chem_shift_completeness. pdbx_nmr_chem_shift_completenessItem Abstract datatype property for pdbx_nmr_chem_shift_completeness items. reference_to_pdbx_nmr_chem_shift_completeness cross-reference to pdbx_nmr_chem_shift_completeness. referenced_by_pdbx_nmr_chem_shift_completeness cross-reference from pdbx_nmr_chem_shift_completeness. pdbx_nmr_chem_shift_completeness.number_assigned_chem_shifts The total number of assigned chemical shifts for the specified atom type and atom group. pdbx_nmr_chem_shift_completeness.number_assigned_chem_shifts_well_formed The total number of assigned chemical shifts for the specified atom type and atom group within polypeptide chain segments structurally well formed. pdbx_nmr_chem_shift_completeness.number_target_shifts The total number of typically assignable chemical shifts for the specified atom type and atom group. pdbx_nmr_chem_shift_completeness.number_target_shifts_well_formed The total number of typically assignable chemical shifts for the specified atom type and atom group within polypeptide chain segments structurally well formed. pdbx_nmr_chem_shift_completeness.number_unassigned_chem_shifts The total number of unassigned chemical shifts for the specified atom type and atom group. pdbx_nmr_chem_shift_completeness.number_unassigned_chem_shifts_well_formed The total number of unassigned chemical shifts for the specified atom type and atom group within polypeptide chain segments structurally well formed. pdbx_nmr_chem_shift_completeness.atom_group The group of atoms within a molecule whose completeness of assigned chemical shifts is calculated. pdbx_nmr_chem_shift_completeness.atom_type The kind of element (or atom) for which the completeness of assigned chemical shifts is calculated. pdbx_nmr_chem_shift_completeness.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_nmr_chem_shift_re_offset Items in the PDBX_NMR_CHEM_SHIFT_RE_OFFSET category provide information about chemical shift reference correction based on assigned chemical shifts. 0 1 0 1 0 1 0 1 1 1 pdbx_nmr_chem_shift_re_offsetCategory This property indicates that datablock has a category holder pdbx_nmr_chem_shift_re_offsetCategory. pdbx_nmr_chem_shift_re_offsetCategory This property indicates that pdbx_nmr_chem_shift_re_offsetCategory. has a category pdbx_nmr_chem_shift_re_offset. pdbx_nmr_chem_shift_re_offsetItem Abstract datatype property for pdbx_nmr_chem_shift_re_offset items. reference_to_pdbx_nmr_chem_shift_re_offset cross-reference to pdbx_nmr_chem_shift_re_offset. referenced_by_pdbx_nmr_chem_shift_re_offset cross-reference from pdbx_nmr_chem_shift_re_offset. pdbx_nmr_chem_shift_re_offset.correction_val An uniform correction value in ppm of assigned chemical shifts for the specified atom. pdbx_nmr_chem_shift_re_offset.correction_val_err Default error of the correction value in ppm. pdbx_nmr_chem_shift_re_offset.correction_val_esd The estimated standard deviation of the correction value in ppm. pdbx_nmr_chem_shift_re_offset.number_chem_shifts The total number of assigned chemical shifts for the specified atom. pdbx_nmr_chem_shift_re_offset.atom_type The kind of atom to which the chemical shift offset value applies. pdbx_nmr_chem_shift_re_offset.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_nmr_constraints This section provides a tabulation of constraint data. This example uses the data from the MCP-1 structure determination. Remember this is a dimer so there are intersubunit constraints as well as intrasubunit constraints. <VRPTx:pdbx_nmr_constraintsCategory> <VRPTx:pdbx_nmr_constraints entry_id="1ABC"> <VRPTx:NOE_constraints_total>4458</VRPTx:NOE_constraints_total> <VRPTx:NOE_intraresidue_total_count>1144</VRPTx:NOE_intraresidue_total_count> <VRPTx:NOE_long_range_total_count>1356</VRPTx:NOE_long_range_total_count> <VRPTx:NOE_medium_range_total_count>1004</VRPTx:NOE_medium_range_total_count> <VRPTx:NOE_sequential_total_count>272</VRPTx:NOE_sequential_total_count> <VRPTx:protein_phi_angle_constraints_total_count>96</VRPTx:protein_phi_angle_constraints_total_count> </VRPTx:pdbx_nmr_constraints> </VRPTx:pdbx_nmr_constraintsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_constraintsCategory This property indicates that datablock has a category holder pdbx_nmr_constraintsCategory. pdbx_nmr_constraintsCategory This property indicates that pdbx_nmr_constraintsCategory. has a category pdbx_nmr_constraints. pdbx_nmr_constraintsItem Abstract datatype property for pdbx_nmr_constraints items. reference_to_pdbx_nmr_constraints cross-reference to pdbx_nmr_constraints. referenced_by_pdbx_nmr_constraints cross-reference from pdbx_nmr_constraints. pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count The total number of nucleic acid alpha-angle constraints used in the final structure calculation. 18 pdbx_nmr_constraints.NA_beta-angle_constraints_total_count The total number of nucleic acid beta-angle constraints used in the final structure calculation. 24 pdbx_nmr_constraints.NA_chi-angle_constraints_total_count The total number of nucleic acid chi-angle constraints used in the final structure calculation. 15 pdbx_nmr_constraints.NA_delta-angle_constraints_total_count The total number of nucleic acid delta-angle constraints used in the final structure calculation. 15 pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count The total number of nucleic acid epsilon-angle constraints used in the final structure calculation. 31 pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count The total number of nucleic acid gamma-angle constraints used in the final structure calculation. 12 pdbx_nmr_constraints.NA_other-angle_constraints_total_count The total number of nucleic acid other-angle constraints used in the final structure calculation. 5 pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count The total number of nucleic acid sugar pucker constraints used in the final structure calculation. 10 pdbx_nmr_constraints.NOE_constraints_total The total number of all NOE constraints used in the final structure calculation. 4458 pdbx_nmr_constraints.NOE_interentity_total_count The total number of interentity, NOE constraints used in the final structure calculation. This field should only be if system is complex -i.e more than one entity e.g. a dimer or ligand-protein complex 272 pdbx_nmr_constraints.NOE_interproton_distance_evaluation Describe the method used to quantify the NOE and ROE values. NOE buildup curves with 50, 75, 150 ms mixing times were analyzed. Noesy cross peak intensities were classified into three different catagories with distances of 1.8-2.7 A, 1.8-3.5 A, 1.8- 5.0 A for strong, medium and weak NOEs. pdbx_nmr_constraints.NOE_intraresidue_total_count The total number of intraresidue, |i-j|=0, NOE constraints used in the final structure calculation. 1144 pdbx_nmr_constraints.NOE_long_range_total_count The total number of long range, |i-j|>=5, NOE constraints used in the final structure calculation. 1356 pdbx_nmr_constraints.NOE_medium_range_total_count The total number of medium range, 1<|i-j|<5, NOE constraints used in the final structure calculation. 682 pdbx_nmr_constraints.NOE_motional_averaging_correction Describe any corrections that were made to the NOE data for motional averaging. Replace with item example text pdbx_nmr_constraints.NOE_pseudoatom_corrections Describe any corrections made for pseudoatoms Pseudo-atoms nomenclature and corrections according to Wuethrich, Billeter, and Braun, J. Mol.Biol.(1983) 169, 949-961. Pseudoatoms were not used. pdbx_nmr_constraints.NOE_sequential_total_count The total number of sequential, |i-j|=1, NOE constraints used in the final structure calculation. 1004 pdbx_nmr_constraints.disulfide_bond_constraints_total_count The total number of disulfide bond constraints used in the final structure calculation. 3 pdbx_nmr_constraints.hydrogen_bond_constraints_total_count The total number of hydrogen bond constraints used in the final structure calculation. 6 pdbx_nmr_constraints.protein_chi_angle_constraints_total_count The total number of chi angle constraints used in the final structure calculation. 66 pdbx_nmr_constraints.protein_other_angle_constraints_total_count The total number of other angle constraints used in the final structure calculation. 0 pdbx_nmr_constraints.protein_phi_angle_constraints_total_count The total number of phi angle constraints used in the final structure calculation 96 pdbx_nmr_constraints.protein_psi_angle_constraints_total_count The total number of psi angle constraints used in the final structure calculation. 0 pdbx_nmr_constraints.entry_id You can leave this blank as an ID will be assigned by the RCSB. 0 pdbx_nmr_details Experimental details of the NMR study that have not been described elsewhere in this deposition. 0 1 1 pdbx_nmr_detailsCategory This property indicates that datablock has a category holder pdbx_nmr_detailsCategory. pdbx_nmr_detailsCategory This property indicates that pdbx_nmr_detailsCategory. has a category pdbx_nmr_details. pdbx_nmr_detailsItem Abstract datatype property for pdbx_nmr_details items. reference_to_pdbx_nmr_details cross-reference to pdbx_nmr_details. referenced_by_pdbx_nmr_details cross-reference from pdbx_nmr_details. pdbx_nmr_details.text Additional details describing the NMR experiment. This structure was determined using standard 2D homonuclear techniques. The structure was determined using triple-resonance NMR spectroscopy. pdbx_nmr_details.entry_id The entry ID for the structure determination. 0 pdbx_nmr_dihedral_angle_violation Data items in the category record all dihedral angle restraint violations of the ensemble. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.5 All violated dihedral-angle restraints 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_nmr_dihedral_angle_violationCategory This property indicates that datablock has a category holder pdbx_nmr_dihedral_angle_violationCategory. pdbx_nmr_dihedral_angle_violationCategory This property indicates that pdbx_nmr_dihedral_angle_violationCategory. has a category pdbx_nmr_dihedral_angle_violation. pdbx_nmr_dihedral_angle_violationItem Abstract datatype property for pdbx_nmr_dihedral_angle_violation items. reference_to_pdbx_nmr_dihedral_angle_violation cross-reference to pdbx_nmr_dihedral_angle_violation. referenced_by_pdbx_nmr_dihedral_angle_violation cross-reference from pdbx_nmr_dihedral_angle_violation. pdbx_nmr_dihedral_angle_violation.PDB_ins_code_1 Optional identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.PDB_ins_code_2 Optional identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.PDB_ins_code_3 Optional identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.PDB_ins_code_4 Optional identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_nmr_dihedral_angle_violation.auth_asym_id This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_atom_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_atom_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_atom_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_atom_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_comp_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_comp_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_comp_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_comp_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_seq_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_seq_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_seq_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.auth_seq_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.entity_id This data item is a pointer to attribute label_entity_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_alt_id_1 An optional identifier of the first of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_alt_id_2 An optional identifier of the second of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_alt_id_3 An optional identifier of the third of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_alt_id_4 An optional identifier of the fourth of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_asym_id This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_seq_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_seq_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_seq_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.label_seq_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation.list_id Pointer to attribute id in category pdbx_nmr_restraint_list. pdbx_nmr_dihedral_angle_violation.restraint_id An integer value that uniquely identifies dihedral angle restraint in a list. pdbx_nmr_dihedral_angle_violation.violation The residual dihedral angle violation value for a particular dihedral angle restraint. pdbx_nmr_dihedral_angle_violation.ordinal The ordered number in the violated restraints. 0 pdbx_nmr_dihedral_angle_violation_ensemble Data items in the category record violations of dihedral angle restraints for each virtual ensemble alternating the size of an ensemble. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.3 Dihedral-angle violation statistics for the ensemble 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_dihedral_angle_violation_ensembleCategory This property indicates that datablock has a category holder pdbx_nmr_dihedral_angle_violation_ensembleCategory. pdbx_nmr_dihedral_angle_violation_ensembleCategory This property indicates that pdbx_nmr_dihedral_angle_violation_ensembleCategory. has a category pdbx_nmr_dihedral_angle_violation_ensemble. pdbx_nmr_dihedral_angle_violation_ensembleItem Abstract datatype property for pdbx_nmr_dihedral_angle_violation_ensemble items. reference_to_pdbx_nmr_dihedral_angle_violation_ensemble cross-reference to pdbx_nmr_dihedral_angle_violation_ensemble. referenced_by_pdbx_nmr_dihedral_angle_violation_ensemble cross-reference from pdbx_nmr_dihedral_angle_violation_ensemble. pdbx_nmr_dihedral_angle_violation_ensemble.alpha_violations_count The total number of all ALPHA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.beta_violations_count The total number of all BETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi1_violations_count The total number of all CHI1 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi21_violations_count The total number of all CHI21 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi22_violations_count The total number of all CHI22 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi2_violations_count The total number of all CHI2 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi31_violations_count The total number of all CHI31 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi32_violations_count The total number of all CHI32 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi3_violations_count The total number of all CHI3 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi42_violations_count The total number of all CHI42 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi4_violations_count The total number of all CHI4 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi5_violations_count The total number of all CHI5 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.chi_violations_count The total number of all CHI dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.delta_violations_count The total number of all DELTA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.epsilon_violations_count The total number of all EPSILON dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.eta_prime_violations_count The total number of all ETA' dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.eta_violations_count The total number of allC ETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.fraction_ensemble_percent The percentage of size of a fraction of an ensemble to the size of the original ensemble provided by author. pdbx_nmr_dihedral_angle_violation_ensemble.gamma_violations_count The total number of all GAMMA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.nu0_violations_count The total number of all NU0/TAU0 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.nu1_violations_count The total number of all NU1/TAU1 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.nu2_violations_count The total number of all NU2/TAU2 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.nu3_violations_count The total number of all NU3/TAU3 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.nu4_violations_count The total number of all NU4/TAU4 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.omega_violations_count The total number of all OMEGA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.other_violations_count The total number of all other dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.phi_violations_count The total number of all PHI dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.psi_violations_count The total number of all PSI dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.theta_prime_violations_count The total number of all THETA' dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.theta_violations_count The total number of all THETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.violations_count The total number of dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.zeta_violations_count The total number of all ZETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_ensemble.fraction_ensemble_size The size of fraction of an ensemble. 0 pdbx_nmr_dihedral_angle_violation_model Data items in the category record violations of dihedral angle restraints for each model. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.2 Dihedral-angle violation statistics for each model 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_dihedral_angle_violation_modelCategory This property indicates that datablock has a category holder pdbx_nmr_dihedral_angle_violation_modelCategory. pdbx_nmr_dihedral_angle_violation_modelCategory This property indicates that pdbx_nmr_dihedral_angle_violation_modelCategory. has a category pdbx_nmr_dihedral_angle_violation_model. pdbx_nmr_dihedral_angle_violation_modelItem Abstract datatype property for pdbx_nmr_dihedral_angle_violation_model items. reference_to_pdbx_nmr_dihedral_angle_violation_model cross-reference to pdbx_nmr_dihedral_angle_violation_model. referenced_by_pdbx_nmr_dihedral_angle_violation_model cross-reference from pdbx_nmr_dihedral_angle_violation_model. pdbx_nmr_dihedral_angle_violation_model.alpha_violations_count The total number of all ALPHA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.average_violation The average value of residual dihedral angle violation in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.beta_violations_count The total number of all BETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi1_violations_count The total number of all CHI1 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi21_violations_count The total number of all CHI21 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi22_violations_count The total number of all CHI22 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi2_violations_count The total number of all CHI2 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi31_violations_count The total number of all CHI31 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi32_violations_count The total number of all CHI32 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi3_violations_count The total number of all CHI3 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi42_violations_count The total number of all CHI42 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi4_violations_count The total number of all CHI4 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi5_violations_count The total number of all CHI5 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.chi_violations_count The total number of all CHI dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.delta_violations_count The total number of all DELTA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.epsilon_violations_count The total number of all EPSILON dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.eta_prime_violations_count The total number of all ETA' dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.eta_violations_count The total number of all ETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.gamma_violations_count The total number of all GAMMA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.maximum_violation The maximum value of residual dihedral angle violation in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.median_violation The median value of residual dihedral angle violation in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.nu0_violations_count The total number of all NU0/TAU0 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.nu1_violations_count The total number of all NU1/TAU1 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.nu2_violations_count The total number of all NU2/TAU2 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.nu3_violations_count The total number of all NU3/TAU3 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.nu4_violations_count The total number of all NU4/TAU4 dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.omega_violations_count The total number of all OMEGA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.other_violations_count The total number of all other dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.phi_violations_count The total number of all PHI dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.psi_violations_count The total number of all PSI dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.standard_deviation The standard deviation of residual dihedral angle violation in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.theta_prime_violations_count The total number of all THETA' dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.theta_violations_count The total number of all THETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.violations_count The total number of dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.zeta_violations_count The total number of all ZETA dihedral angle restraint violations in a particular coordinate model. pdbx_nmr_dihedral_angle_violation_model.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. 0 pdbx_nmr_dihedral_angle_violation_plural Data items in the category record potentially severe violations of dihedral angle restraints, which occurred in multiple coordinate models of the ensemble. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.4 Most violated dihedral angle restraints in the ensemble 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_nmr_dihedral_angle_violation_pluralCategory This property indicates that datablock has a category holder pdbx_nmr_dihedral_angle_violation_pluralCategory. pdbx_nmr_dihedral_angle_violation_pluralCategory This property indicates that pdbx_nmr_dihedral_angle_violation_pluralCategory. has a category pdbx_nmr_dihedral_angle_violation_plural. pdbx_nmr_dihedral_angle_violation_pluralItem Abstract datatype property for pdbx_nmr_dihedral_angle_violation_plural items. reference_to_pdbx_nmr_dihedral_angle_violation_plural cross-reference to pdbx_nmr_dihedral_angle_violation_plural. referenced_by_pdbx_nmr_dihedral_angle_violation_plural cross-reference from pdbx_nmr_dihedral_angle_violation_plural. pdbx_nmr_dihedral_angle_violation_plural.PDB_ins_code_1 Optional identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.PDB_ins_code_2 Optional identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.PDB_ins_code_3 Optional identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.PDB_ins_code_4 Optional identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_asym_id This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_atom_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_atom_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_atom_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_atom_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_comp_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_comp_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_comp_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_comp_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_seq_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_seq_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_seq_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.auth_seq_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.average_violation The average value of residual dihedral angle violation for a particular dihedral angle restraint in the models violated. pdbx_nmr_dihedral_angle_violation_plural.entity_id This data item is a pointer to attribute label_entity_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_alt_id_1 An optional identifier of the first of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_alt_id_2 An optional identifier of the second of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_alt_id_3 An optional identifier of the third of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_alt_id_4 An optional identifier of the fourth of the four atoms that define a dihedral angle restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_asym_id This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_seq_id_1 Part of the identifier of the first of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_seq_id_2 Part of the identifier of the second of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_seq_id_3 Part of the identifier of the third of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.label_seq_id_4 Part of the identifier of the fourth of the four atom sites that define a dihedral angle restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_dihedral_angle_violation_plural.list_id Pointer to attribute id in category pdbx_nmr_restraint_list. pdbx_nmr_dihedral_angle_violation_plural.median_violation The median value of residual dihedral angle violation for a particular dihedral angle restraint in the models violated. pdbx_nmr_dihedral_angle_violation_plural.restraint_id An integer value that uniquely identifies dihedral angle restraint in a list. pdbx_nmr_dihedral_angle_violation_plural.standard_deviation The standard deviation of residual dihedral angle violation for a particular dihedral angle restraint in the models violated. pdbx_nmr_dihedral_angle_violation_plural.violation_models_count The total number of models violated for a particular dihedral angle restraint. pdbx_nmr_dihedral_angle_violation_plural.ordinal The ordered number in the violated restraints. 0 pdbx_nmr_dihedral_angle_violation_summary Data items in the category record violations of dihedral angle restraints. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.1 Summary of dihedral-angle violations 1 1 0 1 0 1 1 1 0 1 1 1 0 1 0 1 1 pdbx_nmr_dihedral_angle_violation_summaryCategory This property indicates that datablock has a category holder pdbx_nmr_dihedral_angle_violation_summaryCategory. pdbx_nmr_dihedral_angle_violation_summaryCategory This property indicates that pdbx_nmr_dihedral_angle_violation_summaryCategory. has a category pdbx_nmr_dihedral_angle_violation_summary. pdbx_nmr_dihedral_angle_violation_summaryItem Abstract datatype property for pdbx_nmr_dihedral_angle_violation_summary items. reference_to_pdbx_nmr_dihedral_angle_violation_summary cross-reference to pdbx_nmr_dihedral_angle_violation_summary. referenced_by_pdbx_nmr_dihedral_angle_violation_summary cross-reference from pdbx_nmr_dihedral_angle_violation_summary. pdbx_nmr_dihedral_angle_violation_summary.consistent_violations_count The total number of consistently violated dihedral angle restraints of the ensemble for a particular restraint type. pdbx_nmr_dihedral_angle_violation_summary.consistent_violations_percent The percentage of consistently violated dihedral angle restraints to the total number of dihedral angle restraints. pdbx_nmr_dihedral_angle_violation_summary.consistent_violations_percent_type The percentage of consistently violated dihedral angle restraints to the number of restraints of a particular restraint type. pdbx_nmr_dihedral_angle_violation_summary.restraints_count The total number of unique dihedral angle restraints to which a particular restraint type belongs. pdbx_nmr_dihedral_angle_violation_summary.restraints_percent The percentage of unique dihedral angle restraints to the total number of dihedral angle restraints. pdbx_nmr_dihedral_angle_violation_summary.violations_count The total number of violated dihedral angle restraints to which a particular restraint type belongs. pdbx_nmr_dihedral_angle_violation_summary.violations_percent The percentage of violated dihedral angle restraints to the total number of dihedral angle restraints. pdbx_nmr_dihedral_angle_violation_summary.violations_percent_type The percentage of violated dihedral angle restraints to the number of restraints of a particular restraint type. phi psi omega chi1 chi2 chi3 chi4 chi5 alpha beta gamma delta epsilon zeta nu0 nu1 nu2 nu3 nu4 chi21 chi22 chi31 chi32 chi42 chi eta theta eta' theta' other all Defines the type of dihedral angle restraints based on the conventional residue number gap. 0 pdbx_nmr_distance_violation Data items in the category record all distance restraint violations of the ensemble. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.5 All violated distance restraints 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_nmr_distance_violationCategory This property indicates that datablock has a category holder pdbx_nmr_distance_violationCategory. pdbx_nmr_distance_violationCategory This property indicates that pdbx_nmr_distance_violationCategory. has a category pdbx_nmr_distance_violation. pdbx_nmr_distance_violationItem Abstract datatype property for pdbx_nmr_distance_violation items. reference_to_pdbx_nmr_distance_violation cross-reference to pdbx_nmr_distance_violation. referenced_by_pdbx_nmr_distance_violation cross-reference from pdbx_nmr_distance_violation. pdbx_nmr_distance_violation.PDB_ins_code_1 Optional identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.PDB_ins_code_2 Optional identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_nmr_distance_violation.auth_asym_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_asym_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_atom_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_atom_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_comp_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_comp_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_seq_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.auth_seq_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.entity_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_entity_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.entity_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_entity_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.label_alt_id_1 An optional identifier of the first of the two atoms that define a distance restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.label_alt_id_2 An optional identifier of the second of the two atoms that define a distance restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.label_asym_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.label_asym_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.label_seq_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.label_seq_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation.list_id Pointer to attribute id in category pdbx_nmr_restraint_list. pdbx_nmr_distance_violation.restraint_id An integer value that uniquely identifies distance restraint in a list. pdbx_nmr_distance_violation.violation The residual distance violation value for a particular distance restraint. pdbx_nmr_distance_violation.ordinal The ordered number in the violated restraints. 0 pdbx_nmr_distance_violation_ensemble Data items in the category record violations of distance restraints for each virtual ensemble alternating the size of an ensemble. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.3 Distance violation statistics for the ensemble 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_distance_violation_ensembleCategory This property indicates that datablock has a category holder pdbx_nmr_distance_violation_ensembleCategory. pdbx_nmr_distance_violation_ensembleCategory This property indicates that pdbx_nmr_distance_violation_ensembleCategory. has a category pdbx_nmr_distance_violation_ensemble. pdbx_nmr_distance_violation_ensembleItem Abstract datatype property for pdbx_nmr_distance_violation_ensemble items. reference_to_pdbx_nmr_distance_violation_ensemble cross-reference to pdbx_nmr_distance_violation_ensemble. referenced_by_pdbx_nmr_distance_violation_ensemble cross-reference from pdbx_nmr_distance_violation_ensemble. pdbx_nmr_distance_violation_ensemble.disulfide_bond_violations_count The total number of disulfide bond distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.fraction_ensemble_percent The percentage of size of a fraction of an ensemble to the size of the original ensemble provided by author. pdbx_nmr_distance_violation_ensemble.hydrogen_bond_violations_count The total number of hydrogen bond distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.interchain_violations_count The total number of interchain distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.intraresidue_violations_count The total number of intraresidue, |i-j|=0, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.long_range_violations_count The total number of long range, |i-j|>=5, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.medium_range_violations_count The total number of medium range, 1<|i-j|<5, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.sequential_violations_count The total number of sequential, |i-j|=1, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.violations_count The total number of distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_ensemble.fraction_ensemble_size The size of fraction of an ensemble. 0 pdbx_nmr_distance_violation_model Data items in the category record violations of distance restraints for each model. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.2 Distance violation statistics for each model 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 0 1 1 pdbx_nmr_distance_violation_modelCategory This property indicates that datablock has a category holder pdbx_nmr_distance_violation_modelCategory. pdbx_nmr_distance_violation_modelCategory This property indicates that pdbx_nmr_distance_violation_modelCategory. has a category pdbx_nmr_distance_violation_model. pdbx_nmr_distance_violation_modelItem Abstract datatype property for pdbx_nmr_distance_violation_model items. reference_to_pdbx_nmr_distance_violation_model cross-reference to pdbx_nmr_distance_violation_model. referenced_by_pdbx_nmr_distance_violation_model cross-reference from pdbx_nmr_distance_violation_model. pdbx_nmr_distance_violation_model.average_violation The average value of residual distance violation in a particular coordinate model. pdbx_nmr_distance_violation_model.disulfide_bond_violations_count The total number of disulfide bond distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.hydrogen_bond_violations_count The total number of hydrogen bond distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.interchain_violations_count The total number of interchain distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.intraresidue_violations_count The total number of intraresidue, |i-j|=0, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.long_range_violations_count The total number of long range, |i-j|>=5, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.maximum_violation The maximum value of residual distance violation in a particular coordinate model. pdbx_nmr_distance_violation_model.median_violation The median value of residual distance violation in a particular coordinate model. pdbx_nmr_distance_violation_model.medium_range_violations_count The total number of medium range, 1<|i-j|<5, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.sequential_violations_count The total number of sequential, |i-j|=1, distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.standard_deviation The standard deviation of residual distance violation in a particular coordinate model. pdbx_nmr_distance_violation_model.violations_count The total number of distance restraint violations in a particular coordinate model. pdbx_nmr_distance_violation_model.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. 0 pdbx_nmr_distance_violation_plural Data items in the category record potentially severe violations of distance restraints, which occurred in multiple coordinate models of the ensemble. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.4 Most violated distance restraints in the ensemble 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_nmr_distance_violation_pluralCategory This property indicates that datablock has a category holder pdbx_nmr_distance_violation_pluralCategory. pdbx_nmr_distance_violation_pluralCategory This property indicates that pdbx_nmr_distance_violation_pluralCategory. has a category pdbx_nmr_distance_violation_plural. pdbx_nmr_distance_violation_pluralItem Abstract datatype property for pdbx_nmr_distance_violation_plural items. reference_to_pdbx_nmr_distance_violation_plural cross-reference to pdbx_nmr_distance_violation_plural. referenced_by_pdbx_nmr_distance_violation_plural cross-reference from pdbx_nmr_distance_violation_plural. pdbx_nmr_distance_violation_plural.PDB_ins_code_1 Optional identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.PDB_ins_code_2 Optional identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_asym_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_asym_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_atom_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_atom_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_comp_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_comp_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_seq_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.auth_seq_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.average_violation The average value of residual distance violation for a particular distance restraint in the models violated. pdbx_nmr_distance_violation_plural.entity_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_entity_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.entity_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_entity_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.label_alt_id_1 An optional identifier of the first of the two atoms that define a distance restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.label_alt_id_2 An optional identifier of the second of the two atoms that define a distance restraint. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.label_asym_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.label_asym_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.label_seq_id_1 Part of the identifier of the first of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.label_seq_id_2 Part of the identifier of the second of the two atom sites that define a distance restraint. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_distance_violation_plural.list_id Pointer to attribute id in category pdbx_nmr_restraint_list. pdbx_nmr_distance_violation_plural.median_violation The median value of residual distance violation for a particular distance restraint in the models violated. pdbx_nmr_distance_violation_plural.restraint_id An integer value that uniquely identifies distance restraint in a list. pdbx_nmr_distance_violation_plural.standard_deviation The standard deviation of residual distance violation for a particular distance restraint in the models violated. pdbx_nmr_distance_violation_plural.violation_models_count The total number of models violated for a particular distance restraint. pdbx_nmr_distance_violation_plural.ordinal The ordered number in the violated restraints. 0 pdbx_nmr_distance_violation_summary Data items in the category record violations of distance restraints. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.1 Summary of distance violations 1 1 0 1 0 1 1 1 0 1 1 1 0 1 0 1 1 1 pdbx_nmr_distance_violation_summaryCategory This property indicates that datablock has a category holder pdbx_nmr_distance_violation_summaryCategory. pdbx_nmr_distance_violation_summaryCategory This property indicates that pdbx_nmr_distance_violation_summaryCategory. has a category pdbx_nmr_distance_violation_summary. pdbx_nmr_distance_violation_summaryItem Abstract datatype property for pdbx_nmr_distance_violation_summary items. reference_to_pdbx_nmr_distance_violation_summary cross-reference to pdbx_nmr_distance_violation_summary. referenced_by_pdbx_nmr_distance_violation_summary cross-reference from pdbx_nmr_distance_violation_summary. pdbx_nmr_distance_violation_summary.consistent_violations_count The total number of consistently violated distance restraints of the ensemble for a particular restraint type/subtype. pdbx_nmr_distance_violation_summary.consistent_violations_percent The percentage of consistently violated distance restraints to the total number of distance restraints. pdbx_nmr_distance_violation_summary.consistent_violations_percent_type The percentage of consistently violated distance restraints to the number of restraints of a particular restraint type and subtype. pdbx_nmr_distance_violation_summary.restraints_count The total number of unique distance restraints to which a particular restraint type/subtype belongs. pdbx_nmr_distance_violation_summary.restraints_percent The percentage of unique distance restraints to the total number of distance restraints. pdbx_nmr_distance_violation_summary.violations_count The total number of violated distance restraints to which a particular restraint type/subtype belongs. pdbx_nmr_distance_violation_summary.violations_percent The percentage of violated distance restraints to the total number of distance restraints. pdbx_nmr_distance_violation_summary.violations_percent_type The percentage of violated distance restraints to the number of restraints of a particular restraint type and subtype. backbone_backbone distance restraints between two backbone atoms backbone_sidechain distance restraints between backbone atom and side chaini atom sidechain_sidechain distance restraints between two side chain atoms all all distance restraints without backbone/side chain classification Defines the type of distance restraints based on atom classification of either backbone or side chain atoms. intraresidue sequential medium_range long_range interchain hydrogen_bond disulfide_bond all Defines the type of distance restraints based on the conventional residue number gap. 0 pdbx_nmr_ensemble This category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section. This example uses the data from the MCP-1 study. <VRPTx:pdbx_nmr_ensembleCategory> <VRPTx:pdbx_nmr_ensemble entry_id="1ABC"> <VRPTx:conformer_selection_criteria>structures with the least restraint violations</VRPTx:conformer_selection_criteria> <VRPTx:conformers_calculated_total_number>40</VRPTx:conformers_calculated_total_number> <VRPTx:conformers_submitted_total_number>20</VRPTx:conformers_submitted_total_number> <VRPTx:representative_conformer>1</VRPTx:representative_conformer> </VRPTx:pdbx_nmr_ensemble> </VRPTx:pdbx_nmr_ensembleCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_ensembleCategory This property indicates that datablock has a category holder pdbx_nmr_ensembleCategory. pdbx_nmr_ensembleCategory This property indicates that pdbx_nmr_ensembleCategory. has a category pdbx_nmr_ensemble. pdbx_nmr_ensembleItem Abstract datatype property for pdbx_nmr_ensemble items. reference_to_pdbx_nmr_ensemble cross-reference to pdbx_nmr_ensemble. referenced_by_pdbx_nmr_ensemble cross-reference from pdbx_nmr_ensemble. Y N Whether all models in the NMR ensemble structure consist entirely of the same atoms (Y) or not (N). pdbx_nmr_ensemble.average_constraint_violations_per_residue The average number of constraint violations on a per residue basis for the ensemble. 0.25 pdbx_nmr_ensemble.average_constraints_per_residue The average number of constraints per residue for the ensemble 30.2 pdbx_nmr_ensemble.average_distance_constraint_violation The average distance restraint violation for the ensemble. 0.11 pdbx_nmr_ensemble.average_torsion_angle_constraint_violation The average torsion angle constraint violation for the ensemble. 2.4 pdbx_nmr_ensemble.conformer_selection_criteria By highlighting the appropriate choice(s), describe how the submitted conformer (models) were selected. structures with the lowest energy structures with the least restraint violations structures with acceptable covalent geometry structures with favorable non-bond energy target function back calculated data agree with experimental NOESY spectrum all calculated structures submitted The submitted conformer models are the 25 structures with the lowest energy. The submitted conformer models are those with the fewest number of constraint violations. pdbx_nmr_ensemble.conformers_calculated_total_number The total number of conformer (models) that were calculated in the final round. 40 pdbx_nmr_ensemble.conformers_submitted_total_number The number of conformer (models) that are submitted for the ensemble. 20 pdbx_nmr_ensemble.distance_constraint_violation_method Describe the method used to calculate the distance constraint violation statistics, i.e. are they calculated over all the distance constraints or calculated for violations only? Statistics were calculated over all of the distance constraints. Statistics were calculated for violations only pdbx_nmr_ensemble.maximum_distance_constraint_violation The maximum distance constraint violation for the ensemble. 0.4 pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation The maximum lower distance constraint violation for the ensemble. 0.3 pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation The maximum torsion angle constraint violation for the ensemble. 4 pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation The maximum upper distance constraint violation for the ensemble. 0.4 pdbx_nmr_ensemble.representative_conformer The number of the conformer identified as most representative. 20 pdbx_nmr_ensemble.torsion_angle_constraint_violation_method This item describes the method used to calculate the torsion angle constraint violation statistics. i.e. are the entered values based on all torsion angle or calculated for violations only? Statistics were calculated over all the torsion angle constraints. Statistics were calculated for torsion angle constraints violations only. pdbx_nmr_ensemble.entry_id You can leave this blank as an ID will be assigned by the RCSB. 0 pdbx_nmr_ensemble_rms Structural statistics are derived from molecular dynamics and simulated annealing programs. This example is derived from the MCP-1 structure calculation statistics. For this structure the statistics were calculated over residues 5-69 for both the monomer and dimer . <VRPTx:pdbx_nmr_ensemble_rmsCategory> <VRPTx:pdbx_nmr_ensemble_rms entry_id="1ABC"> <VRPTx:atom_type>all heavy atoms</VRPTx:atom_type> <VRPTx:chain_range_begin>A</VRPTx:chain_range_begin> <VRPTx:chain_range_end>A</VRPTx:chain_range_end> <VRPTx:distance_rms_dev>0.22</VRPTx:distance_rms_dev> <VRPTx:distance_rms_dev_error>0.06</VRPTx:distance_rms_dev_error> <VRPTx:residue_range_begin>5</VRPTx:residue_range_begin> <VRPTx:residue_range_end>69</VRPTx:residue_range_end> </VRPTx:pdbx_nmr_ensemble_rms> </VRPTx:pdbx_nmr_ensemble_rmsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_ensemble_rmsCategory This property indicates that datablock has a category holder pdbx_nmr_ensemble_rmsCategory. pdbx_nmr_ensemble_rmsCategory This property indicates that pdbx_nmr_ensemble_rmsCategory. has a category pdbx_nmr_ensemble_rms. pdbx_nmr_ensemble_rmsItem Abstract datatype property for pdbx_nmr_ensemble_rms items. reference_to_pdbx_nmr_ensemble_rms cross-reference to pdbx_nmr_ensemble_rms. referenced_by_pdbx_nmr_ensemble_rms cross-reference from pdbx_nmr_ensemble_rms. backbone heavy atoms side chain heavy atoms all heavy atoms all atoms all backbone atoms Statistics are often calculated over only some of the atoms, e.g. backbone, or heavy atoms. Describe which type of atoms are used for the statistical analysis. backbone atoms heavy atoms pdbx_nmr_ensemble_rms.bond_angle_rms_dev The bond angle rmsd to the target values for the ensemble. 0.60 pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error The error in the bond angle rmsd. 0.01 pdbx_nmr_ensemble_rms.chain_range_begin The beginning chain id. A pdbx_nmr_ensemble_rms.chain_range_end The ending chain id: A pdbx_nmr_ensemble_rms.coord_average_rmsd_method Describe the method for calculating the coordinate average rmsd. pdbx_nmr_ensemble_rms.covalent_bond_rms_dev The covalent bond rmsd to the target value for the ensemble. 0.0066 pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error The error in the covalent bond rmsd. 0.0001 pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev The dihedral angle rmsd to the target values for the ensemble. 0.66 pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error The error of the rmsd dihedral angles. 0.07 pdbx_nmr_ensemble_rms.distance_rms_dev The distance rmsd to the mean structure for the ensemble of structures. 0.22 pdbx_nmr_ensemble_rms.distance_rms_dev_error The error in the distance rmsd. 0.07 pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev The improper torsion angle rmsd to the target values for the ensemble. 0.64 pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error The error in the improper torsion angle rmsd. 0.04 pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev The peptide planarity rmsd. 0.11 pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error The error in the peptide planarity rmsd. 0.05 pdbx_nmr_ensemble_rms.residue_range_begin Structure statistics are often calculated only over the well-ordered region(s) of the biopolymer. Portions of the macromolecule are often mobile and disordered, hence they are excluded in calculating the statistics. To define the range(s) over which the statistics are calculated, enter the beginning residue number(s): e.g. if the regions used were 5-32 and 41-69, enter 5,41 5 41 pdbx_nmr_ensemble_rms.residue_range_end The ending residue number: e.g. 32,69. 32 69 pdbx_nmr_ensemble_rms.entry_id You can leave this blank as an ID will be assigned by the RCSB. 0 pdbx_nmr_exptl In this section, enter information on those experiments that were used to generate constraint data. For each NMR experiment indicate which sample and which sample conditions were used for the experiment. This example was taken from the MCP-1 study. <VRPTx:pdbx_nmr_exptlCategory> <VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="1" solution_id="3"> <VRPTx:type>3D_15N-separated_NOESY</VRPTx:type> </VRPTx:pdbx_nmr_exptl> <VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="2" solution_id="1"> <VRPTx:type>3D_13C-separated_NOESY</VRPTx:type> </VRPTx:pdbx_nmr_exptl> <VRPTx:pdbx_nmr_exptl conditions_id="2" experiment_id="3" solution_id="1"> <VRPTx:type>4D_13C/15N-separated_NOESY</VRPTx:type> </VRPTx:pdbx_nmr_exptl> <VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="4" solution_id="1"> <VRPTx:type>4D_13C-separated_NOESY</VRPTx:type> </VRPTx:pdbx_nmr_exptl> <VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="5" solution_id="1"> <VRPTx:type>3D_15N-separated_ROESY</VRPTx:type> </VRPTx:pdbx_nmr_exptl> <VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="6" solution_id="3"> <VRPTx:type>3D_13C-separated_ROESY</VRPTx:type> </VRPTx:pdbx_nmr_exptl> </VRPTx:pdbx_nmr_exptlCategory> 0 1 0 1 0 1 1 1 1 pdbx_nmr_exptlCategory This property indicates that datablock has a category holder pdbx_nmr_exptlCategory. pdbx_nmr_exptlCategory This property indicates that pdbx_nmr_exptlCategory. has a category pdbx_nmr_exptl. pdbx_nmr_exptlItem Abstract datatype property for pdbx_nmr_exptl items. reference_to_pdbx_nmr_exptl cross-reference to pdbx_nmr_exptl. referenced_by_pdbx_nmr_exptl cross-reference from pdbx_nmr_exptl. isotropic anisotropic Physical state of the sample either anisotropic or isotropic. isotropic pdbx_nmr_exptl.spectrometer_id Pointer to '_pdbx_nmr_spectrometer.spectrometer_id' pdbx_nmr_exptl.type The type of NMR experiment. 2D NOESY 3D_15N-separated_NOESY 3D_13C-separated_NOESY 4D_13C-separated_NOESY 4D_13C/15N-separated_NOESY 3D_15N-separated_ROESY 3D_13C-separated_ROESY HNCA-J HNHA DQF-COSY P-COSY PE-COSY E-COSY pdbx_nmr_exptl.conditions_id The number to identify the set of sample conditions. 1 2 3 pdbx_nmr_exptl.experiment_id A numerical ID for each experiment. 1 2 3 pdbx_nmr_exptl.solution_id The solution_id from the Experimental Sample to identify the sample that these conditions refer to. [Remember to save the entries here before returning to the Experimental Sample form] 1 2 3 0 pdbx_nmr_exptl_sample The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name. Example 1 - This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <VRPTx:pdbx_nmr_exptl_sampleCategory> <VRPTx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="1"> <VRPTx:concentration>2</VRPTx:concentration> <VRPTx:concentration_units>mM</VRPTx:concentration_units> <VRPTx:isotopic_labeling>U-15N,13C</VRPTx:isotopic_labeling> </VRPTx:pdbx_nmr_exptl_sample> <VRPTx:pdbx_nmr_exptl_sample component="H2O" solution_id="1"> <VRPTx:concentration>90</VRPTx:concentration> <VRPTx:concentration_units>&#37;</VRPTx:concentration_units> <VRPTx:isotopic_labeling xsi:nil="true" /> </VRPTx:pdbx_nmr_exptl_sample> <VRPTx:pdbx_nmr_exptl_sample component="D2O" solution_id="1"> <VRPTx:concentration>10</VRPTx:concentration> <VRPTx:concentration_units>&#37;</VRPTx:concentration_units> <VRPTx:isotopic_labeling xsi:nil="true" /> </VRPTx:pdbx_nmr_exptl_sample> </VRPTx:pdbx_nmr_exptl_sampleCategory> Example 2 - This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <VRPTx:pdbx_nmr_exptl_sampleCategory> <VRPTx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="2"> <VRPTx:concentration>1</VRPTx:concentration> <VRPTx:concentration_units>mM</VRPTx:concentration_units> <VRPTx:isotopic_labeling>U-50&#37; 15N</VRPTx:isotopic_labeling> </VRPTx:pdbx_nmr_exptl_sample> <VRPTx:pdbx_nmr_exptl_sample component="H2O" solution_id="2"> <VRPTx:concentration>90</VRPTx:concentration> <VRPTx:concentration_units>&#37;</VRPTx:concentration_units> <VRPTx:isotopic_labeling xsi:nil="true" /> </VRPTx:pdbx_nmr_exptl_sample> <VRPTx:pdbx_nmr_exptl_sample component="D2O" solution_id="2"> <VRPTx:concentration>10</VRPTx:concentration> <VRPTx:concentration_units>&#37;</VRPTx:concentration_units> <VRPTx:isotopic_labeling xsi:nil="true" /> </VRPTx:pdbx_nmr_exptl_sample> </VRPTx:pdbx_nmr_exptl_sampleCategory> 0 1 0 1 0 1 0 1 1 1 pdbx_nmr_exptl_sampleCategory This property indicates that datablock has a category holder pdbx_nmr_exptl_sampleCategory. pdbx_nmr_exptl_sampleCategory This property indicates that pdbx_nmr_exptl_sampleCategory. has a category pdbx_nmr_exptl_sample. pdbx_nmr_exptl_sampleItem Abstract datatype property for pdbx_nmr_exptl_sample items. reference_to_pdbx_nmr_exptl_sample cross-reference to pdbx_nmr_exptl_sample. referenced_by_pdbx_nmr_exptl_sample cross-reference from pdbx_nmr_exptl_sample. pdbx_nmr_exptl_sample.concentration The concentration value of the component. 2.0 2.7 0.01 pdbx_nmr_exptl_sample.concentration_range The concentration range for the component. 2.0-2.2 2.7-3.5 0.01-0.05 % mM mg/mL nM pM M g/L ug/mL mg mg/L mg/uL ug/uL uM v/v w/v w/w % w/v % w/w % v/v saturated na The concentration units of the component. mg/mL for mg per milliliter mM for millimolar % for percent by volume pdbx_nmr_exptl_sample.isotopic_labeling The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H U-13C,15N U-2H pdbx_nmr_exptl_sample.component The name of each component in the sample ribonuclease DNA strand 1 TRIS buffer sodium chloride H2O D2O pdbx_nmr_exptl_sample.solution_id The name (number) of the sample. 1 2 3 0 pdbx_nmr_exptl_sample_conditions The experimental conditions used to for each sample. Each set of conditions is identified by a numerical code. This example was taken from a pH stability study. <VRPTx:pdbx_nmr_exptl_sample_conditionsCategory> <VRPTx:pdbx_nmr_exptl_sample_conditions conditions_id="1"> <VRPTx:ionic_strength>25mM NaCl</VRPTx:ionic_strength> <VRPTx:pH>7</VRPTx:pH> <VRPTx:pressure>ambient</VRPTx:pressure> <VRPTx:temperature>298</VRPTx:temperature> </VRPTx:pdbx_nmr_exptl_sample_conditions> <VRPTx:pdbx_nmr_exptl_sample_conditions conditions_id="2"> <VRPTx:ionic_strength>25mM NaCl</VRPTx:ionic_strength> <VRPTx:pH>3</VRPTx:pH> <VRPTx:pressure>ambient</VRPTx:pressure> <VRPTx:temperature>298</VRPTx:temperature> </VRPTx:pdbx_nmr_exptl_sample_conditions> </VRPTx:pdbx_nmr_exptl_sample_conditionsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_exptl_sample_conditionsCategory This property indicates that datablock has a category holder pdbx_nmr_exptl_sample_conditionsCategory. pdbx_nmr_exptl_sample_conditionsCategory This property indicates that pdbx_nmr_exptl_sample_conditionsCategory. has a category pdbx_nmr_exptl_sample_conditions. pdbx_nmr_exptl_sample_conditionsItem Abstract datatype property for pdbx_nmr_exptl_sample_conditions items. reference_to_pdbx_nmr_exptl_sample_conditions cross-reference to pdbx_nmr_exptl_sample_conditions. referenced_by_pdbx_nmr_exptl_sample_conditions cross-reference from pdbx_nmr_exptl_sample_conditions. pdbx_nmr_exptl_sample_conditions.details General details describing conditions of both the sample and the environment during measurements. The high salinity of the sample may have contributed to overheating of the sample during experiments with long saturation periods like the TOCSY experiments. pdbx_nmr_exptl_sample_conditions.ionic_strength The ionic strength at which the NMR data were collected -in lieu of this enter the concentration and identity of the salt in the sample. pdbx_nmr_exptl_sample_conditions.ionic_strength_err Estimate of the standard error for the value for the sample ionic strength. 0.2 M mM Not defined Units for the value of the sample condition ionic strength.. M pdbx_nmr_exptl_sample_conditions.label A descriptive label that uniquely identifies this set of sample conditions. conditions_1 pdbx_nmr_exptl_sample_conditions.pH The pH at which the NMR data were collected. 3.1 7.0 pdbx_nmr_exptl_sample_conditions.pH_err Estimate of the standard error for the value for the sample pH. 0.05 pH pD pH* Not defined Units for the value of the sample condition pH. pH pdbx_nmr_exptl_sample_conditions.pressure The pressure at which NMR data were collected. ambient 1atm pdbx_nmr_exptl_sample_conditions.pressure_err Estimate of the standard error for the value for the sample pressure. 0.01 pdbx_nmr_exptl_sample_conditions.pressure_units The units of pressure at which NMR data were collected. Pa atm Torr pdbx_nmr_exptl_sample_conditions.temperature The temperature (in kelvin) at which NMR data were collected. 298 pdbx_nmr_exptl_sample_conditions.temperature_err Estimate of the standard error for the value for the sample temperature. 0.2 K C Not defined Units for the value of the sample condition temperature. K pdbx_nmr_exptl_sample_conditions.conditions_id The condition number as defined above. 1 2 3 0 pdbx_nmr_force_constants The final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing. This example is taken from a study of BAF, a dimeric DNA binding protein. The final force constants in the target function used for simulated annealing are: Experimental Constraint terms: Distance (NOE,H-bonds), Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling, D isotope shifts Covalent Geometry Constraint terms: Bond lengths, Angles, Impropers Non-bonded Interaction terms: van der Waals, Type of van der Waals term, Conformational database potential, Radius of gyration. <VRPTx:pdbx_nmr_force_constantsCategory> <VRPTx:pdbx_nmr_force_constants entry_id="1ABC"> <VRPTx:covalent_geom_bond_term>1000.</VRPTx:covalent_geom_bond_term> <VRPTx:covalent_geom_bond_term_units>kcal/mol/A**2</VRPTx:covalent_geom_bond_term_units> <VRPTx:exptl_13C_shift_term>0.5</VRPTx:exptl_13C_shift_term> <VRPTx:exptl_13C_shift_term_units>kcal/mol/ppm**2</VRPTx:exptl_13C_shift_term_units> <VRPTx:exptl_1H_shift_term>7.5</VRPTx:exptl_1H_shift_term> <VRPTx:exptl_1H_shift_term_units>kcal/mol/ppm**2</VRPTx:exptl_1H_shift_term_units> <VRPTx:exptl_J_coupling_term>1.</VRPTx:exptl_J_coupling_term> <VRPTx:exptl_J_coupling_term_units>kcal/mol/Hz**2</VRPTx:exptl_J_coupling_term_units> <VRPTx:exptl_distance_term>30.</VRPTx:exptl_distance_term> <VRPTx:exptl_distance_term_units>kcal/mol/A**2</VRPTx:exptl_distance_term_units> <VRPTx:exptl_torsion_angles_term>200.</VRPTx:exptl_torsion_angles_term> <VRPTx:exptl_torsion_angles_term_units>kcal/mol/rad**2</VRPTx:exptl_torsion_angles_term_units> <VRPTx:non-bonded_inter_van_der_Waals_term_type>4.</VRPTx:non-bonded_inter_van_der_Waals_term_type> <VRPTx:non-bonded_inter_van_der_Waals_term_units>kcal/mol/A**4</VRPTx:non-bonded_inter_van_der_Waals_term_units> </VRPTx:pdbx_nmr_force_constants> </VRPTx:pdbx_nmr_force_constantsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_force_constantsCategory This property indicates that datablock has a category holder pdbx_nmr_force_constantsCategory. pdbx_nmr_force_constantsCategory This property indicates that pdbx_nmr_force_constantsCategory. has a category pdbx_nmr_force_constants. pdbx_nmr_force_constantsItem Abstract datatype property for pdbx_nmr_force_constants items. reference_to_pdbx_nmr_force_constants cross-reference to pdbx_nmr_force_constants. referenced_by_pdbx_nmr_force_constants cross-reference from pdbx_nmr_force_constants. pdbx_nmr_force_constants.covalent_geom_angles_term The final force constant for covalent geometry angle constraints term employed in the target function used for simulated annealing. 500 kcal/mol/rad**2 kJ/mol/rad**2 other The units for the force constant for the covalent geometry angle constraints term. kcal/mol/rad**2 pdbx_nmr_force_constants.covalent_geom_bond_term The final force constant for the covalent geometry bond length constraints term employed in the target function used for simulated annealing. 1000 kcal/mol/A**2 kJ/mol/nm**2 other The units for the force constant for the covalent geometry bond length constraints term. kcal/mol/A**2 pdbx_nmr_force_constants.covalent_geom_impropers_term The final force constant for covalent geometry impropers contstraints term employed in the target function used for simulated annealing. 500 kcal/mol/rad**2 kJ/mol/rad**2 other The units for the force constant for the covalent geometry impropers constraints term. kcal/mol/rad**2 pdbx_nmr_force_constants.exptl_13C_shift_term The final force constant for 13C shift constraints term employed in the target function used for simulated annealing. 0.5 kcal/mol/ppm**2 kJ/mol/ppm**2 other The units for the force constant for the 13C shift constraints term. kcal/mol/ppm**2 pdbx_nmr_force_constants.exptl_1H_shift_term The final force constant for 1H shift constraints term employed in the target function used for simulated annealing. 7.5 kcal/mol/ppm**2 kJ/mol/ppm**2 other The units for the force constant for the 1H shift constraints term. kcal/mol/ppm**2 pdbx_nmr_force_constants.exptl_D_isotope_shift_term The final force constant for Deuterium isotope shift constraints term employed in the target function used for simulated annealing. 0.5 kcal/mol/ppb**2 kJ/mol/ppb**2 other The units for the force constant for the Deuterium isotope shift constraints term. kcal/mol/ppb**2 pdbx_nmr_force_constants.exptl_J_coupling_term The final force constant for J coupling term employed in the target function used for simulated annealing. 1 kcal/mol/Hz**2 kJ/mol/Hz**2 other The units for the force constant for the J coupling term. kcal/mol/Hz**2 pdbx_nmr_force_constants.exptl_dipolar_coupling_term The final force constant for dipolar coupling constraint term employed in the target function used for simulated annealing. 1 kcal/mol/Hz**2 kJ/mol/Hz**2 other The units for the force constant for the dipolar coupling constraints term. kcal/mol/Hz**2 pdbx_nmr_force_constants.exptl_distance_term The final force constant for distance (NOEs) constraints term employed in the target function used for simulated annealing. 30 kcal/mol/A**2 kJ/mol/nm**2 other The units for the force constant for the distance constraints term. kcal/mol/ A**2 pdbx_nmr_force_constants.exptl_torsion_angles_term The final force constant for the torsion angle term employed in the target function used for simulated annealing. 200 kcal/mol/rad**2 kJ/mol/rad**2 author The units for the force constant for the torsion angle constraints term. kcal/mol/rad**2 pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term The force constant used for the non-bonded interaction conformational database potential term employed in the target function used for simulated annealing. 1.0 pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term The force constant used for the non-bonded interaction radius of gyration term employed in the target function used for simulated annealing. 100 kcal/mol/ A**2 kJ/mol/ nm**4 other The units for the force constant for the radius of gyration term. kcal/mol/ A**2 pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term The force constant used for the non-bonded interaction van der Waals term employed in the target function used for simulated annealing. 4 quartic other The type of van der Waals term employed in the target function used for simulated annealing. quartic kcal/mol/A**4 kJ/mol/nm**4 other The units for the force constant for the van der Waals term. kcal/mol/ A**4 pdbx_nmr_force_constants.entry_id You can leave this blank as an ID will be assigned by the RCSB. 0 pdbx_nmr_refine Describe the method and details of the refinement of the deposited structure. This example is drawn from the MCP-1 structure. <VRPTx:pdbx_nmr_refineCategory> <VRPTx:pdbx_nmr_refine entry_id="1ABC" software_ordinal="1"> <VRPTx:method>torsion angle dynamics</VRPTx:method> </VRPTx:pdbx_nmr_refine> </VRPTx:pdbx_nmr_refineCategory> 0 1 0 1 1 1 pdbx_nmr_refineCategory This property indicates that datablock has a category holder pdbx_nmr_refineCategory. pdbx_nmr_refineCategory This property indicates that pdbx_nmr_refineCategory. has a category pdbx_nmr_refine. pdbx_nmr_refineItem Abstract datatype property for pdbx_nmr_refine items. reference_to_pdbx_nmr_refine cross-reference to pdbx_nmr_refine. referenced_by_pdbx_nmr_refine cross-reference from pdbx_nmr_refine. pdbx_nmr_refine.details Additional details about the NMR refinement. Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 3344 restraints, 3167 are NOE-derived distance constraints, 68 dihedral angle restraints,109 distance restraints from hydrogen bonds. pdbx_nmr_refine.method The method used to determine the structure. distance geometry simulated annealing molecular dynamics matrix relaxation torsion angle dynamics pdbx_nmr_refine.entry_id You can leave this blank as an ID will be assigned by the RCSB. pdbx_nmr_refine.software_ordinal Pointer to attribute ordinal in category software 0 pdbx_nmr_representative An average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure. This section describes selection of the representative structure. This example is drawn from the MCP-1 structure. <VRPTx:pdbx_nmr_representativeCategory> <VRPTx:pdbx_nmr_representative entry_id="1ABC"> <VRPTx:conformer_id>15</VRPTx:conformer_id> <VRPTx:selection_criteria>lowest energy</VRPTx:selection_criteria> </VRPTx:pdbx_nmr_representative> </VRPTx:pdbx_nmr_representativeCategory> 0 1 0 1 1 pdbx_nmr_representativeCategory This property indicates that datablock has a category holder pdbx_nmr_representativeCategory. pdbx_nmr_representativeCategory This property indicates that pdbx_nmr_representativeCategory. has a category pdbx_nmr_representative. pdbx_nmr_representativeItem Abstract datatype property for pdbx_nmr_representative items. reference_to_pdbx_nmr_representative cross-reference to pdbx_nmr_representative. referenced_by_pdbx_nmr_representative cross-reference from pdbx_nmr_representative. pdbx_nmr_representative.conformer_id If a member of the ensemble has been selected as a representative structure, identify it by its model number. 15 pdbx_nmr_representative.selection_criteria By highlighting the appropriate choice(s), describe the criteria used to select this structure as a representative structure, or if an average structure has been calculated describe how this was done. The structure closest to the average. The structure with the lowest energy was selected. The structure with the fewest number of violations was selected. A minimized average structure was calculated. pdbx_nmr_representative.entry_id You can leave this blank as an ID will be assigned by the RCSB. 0 pdbx_nmr_restraint_list Items in the PDBX_NMR_RESTRAINT_LIST category provide information about a list of NMR restraints. 0 1 1 1 pdbx_nmr_restraint_listCategory This property indicates that datablock has a category holder pdbx_nmr_restraint_listCategory. pdbx_nmr_restraint_listCategory This property indicates that pdbx_nmr_restraint_listCategory. has a category pdbx_nmr_restraint_list. pdbx_nmr_restraint_listItem Abstract datatype property for pdbx_nmr_restraint_list items. reference_to_pdbx_nmr_restraint_list cross-reference to pdbx_nmr_restraint_list. referenced_by_pdbx_nmr_restraint_list cross-reference from pdbx_nmr_restraint_list. pdbx_nmr_restraint_list.label A descriptive label that uniquely identifies a list of NMR restraints. nef_distance_restraint_list_2loy.mr pdbx_nmr_restraint_list.id An integer value that uniquely identifies a list of NMR restraints from other sets in the entry. distance dihedral_angle RDC Defines type of NMR restraints in a list. 0 pdbx_nmr_restraint_summary Data items in the category record NMR restraints analysis. Ref: User guide to the wwPDB NMR validation reports 8. NMR restraints analysis 8.1 Conformationally restricting restraints 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_restraint_summaryCategory This property indicates that datablock has a category holder pdbx_nmr_restraint_summaryCategory. pdbx_nmr_restraint_summaryCategory This property indicates that pdbx_nmr_restraint_summaryCategory. has a category pdbx_nmr_restraint_summary. pdbx_nmr_restraint_summaryItem Abstract datatype property for pdbx_nmr_restraint_summary items. reference_to_pdbx_nmr_restraint_summary cross-reference to pdbx_nmr_restraint_summary. referenced_by_pdbx_nmr_restraint_summary cross-reference from pdbx_nmr_restraint_summary. pdbx_nmr_restraint_summary.dihedral_angle_restraints_total The total number of dihedral angle restraints used in the final structure calculation. 0 pdbx_nmr_restraint_summary.distance_restraints_total The total number of all distance restraints used in the final structure calculation. All redundant and duplicate restraints are filtered. 4458 pdbx_nmr_restraint_summary.disulfide_bond_restraints_total The total number of disulfide bond restraints used in the final structure calculation. 3 pdbx_nmr_restraint_summary.hydrogen_bond_restraints_total The total number of hydrogen bond restraints used in the final structure calculation. 6 pdbx_nmr_restraint_summary.interchain_total_count The total number of interchain distance restraints used in the final structure calculation. This field should only be if system is complex -i.e more than one entity e.g. a dimer or ligand-protein complex 272 pdbx_nmr_restraint_summary.intraresidue_total_count The total number of intraresidue, |i-j|=0, distance restraints used in the final structure calculation. 1144 pdbx_nmr_restraint_summary.long_range_restraints_per_residue The average number of long range restraints per residue. 2.2 pdbx_nmr_restraint_summary.long_range_total_count The total number of long range, |i-j|>=5, distance restraints used in the final structure calculation. 1356 pdbx_nmr_restraint_summary.medium_range_total_count The total number of medium range, 1<|i-j|<5, distance restraints used in the final structure calculation. 682 pdbx_nmr_restraint_summary.restraints_per_residue The average number of restraints per residue. 5.8 pdbx_nmr_restraint_summary.sequential_total_count The total number of sequential, |i-j|=1, distance restraints used in the final structure calculation. 1004 pdbx_nmr_restraint_summary.unmapped_restraints_total The total number of unmapped restraints to the coordinates. pdbx_nmr_restraint_summary.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_nmr_restraint_violation Data items in the category record residual violations of conformationally restricting restraints in different bins based on its magnitude of violation. Ref: User guide to the wwPDB NMR validation reports 8. NMR restraints analysis 8.2 Residual restraint violations 1 1 0 1 1 1 0 1 0 1 1 1 pdbx_nmr_restraint_violationCategory This property indicates that datablock has a category holder pdbx_nmr_restraint_violationCategory. pdbx_nmr_restraint_violationCategory This property indicates that pdbx_nmr_restraint_violationCategory. has a category pdbx_nmr_restraint_violation. pdbx_nmr_restraint_violationItem Abstract datatype property for pdbx_nmr_restraint_violation items. reference_to_pdbx_nmr_restraint_violation cross-reference to pdbx_nmr_restraint_violation. referenced_by_pdbx_nmr_restraint_violation cross-reference from pdbx_nmr_restraint_violation. A degrees Hz The units used for both a defined range of a particular bin and the maximum value of residual violation. pdbx_nmr_restraint_violation.limit_bin_max The maximum limit for a particular bin used for the overall assessment of residual violations between the restraints and the coordinate model. The value defines an exclusive maximum limit of a bin. pdbx_nmr_restraint_violation.limit_bin_min The minimum limit for a particular bin used for the overall assessment of residual violations between the restraints and the coordinate model. The value defines an inclusive minimum limit of a bin. pdbx_nmr_restraint_violation.maximum_violation_in_bin The maximum value of residual violation in a particular bin. pdbx_nmr_restraint_violation.violations_per_model The average number of residual violations per model in a particular bin. pdbx_nmr_restraint_violation.ordinal The ordered number of the bin for counting the violated restraints. distance dihedral_angle RDC Defines the type of conformationally restricting restraints. 0 pdbx_nmr_software Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. This example describes the software used in the MCP-1 study. <VRPTx:pdbx_nmr_softwareCategory> <VRPTx:pdbx_nmr_software ordinal="1"> <VRPTx:authors>Bruker</VRPTx:authors> <VRPTx:classification>collection</VRPTx:classification> <VRPTx:name>UXNMR</VRPTx:name> <VRPTx:version>940501.3</VRPTx:version> </VRPTx:pdbx_nmr_software> <VRPTx:pdbx_nmr_software ordinal="2"> <VRPTx:authors>Hare</VRPTx:authors> <VRPTx:classification>processing</VRPTx:classification> <VRPTx:name>FELIX</VRPTx:name> <VRPTx:version>1.1</VRPTx:version> </VRPTx:pdbx_nmr_software> <VRPTx:pdbx_nmr_software ordinal="3"> <VRPTx:authors>Kraulis</VRPTx:authors> <VRPTx:classification>data analysis</VRPTx:classification> <VRPTx:name>ANSIG</VRPTx:name> <VRPTx:version>3.0</VRPTx:version> </VRPTx:pdbx_nmr_software> <VRPTx:pdbx_nmr_software ordinal="4"> <VRPTx:authors>Brunger</VRPTx:authors> <VRPTx:classification>structure calculation</VRPTx:classification> <VRPTx:name>X-PLOR</VRPTx:name> <VRPTx:version>3.8</VRPTx:version> </VRPTx:pdbx_nmr_software> </VRPTx:pdbx_nmr_softwareCategory> 0 1 1 1 1 1 0 1 1 pdbx_nmr_softwareCategory This property indicates that datablock has a category holder pdbx_nmr_softwareCategory. pdbx_nmr_softwareCategory This property indicates that pdbx_nmr_softwareCategory. has a category pdbx_nmr_software. pdbx_nmr_softwareItem Abstract datatype property for pdbx_nmr_software items. reference_to_pdbx_nmr_software cross-reference to pdbx_nmr_software. referenced_by_pdbx_nmr_software cross-reference from pdbx_nmr_software. pdbx_nmr_software.authors The name of the authors of the software used in this procedure. Brunger Guentert pdbx_nmr_software.classification The purpose of the software. collection processing data analysis structure solution refinement iterative matrix relaxation pdbx_nmr_software.name The name of the software used for the task. ANSIG AURELIA AZARA CHARMM CoMAND CORMA DIANA DYANA DSPACE DISGEO DGII DISMAN DINOSAUR DISCOVER FELIX FT_NMR GROMOS IRMA MARDIGRAS NMRPipe SA UXNMR VNMR X-PLOR XWINNMR pdbx_nmr_software.version The version of the software. 940501.3 2.1 pdbx_nmr_software.ordinal An ordinal index for this category 1 2 0 pdbx_nmr_spectrometer The details about each spectrometer used to collect data for this deposition. The instruments described here are the ones used for the MCP-1 studies. <VRPTx:pdbx_nmr_spectrometerCategory> <VRPTx:pdbx_nmr_spectrometer spectrometer_id="1"> <VRPTx:field_strength>600</VRPTx:field_strength> <VRPTx:type>Bruker AMX</VRPTx:type> </VRPTx:pdbx_nmr_spectrometer> <VRPTx:pdbx_nmr_spectrometer spectrometer_id="2"> <VRPTx:field_strength>500</VRPTx:field_strength> <VRPTx:type>Bruker AMX</VRPTx:type> </VRPTx:pdbx_nmr_spectrometer> </VRPTx:pdbx_nmr_spectrometerCategory> 0 1 0 1 0 1 0 1 0 1 1 pdbx_nmr_spectrometerCategory This property indicates that datablock has a category holder pdbx_nmr_spectrometerCategory. pdbx_nmr_spectrometerCategory This property indicates that pdbx_nmr_spectrometerCategory. has a category pdbx_nmr_spectrometer. pdbx_nmr_spectrometerItem Abstract datatype property for pdbx_nmr_spectrometer items. reference_to_pdbx_nmr_spectrometer cross-reference to pdbx_nmr_spectrometer. referenced_by_pdbx_nmr_spectrometer cross-reference from pdbx_nmr_spectrometer. pdbx_nmr_spectrometer.details A text description of the NMR spectrometer. pdbx_nmr_spectrometer.field_strength The field strength in MHz of the spectrometer. 360 400 500 600 750 800 850 900 950 1000 pdbx_nmr_spectrometer.manufacturer The name of the manufacturer of the spectrometer. Varian Bruker JEOL GE pdbx_nmr_spectrometer.model The model of the NMR spectrometer. AVANCE AVANCE II AVANCE III AVANCE III HD WH WM AC+ Alpha AM AMX AMX II DMX DRX DSX MSL OMEGA OMEGA PSG GX GSX A AL EC EX LA ECP Infinityplus Mercury VNMRS VXR UNITY INOVA UNITYPLUS INOVA home-built pdbx_nmr_spectrometer.type Select the instrument manufacturer(s) and the model(s) of the NMR(s) used for this work. Bruker WH Bruker WM Bruker AM Bruker AMX Bruker DMX Bruker DRX Bruker MSL Bruker AVANCE GE Omega GE Omega PSG JEOL GX JEOL GSX JEOL A JEOL AL JEOL EC JEOL EX JEOL LA JEOL ECP Varian VXRS Varian UNITY Varian UNITYplus Varian INOVA other pdbx_nmr_spectrometer.spectrometer_id Assign a numerical ID to each instrument. 1 2 3 0 pdbx_nmr_unmapped_chem_shift Items in the PDBX_NMR_UNMAPPED_CHEM_SHIFT category provide information about assigned chemical shifts not mapped to atoms in the NMR structure. 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_nmr_unmapped_chem_shiftCategory This property indicates that datablock has a category holder pdbx_nmr_unmapped_chem_shiftCategory. pdbx_nmr_unmapped_chem_shiftCategory This property indicates that pdbx_nmr_unmapped_chem_shiftCategory. has a category pdbx_nmr_unmapped_chem_shift. pdbx_nmr_unmapped_chem_shiftItem Abstract datatype property for pdbx_nmr_unmapped_chem_shift items. reference_to_pdbx_nmr_unmapped_chem_shift cross-reference to pdbx_nmr_unmapped_chem_shift. referenced_by_pdbx_nmr_unmapped_chem_shift cross-reference from pdbx_nmr_unmapped_chem_shift. 1 2 3 4 5 6 9 Ambiguity codes are used to define chemical shifts that have not been assigned to specific atoms in the molecule studied. Ambiguity in chemical shifts may exist at several different levels, stereospecific ambiguity, intra and inter residue ambiguities, etc. pdbx_nmr_unmapped_chem_shift.auth_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unmapped_chem_shift.auth_atom_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unmapped_chem_shift.auth_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unmapped_chem_shift.auth_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unmapped_chem_shift.details A diagnostic message while mapping assigned chemical shifts to atoms in the NMR structure. pdbx_nmr_unmapped_chem_shift.val Assigned chemical shift value in ppm. pdbx_nmr_unmapped_chem_shift.val_err Estimated or measured error in the assigned chemical shift value in ppm. pdbx_nmr_unmapped_chem_shift.id The value of attribute id in category pdbx_nmr_unmapped_chem_shift must uniquely identify each item in the PDBX_NMR_UNMAPPED_CHEM_SHIFT list. This is an integer serial number. pdbx_nmr_unmapped_chem_shift.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_nmr_unparsed_chem_shift Items in the PDBX_NMR_UNPARSED_CHEM_SHIFT category provide information about assigned chemical shifts not parsed. 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_nmr_unparsed_chem_shiftCategory This property indicates that datablock has a category holder pdbx_nmr_unparsed_chem_shiftCategory. pdbx_nmr_unparsed_chem_shiftCategory This property indicates that pdbx_nmr_unparsed_chem_shiftCategory. has a category pdbx_nmr_unparsed_chem_shift. pdbx_nmr_unparsed_chem_shiftItem Abstract datatype property for pdbx_nmr_unparsed_chem_shift items. reference_to_pdbx_nmr_unparsed_chem_shift cross-reference to pdbx_nmr_unparsed_chem_shift. referenced_by_pdbx_nmr_unparsed_chem_shift cross-reference from pdbx_nmr_unparsed_chem_shift. 1 2 3 4 5 6 9 Ambiguity codes are used to define chemical shifts that have not been assigned to specific atoms in the molecule studied. Ambiguity in chemical shifts may exist at several different levels, stereospecific ambiguity, intra and inter residue ambiguities, etc. pdbx_nmr_unparsed_chem_shift.auth_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unparsed_chem_shift.auth_atom_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unparsed_chem_shift.auth_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unparsed_chem_shift.auth_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_nmr_unparsed_chem_shift.chem_shift_id An integer value that is a unique identifier for the assigned chemical shift value in the assigned chemical shift list. pdbx_nmr_unparsed_chem_shift.details A diagnostic message while parsing assigned chemical shifts. pdbx_nmr_unparsed_chem_shift.val Assigned chemical shift value in ppm. pdbx_nmr_unparsed_chem_shift.val_err Estimated or measured error in the assigned chemical shift value in ppm. pdbx_nmr_unparsed_chem_shift.id The value of attribute id in category pdbx_nmr_unparsed_chem_shift must uniquely identify each item in the PDBX_NMR_UNPARSED_CHEM_SHIFT list. This is an integer serial number. pdbx_nmr_unparsed_chem_shift.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_nonpoly_scheme The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities. Example 1 - <VRPTx:pdbx_nonpoly_schemeCategory> <VRPTx:pdbx_nonpoly_scheme asym_id="C" ndb_seq_num="100"> <VRPTx:auth_mon_id>HOH</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>100</VRPTx:auth_seq_num> <VRPTx:entity_id>3</VRPTx:entity_id> <VRPTx:mon_id>HOH</VRPTx:mon_id> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>HOH</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>100</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>C</VRPTx:pdb_strand_id> </VRPTx:pdbx_nonpoly_scheme> </VRPTx:pdbx_nonpoly_schemeCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_nonpoly_schemeCategory This property indicates that datablock has a category holder pdbx_nonpoly_schemeCategory. pdbx_nonpoly_schemeCategory This property indicates that pdbx_nonpoly_schemeCategory. has a category pdbx_nonpoly_scheme. pdbx_nonpoly_schemeItem Abstract datatype property for pdbx_nonpoly_scheme items. reference_to_pdbx_nonpoly_scheme cross-reference to pdbx_nonpoly_scheme. referenced_by_pdbx_nonpoly_scheme cross-reference from pdbx_nonpoly_scheme. pdbx_nonpoly_scheme.auth_mon_id Author provided residue identifier. This value may differ from the PDB residue identifier and may not correspond to residue identification within the coordinate records. pdbx_nonpoly_scheme.auth_seq_num Author provided residue numbering. This value may differ from the PDB residue number and may not correspond to residue numbering within the coordinate records. pdbx_nonpoly_scheme.entity_id Pointer to attribute label_entity_id in category atom_site. pdbx_nonpoly_scheme.mon_id Pointer to attribute label_comp_id in category atom_site. pdbx_nonpoly_scheme.pdb_ins_code PDB insertion code. pdbx_nonpoly_scheme.pdb_mon_id PDB residue identifier. pdbx_nonpoly_scheme.pdb_seq_num PDB residue number. pdbx_nonpoly_scheme.pdb_strand_id PDB strand/chain id. pdbx_nonpoly_scheme.asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 pdbx_nonpoly_scheme.ndb_seq_num NDB/RCSB residue number. 0 pdbx_percentile_conditions Data items in the PDBX_PERCENTILE_CONDITIONS category describe conditions to calculate percentile rank representations of each validation metric in the wwPDB validation report. For example, relative evaluation for X-ray structure is obtained by by comparing other X-ray structures having similar resolution. If there are no conditions by default, absolute evaluation is calculated based on all available PDB structures determined by the same methodology. Example 1 - <VRPTx:pdbx_percentile_conditionsCategory> <VRPTx:pdbx_percentile_conditions id="1"> <VRPTx:ls_d_res_high xsi:nil="true" /> <VRPTx:ls_d_res_low xsi:nil="true" /> <VRPTx:number_entries_total>101464</VRPTx:number_entries_total> </VRPTx:pdbx_percentile_conditions> <VRPTx:pdbx_percentile_conditions id="2"> <VRPTx:ls_d_res_high>1.9</VRPTx:ls_d_res_high> <VRPTx:ls_d_res_low>1.9</VRPTx:ls_d_res_low> <VRPTx:number_entries_total>5100</VRPTx:number_entries_total> </VRPTx:pdbx_percentile_conditions> </VRPTx:pdbx_percentile_conditionsCategory> 0 1 0 1 0 1 1 pdbx_percentile_conditionsCategory This property indicates that datablock has a category holder pdbx_percentile_conditionsCategory. pdbx_percentile_conditionsCategory This property indicates that pdbx_percentile_conditionsCategory. has a category pdbx_percentile_conditions. pdbx_percentile_conditionsItem Abstract datatype property for pdbx_percentile_conditions items. reference_to_pdbx_percentile_conditions cross-reference to pdbx_percentile_conditions. referenced_by_pdbx_percentile_conditions cross-reference from pdbx_percentile_conditions. pdbx_percentile_conditions.ls_d_res_high The highest resolution to set up condition of calculation of validation metric. See also the definition of attribute ls_d_res_high in category refine. pdbx_percentile_conditions.ls_d_res_low The lowest resolution to set up condition of calculation of validation metric. See also the definition of attribute ls_d_res_low in category refine. pdbx_percentile_conditions.number_entries_total The total number of entries used to generate this validation information in the condition. pdbx_percentile_conditions.id Unique identifier for conditions of calculation of validation metric. 0 pdbx_percentile_entity_view Data items in the PDBX_PERCENTILE_ENTITY_VIEW category describe a percentile rank representation of defined validation metric for each entity in the wwPDB validation report. Example 1 - <VRPTx:pdbx_percentile_entity_viewCategory> <VRPTx:pdbx_percentile_entity_view conditions_id="1" label_asym_id="A" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> <VRPTx:pdbx_percentile_entity_view conditions_id="2" label_asym_id="A" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> <VRPTx:pdbx_percentile_entity_view conditions_id="1" label_asym_id="B" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> <VRPTx:pdbx_percentile_entity_view conditions_id="2" label_asym_id="B" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> </VRPTx:pdbx_percentile_entity_viewCategory> 1 1 0 1 1 1 1 1 1 1 1 1 pdbx_percentile_entity_viewCategory This property indicates that datablock has a category holder pdbx_percentile_entity_viewCategory. pdbx_percentile_entity_viewCategory This property indicates that pdbx_percentile_entity_viewCategory. has a category pdbx_percentile_entity_view. pdbx_percentile_entity_viewItem Abstract datatype property for pdbx_percentile_entity_view items. reference_to_pdbx_percentile_entity_view cross-reference to pdbx_percentile_entity_view. referenced_by_pdbx_percentile_entity_view cross-reference from pdbx_percentile_entity_view. pdbx_percentile_entity_view.auth_asym_id Pointer to attribute auth_asym_id in category atom_site. absolute relative A short descriptive label that identifies applied conditions for calculation of validation metric. pdbx_percentile_entity_view.entity_id Pointer to attribute label_entity_id in category atom_site. pdbx_percentile_entity_view.rank The percentile rank of the validation metric defined. pdbx_percentile_entity_view.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. pdbx_percentile_entity_view.conditions_id Pointer to attribute id in category pdbx_percentile_conditions. pdbx_percentile_entity_view.label_asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 RSRZ_outliers_percent Ramachandran_outlier_percent rotamer_outliers_percent The validation metric of the percentile rank representation. 0 pdbx_percentile_list Data items in the PDBX_PERCENTILE_LIST category describe a set of percentile rank representations of each validation metric in the wwPDB validation report. Example 1 - <VRPTx:pdbx_percentile_listCategory> <VRPTx:pdbx_percentile_list entry_id="5U9B"> <VRPTx:name>all,1.8,xray</VRPTx:name> </VRPTx:pdbx_percentile_list> </VRPTx:pdbx_percentile_listCategory> 1 1 1 pdbx_percentile_listCategory This property indicates that datablock has a category holder pdbx_percentile_listCategory. pdbx_percentile_listCategory This property indicates that pdbx_percentile_listCategory. has a category pdbx_percentile_list. pdbx_percentile_listItem Abstract datatype property for pdbx_percentile_list items. reference_to_pdbx_percentile_list cross-reference to pdbx_percentile_list. referenced_by_pdbx_percentile_list cross-reference from pdbx_percentile_list. pdbx_percentile_list.name A comma separated name to indicate a set of percentile ranks. Example 1 - "all,1.8,xray" that include all geometric validation metrics and X-ray specific metrics recommended by X-ray VTF with the criteria determined by the higher resolution 1.8 angstroms. Example 2 - "all,em": that include all geometric validation metrics and EM specific metrics recommended by EM VTF. Example 3 - "all,nmr": that include all geometric validation metrics and NMR specific metrics recommended by NMR VTF. all,1.8,xray all,em all,nmr pdbx_percentile_list.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_percentile_view Data items in the PDBX_PERCENTILE_VIEW category describe a percentile rank representation of defined validation metric in the wwPDB validation report. Example 1 - <VRPTx:pdbx_percentile_viewCategory> <VRPTx:pdbx_percentile_view conditions_id="1" entry_id="5B1L" type="&apos;all_atom_clashscore"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:rank>66.9</VRPTx:rank> </VRPTx:pdbx_percentile_view> <VRPTx:pdbx_percentile_view conditions_id="1" entry_id="5B1L" type="&apos;RSRZ_outliers_percent"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_view> <VRPTx:pdbx_percentile_view conditions_id="2" entry_id="5B1L" type="&apos;all_atom_clashscore"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:rank>62.5</VRPTx:rank> </VRPTx:pdbx_percentile_view> <VRPTx:pdbx_percentile_view conditions_id="2" entry_id="5B1L" type="&apos;RSRZ_outliers_percent"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_view> </VRPTx:pdbx_percentile_viewCategory> 0 1 1 1 1 1 1 pdbx_percentile_viewCategory This property indicates that datablock has a category holder pdbx_percentile_viewCategory. pdbx_percentile_viewCategory This property indicates that pdbx_percentile_viewCategory. has a category pdbx_percentile_view. pdbx_percentile_viewItem Abstract datatype property for pdbx_percentile_view items. reference_to_pdbx_percentile_view cross-reference to pdbx_percentile_view. referenced_by_pdbx_percentile_view cross-reference from pdbx_percentile_view. absolute relative A short descriptive label that identifies applied conditions for calculation of validation metric. pdbx_percentile_view.rank The percentile rank of the validation metric defined. pdbx_percentile_view.conditions_id Pointer to attribute id in category pdbx_percentile_conditions. pdbx_percentile_view.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. R_value_R_free RNA_suiteness_score all_atom_clashscore RSRZ_outliers_percent Ramachandran_outlier_percent rotamer_outliers_percent The validation metric of the percentile rank representation. 0 pdbx_phasing_MAD_set Record details about each phasing set: (Note: the phasing set is different from data set. for example: if there are three data sets, the inflection point (IP), the peak (PK) and the high remote (HR), the combination of the phasing set will be IP_iso, PK_iso (the isomorphous repleacement with HR as 'native'), IP_ano, PK_ano and HR_ano (the anomalous difference with itself). Therefore, there are five set used for phasing. Example 1 - three wavelengths <VRPTx:pdbx_phasing_MAD_setCategory> <VRPTx:pdbx_phasing_MAD_set id="ISO_1"> <VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:d_res_high>2.00</VRPTx:d_res_high> <VRPTx:d_res_low>22.60</VRPTx:d_res_low> <VRPTx:reflns_acentric>5387</VRPTx:reflns_acentric> <VRPTx:reflns_centric>471</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set> <VRPTx:pdbx_phasing_MAD_set id="ISO_2"> <VRPTx:R_cullis_acentric>0.803</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.718</VRPTx:R_cullis_centric> <VRPTx:d_res_high>2.00</VRPTx:d_res_high> <VRPTx:d_res_low>22.60</VRPTx:d_res_low> <VRPTx:reflns_acentric>5365</VRPTx:reflns_acentric> <VRPTx:reflns_centric>469</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set> <VRPTx:pdbx_phasing_MAD_set id="ISO_3"> <VRPTx:R_cullis_acentric>0.658</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.500</VRPTx:R_cullis_centric> <VRPTx:d_res_high>2.00</VRPTx:d_res_high> <VRPTx:d_res_low>22.60</VRPTx:d_res_low> <VRPTx:reflns_acentric>5317</VRPTx:reflns_acentric> <VRPTx:reflns_centric>460</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set> <VRPTx:pdbx_phasing_MAD_set id="ANO_1"> <VRPTx:R_cullis_acentric>0.841</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:d_res_high>2.00</VRPTx:d_res_high> <VRPTx:d_res_low>22.60</VRPTx:d_res_low> <VRPTx:reflns_acentric>5278</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set> <VRPTx:pdbx_phasing_MAD_set id="ANO_2"> <VRPTx:R_cullis_acentric>0.649</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:d_res_high>2.00</VRPTx:d_res_high> <VRPTx:d_res_low>22.60</VRPTx:d_res_low> <VRPTx:reflns_acentric>5083</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set> <VRPTx:pdbx_phasing_MAD_set id="ANO_3"> <VRPTx:R_cullis_acentric>0.829</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:d_res_high>2.00</VRPTx:d_res_high> <VRPTx:d_res_low>22.60</VRPTx:d_res_low> <VRPTx:reflns_acentric>5329</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set> </VRPTx:pdbx_phasing_MAD_setCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_phasing_MAD_setCategory This property indicates that datablock has a category holder pdbx_phasing_MAD_setCategory. pdbx_phasing_MAD_setCategory This property indicates that pdbx_phasing_MAD_setCategory. has a category pdbx_phasing_MAD_set. pdbx_phasing_MAD_setItem Abstract datatype property for pdbx_phasing_MAD_set items. reference_to_pdbx_phasing_MAD_set cross-reference to pdbx_phasing_MAD_set. referenced_by_pdbx_phasing_MAD_set cross-reference from pdbx_phasing_MAD_set. pdbx_phasing_MAD_set.R_cullis attribute R_cullis in category pdbx_phasing_MAD_set records R_cullis for MAD phasing. pdbx_phasing_MAD_set.R_cullis_acentric attribute R_cullis_acentric in category pdbx_phasing_MAD_set records R_cullis using acentric data for MAD phasing. pdbx_phasing_MAD_set.R_cullis_centric attribute R_cullis_centric in category pdbx_phasing_MAD_set records R_cullis using centric data for MAD phasing. pdbx_phasing_MAD_set.R_kraut attribute R_kraut in category pdbx_phasing_MAD_set records R_kraut for MAD phasing. pdbx_phasing_MAD_set.R_kraut_acentric attribute r_kraut_acentric in category pdbx_phasing_MAD_set records r_kraut using acentric data for MAD phasing. pdbx_phasing_MAD_set.R_kraut_centric attribute R_kraut_centric in category pdbx_phasing_MAD_set records r_kraut using centric data for MAD phasing. pdbx_phasing_MAD_set.d_res_high attribute d_res_high in category pdbx_phasing_MAD_set records the highest resolution for the phasing set. pdbx_phasing_MAD_set.d_res_low attribute d_res_low in category pdbx_phasing_MAD_set records the lowerest resolution for phasing set. pdbx_phasing_MAD_set.fom attribute fom in category pdbx_phasing_MAD_set records the figure of merit for MAD phasing. pdbx_phasing_MAD_set.fom_acentric attribute fom_acentric in category pdbx_phasing_MAD_set records the figure of merit using acentric data for MAD phasing. pdbx_phasing_MAD_set.fom_centric attribute fom_centric in category pdbx_phasing_MAD_set records the figure of merit using centric data for MAD phasing. pdbx_phasing_MAD_set.loc attribute loc in category pdbx_phasing_MAD_set records lack of closure for MAD phasing. pdbx_phasing_MAD_set.loc_acentric attribute loc_acentric in category pdbx_phasing_MAD_set records lack of closure using acentric data for MAD phasing. pdbx_phasing_MAD_set.loc_centric attribute loc_centric in category pdbx_phasing_MAD_set records lack of closure using centric data for MAD phasing. pdbx_phasing_MAD_set.number_of_sites attribute number_of_sites in category pdbx_phasing_MAD_set records the number of site refined for the phasing set. pdbx_phasing_MAD_set.power attribute power in category pdbx_phasing_MAD_set records phasing power for MAD phasing. pdbx_phasing_MAD_set.power_acentric attribute power_acentric in category pdbx_phasing_MAD_set records phasing powe using acentric data for MAD phasing. pdbx_phasing_MAD_set.power_centric attribute power_centric in category pdbx_phasing_MAD_set records phasing powe using centric data for MAD phasing. pdbx_phasing_MAD_set.reflns attribute reflns in category pdbx_phasing_MAD_set records the number of reflections used for MAD phasing. pdbx_phasing_MAD_set.reflns_acentric attribute reflns_acentric in category pdbx_phasing_MAD_set records the number of acentric reflections for MAD phasing. pdbx_phasing_MAD_set.reflns_centric attribute reflns_centric in category pdbx_phasing_MAD_set records the number of centric reflections for MAD phasing. pdbx_phasing_MAD_set.id attribute id in category pdbx_phasing_MAD_set records phase set name for MAD phasing. 0 pdbx_phasing_MAD_set_shell The same as category pdbx_phasing_MAD_set, but broken into shells. Example 1 - three wavelengths (SHARP example) <VRPTx:pdbx_phasing_MAD_set_shellCategory> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ISO_1"> <VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>0.000</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>64</VRPTx:reflns_acentric> <VRPTx:reflns_centric>23</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ISO_1"> <VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>0.000</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>130</VRPTx:reflns_acentric> <VRPTx:reflns_centric>32</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ISO_1"> <VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>0.000</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>182</VRPTx:reflns_acentric> <VRPTx:reflns_centric>27</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ISO_1"> <VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>0.000</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>207</VRPTx:reflns_acentric> <VRPTx:reflns_centric>24</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ANO_1"> <VRPTx:R_cullis_acentric>0.610</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>1.804</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>62</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ANO_1"> <VRPTx:R_cullis_acentric>0.532</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>2.382</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>129</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ANO_1"> <VRPTx:R_cullis_acentric>0.673</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>1.858</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>178</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> <VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ANO_1"> <VRPTx:R_cullis_acentric>0.755</VRPTx:R_cullis_acentric> <VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric> <VRPTx:power_acentric>1.605</VRPTx:power_acentric> <VRPTx:power_centric>0.000</VRPTx:power_centric> <VRPTx:reflns_acentric>204</VRPTx:reflns_acentric> <VRPTx:reflns_centric>0</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_set_shell> </VRPTx:pdbx_phasing_MAD_set_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_phasing_MAD_set_shellCategory This property indicates that datablock has a category holder pdbx_phasing_MAD_set_shellCategory. pdbx_phasing_MAD_set_shellCategory This property indicates that pdbx_phasing_MAD_set_shellCategory. has a category pdbx_phasing_MAD_set_shell. pdbx_phasing_MAD_set_shellItem Abstract datatype property for pdbx_phasing_MAD_set_shell items. reference_to_pdbx_phasing_MAD_set_shell cross-reference to pdbx_phasing_MAD_set_shell. referenced_by_pdbx_phasing_MAD_set_shell cross-reference from pdbx_phasing_MAD_set_shell. pdbx_phasing_MAD_set_shell.R_cullis attribute R_cullis in category pdbx_phasing_MAD_set_shell records R_cullis for MAD phasing. pdbx_phasing_MAD_set_shell.R_cullis_acentric attribute R_cullis_acentric in category pdbx_phasing_MAD_set_shell records R_cullis using acentric data for MAD phasing. pdbx_phasing_MAD_set_shell.R_cullis_centric attribute R_cullis_centric in category pdbx_phasing_MAD_set_shell records R_cullis using centric data for MAD phasing. pdbx_phasing_MAD_set_shell.R_kraut attribute R_kraut in category pdbx_phasing_MAD_set_shell records R_kraut for MAD phasing. pdbx_phasing_MAD_set_shell.R_kraut_acentric attribute R_kraut_acentric in category pdbx_phasing_MAD_set_shell records R_kraut using acentric data for MAD phasing. pdbx_phasing_MAD_set_shell.R_kraut_centric attribute R_kraut_centric in category pdbx_phasing_MAD_set_shell records R_kraut using centric data for MAD phasing. pdbx_phasing_MAD_set_shell.fom attribute fom in category pdbx_phasing_MAD_set_shell records the figure of merit for MAD phasing. pdbx_phasing_MAD_set_shell.fom_acentric attribute fom_acentric in category pdbx_phasing_MAD_set_shell records the figure of merit using acentric data for MAD phasing. pdbx_phasing_MAD_set_shell.fom_centric attribute fom_centric in category pdbx_phasing_MAD_set_shell records the figure of merit using centric data for MAD phasing. pdbx_phasing_MAD_set_shell.loc attribute loc in category pdbx_phasing_MAD_set_shell records lack of closure for MAD phasing. pdbx_phasing_MAD_set_shell.loc_acentric attribute loc_acentric in category pdbx_phasing_MAD_set_shell records lack of closure using acentric data for MAD phasing. pdbx_phasing_MAD_set_shell.loc_centric attribute loc_centric in category pdbx_phasing_MAD_set_shell records lack of closure using centric data for MAD phasing. pdbx_phasing_MAD_set_shell.power attribute power in category pdbx_phasing_MAD_set_shell records phasing power for MAD phasing. pdbx_phasing_MAD_set_shell.power_acentric attribute power_acentric in category pdbx_phasing_MAD_set_shell records phasing power using acentric data for MAD phasing. pdbx_phasing_MAD_set_shell.power_centric attribute power_centric in category pdbx_phasing_MAD_set_shell records phasing power using centric data for MAD phasing. pdbx_phasing_MAD_set_shell.reflns attribute reflns in category pdbx_phasing_MAD_set_shell records the number of reflections used for MAD phasing. pdbx_phasing_MAD_set_shell.reflns_acentric attribute reflns_acentric in category pdbx_phasing_MAD_set_shell records the number of acentric reflections for MAD phasing. pdbx_phasing_MAD_set_shell.reflns_centric attribute reflns_centric in category pdbx_phasing_MAD_set_shell records the number of centric reflections for MAD phasing. pdbx_phasing_MAD_set_shell.d_res_high attribute d_res_high in category pdbx_phasing_MAD_set_shell records the highest resolution for the phasing set. pdbx_phasing_MAD_set_shell.d_res_low attribute d_res_low in category pdbx_phasing_MAD_set_shell records the lowerest resolution for phasing set. pdbx_phasing_MAD_set_shell.id attribute id in category pdbx_phasing_MAD_set_shell records phase set name for MAD phasing. 0 pdbx_phasing_MAD_set_site Record the details (coordinates etc.) of anomalous scatters. Example 1 - anomalous scatters is Se <VRPTx:pdbx_phasing_MAD_set_siteCategory> <VRPTx:pdbx_phasing_MAD_set_site id="1"> <VRPTx:Cartn_x>25.9407</VRPTx:Cartn_x> <VRPTx:Cartn_y>-0.103471</VRPTx:Cartn_y> <VRPTx:Cartn_z>17.4094</VRPTx:Cartn_z> <VRPTx:atom_type_symbol>SE</VRPTx:atom_type_symbol> <VRPTx:b_iso>15.2561</VRPTx:b_iso> <VRPTx:occupancy>1</VRPTx:occupancy> </VRPTx:pdbx_phasing_MAD_set_site> <VRPTx:pdbx_phasing_MAD_set_site id="2"> <VRPTx:Cartn_x>30.6534</VRPTx:Cartn_x> <VRPTx:Cartn_y>6.62359</VRPTx:Cartn_y> <VRPTx:Cartn_z>9.93063</VRPTx:Cartn_z> <VRPTx:atom_type_symbol>SE</VRPTx:atom_type_symbol> <VRPTx:b_iso>12.9102</VRPTx:b_iso> <VRPTx:occupancy>1</VRPTx:occupancy> </VRPTx:pdbx_phasing_MAD_set_site> <VRPTx:pdbx_phasing_MAD_set_site id="3"> <VRPTx:Cartn_x>-3.26506</VRPTx:Cartn_x> <VRPTx:Cartn_y>15.5546</VRPTx:Cartn_y> <VRPTx:Cartn_z>53.9529</VRPTx:Cartn_z> <VRPTx:atom_type_symbol>SE</VRPTx:atom_type_symbol> <VRPTx:b_iso>30.5239</VRPTx:b_iso> <VRPTx:occupancy>1</VRPTx:occupancy> </VRPTx:pdbx_phasing_MAD_set_site> </VRPTx:pdbx_phasing_MAD_set_siteCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_phasing_MAD_set_siteCategory This property indicates that datablock has a category holder pdbx_phasing_MAD_set_siteCategory. pdbx_phasing_MAD_set_siteCategory This property indicates that pdbx_phasing_MAD_set_siteCategory. has a category pdbx_phasing_MAD_set_site. pdbx_phasing_MAD_set_siteItem Abstract datatype property for pdbx_phasing_MAD_set_site items. reference_to_pdbx_phasing_MAD_set_site cross-reference to pdbx_phasing_MAD_set_site. referenced_by_pdbx_phasing_MAD_set_site cross-reference from pdbx_phasing_MAD_set_site. pdbx_phasing_MAD_set_site.Cartn_x attribute Cartn_x in category pdbx_phasing_MAD_set_site records the X Cartesian coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.Cartn_x_esd attribute Cartn_x_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation X Cartesian coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.Cartn_y attribute Cartn_y in category pdbx_phasing_MAD_set_site records the Y Cartesian coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.Cartn_y_esd attribute Cartn_y_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Y Cartesian coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.Cartn_z attribute Cartn_z in category pdbx_phasing_MAD_set_site records the Z Cartesian coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.Cartn_z_esd attribute Cartn_z_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Z Cartesian coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.atom_type_symbol attribute atom_type_symbol in category pdbx_phasing_MAD_set_site records the name of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.b_iso attribute b_iso in category pdbx_phasing_MAD_set_site records isotropic temperature factor parameterthe for the site obtained from MAD phasing. pdbx_phasing_MAD_set_site.b_iso_esd attribute b_iso_esd in category pdbx_phasing_MAD_set_site records estimated standard deviation of isotropic temperature factor parameterthe for the site obtained from MAD phasing. pdbx_phasing_MAD_set_site.fract_x attribute fract_x in category pdbx_phasing_MAD_set_site records the X fractional coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.fract_x_esd attribute fract_x_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation X fractional coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.fract_y attribute fract_y in category pdbx_phasing_MAD_set_site records the Y fractional coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.fract_y_esd attribute fract_y_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Y fractional coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.fract_z attribute fract_z in category pdbx_phasing_MAD_set_site records the Z fractional coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.fract_z_esd attribute fract_z_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Z fractional coordinate of site obtained from MAD phasing. pdbx_phasing_MAD_set_site.occupancy attribute occupancy in category pdbx_phasing_MAD_set_site records the fraction of the atom type presented at this site. pdbx_phasing_MAD_set_site.occupancy_esd attribute occupancy_esd in category pdbx_phasing_MAD_set_site records estimated standard deviation of the fraction of the atom type presented at this site. pdbx_phasing_MAD_set_site.occupancy_iso The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given atom site. pdbx_phasing_MAD_set_site.set_id Record the phasing set. pdbx_phasing_MAD_set_site.id attribute id in category pdbx_phasing_MAD_set_site records the number of site obtained from MAD phasing. 0 pdbx_phasing_MAD_shell Data items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution) Example 1 - <VRPTx:pdbx_phasing_MAD_shellCategory> <VRPTx:pdbx_phasing_MAD_shell d_res_high="7.77" d_res_low="22.60"> <VRPTx:fom_acentric>0.886</VRPTx:fom_acentric> <VRPTx:fom_centric>0.641</VRPTx:fom_centric> <VRPTx:reflns_acentric>64</VRPTx:reflns_acentric> <VRPTx:reflns_centric>23</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_shell> <VRPTx:pdbx_phasing_MAD_shell d_res_high="5.67" d_res_low="7.77"> <VRPTx:fom_acentric>0.863</VRPTx:fom_acentric> <VRPTx:fom_centric>0.642</VRPTx:fom_centric> <VRPTx:reflns_acentric>132</VRPTx:reflns_acentric> <VRPTx:reflns_centric>32</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_shell> <VRPTx:pdbx_phasing_MAD_shell d_res_high="4.68" d_res_low="5.67"> <VRPTx:fom_acentric>0.842</VRPTx:fom_acentric> <VRPTx:fom_centric>0.737</VRPTx:fom_centric> <VRPTx:reflns_acentric>182</VRPTx:reflns_acentric> <VRPTx:reflns_centric>27</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_shell> <VRPTx:pdbx_phasing_MAD_shell d_res_high="4.07" d_res_low="4.68"> <VRPTx:fom_acentric>0.789</VRPTx:fom_acentric> <VRPTx:fom_centric>0.682</VRPTx:fom_centric> <VRPTx:reflns_acentric>209</VRPTx:reflns_acentric> <VRPTx:reflns_centric>24</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_shell> <VRPTx:pdbx_phasing_MAD_shell d_res_high="3.65" d_res_low="4.07"> <VRPTx:fom_acentric>0.772</VRPTx:fom_acentric> <VRPTx:fom_centric>0.633</VRPTx:fom_centric> <VRPTx:reflns_acentric>246</VRPTx:reflns_acentric> <VRPTx:reflns_centric>27</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_shell> <VRPTx:pdbx_phasing_MAD_shell d_res_high="3.34" d_res_low="3.65"> <VRPTx:fom_acentric>0.752</VRPTx:fom_acentric> <VRPTx:fom_centric>0.700</VRPTx:fom_centric> <VRPTx:reflns_acentric>260</VRPTx:reflns_acentric> <VRPTx:reflns_centric>31</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_MAD_shell> </VRPTx:pdbx_phasing_MAD_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_phasing_MAD_shellCategory This property indicates that datablock has a category holder pdbx_phasing_MAD_shellCategory. pdbx_phasing_MAD_shellCategory This property indicates that pdbx_phasing_MAD_shellCategory. has a category pdbx_phasing_MAD_shell. pdbx_phasing_MAD_shellItem Abstract datatype property for pdbx_phasing_MAD_shell items. reference_to_pdbx_phasing_MAD_shell cross-reference to pdbx_phasing_MAD_shell. referenced_by_pdbx_phasing_MAD_shell cross-reference from pdbx_phasing_MAD_shell. pdbx_phasing_MAD_shell.R_cullis attribute R_cullis in category pdbx_phasing_MAD_shell records R_cullis for MAD phasing. pdbx_phasing_MAD_shell.R_cullis_acentric attribute R_cullis_acentric in category pdbx_phasing_MAD_shell records R_cullis using acentric data for MAD phasing. pdbx_phasing_MAD_shell.R_cullis_centric attribute R_cullis_centric in category pdbx_phasing_MAD_shell records R_cullis using centric data for MAD phasing. pdbx_phasing_MAD_shell.R_kraut attribute R_kraut in category pdbx_phasing_MAD_shell records R_kraut for MAD phasing. pdbx_phasing_MAD_shell.R_kraut_acentric attribute r_kraut_acentric in category pdbx_phasing_MAD_shell records R_kraut using acentric data for MAD phasing. pdbx_phasing_MAD_shell.R_kraut_centric attribute R_kraut_centric in category pdbx_phasing_MAD_shell records R_kraut using centric data for MAD phasing. pdbx_phasing_MAD_shell.fom attribute fom in category pdbx_phasing_MAD_shell records the figure of merit for MAD phasing. pdbx_phasing_MAD_shell.fom_acentric attribute fom_acentric in category pdbx_phasing_MAD_shell records the figure of merit using acentric data for MAD phasing. pdbx_phasing_MAD_shell.fom_centric attribute fom_centric in category pdbx_phasing_MAD_shell records the figure of merit using centric data for MAD phasing. pdbx_phasing_MAD_shell.loc attribute loc in category pdbx_phasing_MAD_shell records lack of closure for MAD phasing. pdbx_phasing_MAD_shell.loc_acentric attribute loc_acentric in category pdbx_phasing_MAD_shell records lack of closure using acentric data for MAD phasing. pdbx_phasing_MAD_shell.loc_centric attribute loc_centric in category pdbx_phasing_MAD_shell records lack of closure using centric data for MAD phasing. pdbx_phasing_MAD_shell.power attribute loc in category pdbx_phasing_MAD_shell records phasing power for MAD phasing. pdbx_phasing_MAD_shell.power_acentric attribute power_acentric in category pdbx_phasing_MAD_shell records phasing powe using acentric data for MAD phasing. pdbx_phasing_MAD_shell.power_centric attribute power_centric in category pdbx_phasing_MAD_shell records phasing powe using centric data for MAD phasing. pdbx_phasing_MAD_shell.reflns attribute reflns in category pdbx_phasing_MAD_shell records the number of reflections used for MAD phasing. pdbx_phasing_MAD_shell.reflns_acentric attribute reflns_acentric in category pdbx_phasing_MAD_shell records the number of acentric reflections for MAD phasing. pdbx_phasing_MAD_shell.reflns_centric attribute reflns_centric in category pdbx_phasing_MAD_shell records the number of centric reflections for MAD phasing. pdbx_phasing_MAD_shell.d_res_high attribute d_res_high in category pdbx_phasing_MAD_shell records the higher resolution for the shell. pdbx_phasing_MAD_shell.d_res_low attribute d_res_low in category pdbx_phasing_MAD_shell records the lower resolution for the shell. 0 pdbx_phasing_MR Data items in the PDBX_PHASING_MR category record details about molecular replacement. Example 1 - molecular replacement example from program CNS. <VRPTx:pdbx_phasing_MRCategory> <VRPTx:pdbx_phasing_MR entry_id="ABC001"> <VRPTx:correlation_coeff_Fo_to_Fc>0.586</VRPTx:correlation_coeff_Fo_to_Fc> <VRPTx:d_res_high_rotation>3.8</VRPTx:d_res_high_rotation> <VRPTx:d_res_high_translation>4.0</VRPTx:d_res_high_translation> <VRPTx:d_res_low_rotation>13.0</VRPTx:d_res_low_rotation> <VRPTx:d_res_low_translation>15.0</VRPTx:d_res_low_translation> <VRPTx:method_rotation>real-space rotation search</VRPTx:method_rotation> <VRPTx:method_translation>gerneral using PC-refinement= e2e2</VRPTx:method_translation> <VRPTx:packing>0.3086</VRPTx:packing> <VRPTx:reflns_percent_rotation>97.8</VRPTx:reflns_percent_rotation> <VRPTx:reflns_percent_translation>97.7</VRPTx:reflns_percent_translation> <VRPTx:sigma_F_rotation>1.0</VRPTx:sigma_F_rotation> <VRPTx:sigma_F_translation>0</VRPTx:sigma_F_translation> </VRPTx:pdbx_phasing_MR> </VRPTx:pdbx_phasing_MRCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_phasing_MRCategory This property indicates that datablock has a category holder pdbx_phasing_MRCategory. pdbx_phasing_MRCategory This property indicates that pdbx_phasing_MRCategory. has a category pdbx_phasing_MR. pdbx_phasing_MRItem Abstract datatype property for pdbx_phasing_MR items. reference_to_pdbx_phasing_MR cross-reference to pdbx_phasing_MR. referenced_by_pdbx_phasing_MR cross-reference from pdbx_phasing_MR. pdbx_phasing_MR.R_factor The value of attribute R_factor in category pdbx_phasing_MR identifies the R factor (defined as uasual) after rotation and translation. pdbx_phasing_MR.R_rigid_body The value of attribute R_rigid_body in category pdbx_phasing_MR identifies the R factor for rigid body refinement after rotation and translation.(In general, rigid body refinement has to be carried out after molecular replacement. pdbx_phasing_MR.correlation_coeff_Fo_to_Fc The value of attribute correlation_coeff_Fo_to_Fc in category pdbx_phasing_MR identifies the correlation between the observed and the calculated structure factor after rotation and translation. pdbx_phasing_MR.correlation_coeff_Io_to_Ic The value of attribute correlation_coeff_Io_to_Ic in category pdbx_phasing_MR identifies the correlation between the observed and the calculated intensity (~|F|^2) after rotation and translation. pdbx_phasing_MR.d_res_high_rotation The value of attribute d_res_high_rotation in category pdbx_phasing_MR identifies the highest resolution used for rotation search. pdbx_phasing_MR.d_res_high_translation The value of attribute d_res_high_translation in category pdbx_phasing_MR identifies the highest resolution used for translation search. pdbx_phasing_MR.d_res_low_rotation The value of attribute d_res_low_rotation in category pdbx_phasing_MR identifies the lowest resolution used for rotation search. pdbx_phasing_MR.d_res_low_translation The value of attribute d_res_low_translation in category pdbx_phasing_MR identifies the lowest resolution used for translation search. pdbx_phasing_MR.method_rotation The value of attribute method_rotation in category pdbx_phasing_MR identifies the method used for rotation search. For example, the rotation method may be realspace, fastdirect, or direct. . pdbx_phasing_MR.method_translation The value of attribute method_translation in category pdbx_phasing_MR identifies the method used for translation search. For example in CNS, the translation method may be "general" or "phased" with PC refinement target using "fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector". pdbx_phasing_MR.model_details The value of attribute model_details in category pdbx_phasing_MR records the details of model used. For example, the original model can be truncated by deleting side chains, doubtful parts, using the monomer if the original model was an oligomer. The search model may be one domain of a large molecule. What is the pdb IDs. pdbx_phasing_MR.native_set_id The data set that was treated as the native in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. pdbx_phasing_MR.packing The value of attribute packing in category pdbx_phasing_MR identifies the packing of search model in the unit cell. Too many crystallographic contacts may indicate a bad search. pdbx_phasing_MR.reflns_percent_rotation The value of attribute reflns_percent_rotation in category pdbx_phasing_MR identifies the completness of data used for rotation search. pdbx_phasing_MR.reflns_percent_translation The value of attribute reflns_percent_translation in category pdbx_phasing_MR identifies the completness of data used for translation search. pdbx_phasing_MR.sigma_F_rotation The value of attribute sigma_F_rotation in category pdbx_phasing_MR identifies the sigma cut off of structure factor used for rotation search. pdbx_phasing_MR.sigma_F_translation The value of attribute sigma_F_translation in category pdbx_phasing_MR identifies the sigma cut off of structure factor used for translation search. pdbx_phasing_MR.sigma_I_rotation The value of attribute sigma_I_rotation in category pdbx_phasing_MR identifies the sigma cut off of intensity used for rotation search. pdbx_phasing_MR.sigma_I_translation The value of attribute sigma_I_translation in category pdbx_phasing_MR identifies the sigma cut off of intensity used for translation search. pdbx_phasing_MR.entry_id The value of attribute entry_id in category pdbx_phasing_MR identifies the data block. 0 pdbx_phasing_dm Data items in the PDBX_PHASING_DM category record details about density modification Example 1 - density modification from resolve <VRPTx:pdbx_phasing_dmCategory> <VRPTx:pdbx_phasing_dm entry_id="ABC001"> <VRPTx:fom>0.85</VRPTx:fom> <VRPTx:fom_acentric>0.85</VRPTx:fom_acentric> <VRPTx:fom_centric>0.79</VRPTx:fom_centric> <VRPTx:reflns>12486</VRPTx:reflns> <VRPTx:reflns_acentric>11351</VRPTx:reflns_acentric> <VRPTx:reflns_centric>1135</VRPTx:reflns_centric> </VRPTx:pdbx_phasing_dm> </VRPTx:pdbx_phasing_dmCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_phasing_dmCategory This property indicates that datablock has a category holder pdbx_phasing_dmCategory. pdbx_phasing_dmCategory This property indicates that pdbx_phasing_dmCategory. has a category pdbx_phasing_dm. pdbx_phasing_dmItem Abstract datatype property for pdbx_phasing_dm items. reference_to_pdbx_phasing_dm cross-reference to pdbx_phasing_dm. referenced_by_pdbx_phasing_dm cross-reference from pdbx_phasing_dm. pdbx_phasing_dm.delta_phi_final The value of attribute delta_phi_final in category pdbx_phasing_dm identifies phase difference after density modification pdbx_phasing_dm.delta_phi_initial The value of attribute delta_phi_initial in category pdbx_phasing_dm identifies phase difference before density modification pdbx_phasing_dm.fom The value of attribute fom in category pdbx_phasing_dm identifies the figure of merit for all the data pdbx_phasing_dm.fom_acentric The value of attribute fom_acentric in category pdbx_phasing_dm identifies the figure of merit for acentric data pdbx_phasing_dm.fom_centric The value of attribute fom_centric in category pdbx_phasing_dm identifies the figure of merit for acentric data pdbx_phasing_dm.mask_type The value of attribute mask_type in category pdbx_phasing_dm identifies the type of mask used for density modification pdbx_phasing_dm.method The value of attribute method in category pdbx_phasing_dm identifies the method used for density modification pdbx_phasing_dm.reflns The value of attribute reflns in category pdbx_phasing_dm identifies the number of centric and acentric reflections. pdbx_phasing_dm.reflns_acentric The value of attribute reflns_acentric in category pdbx_phasing_dm identifies the number of acentric reflections. pdbx_phasing_dm.reflns_centric The value of attribute reflns_centric in category pdbx_phasing_dm identifies the number of centric reflections. pdbx_phasing_dm.entry_id The value of attribute entry_id in category pdbx_phasing_dm identifies the data block. 0 pdbx_phasing_dm_shell Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell. Example 1 - density modification with shells <VRPTx:pdbx_phasing_dm_shellCategory> <VRPTx:pdbx_phasing_dm_shell d_res_high="7.73" d_res_low="100.00"> <VRPTx:delta_phi_final>24.7</VRPTx:delta_phi_final> <VRPTx:fom>0.879</VRPTx:fom> <VRPTx:reflns>502</VRPTx:reflns> </VRPTx:pdbx_phasing_dm_shell> <VRPTx:pdbx_phasing_dm_shell d_res_high="6.24" d_res_low="7.73"> <VRPTx:delta_phi_final>29.2</VRPTx:delta_phi_final> <VRPTx:fom>0.857</VRPTx:fom> <VRPTx:reflns>506</VRPTx:reflns> </VRPTx:pdbx_phasing_dm_shell> <VRPTx:pdbx_phasing_dm_shell d_res_high="5.50" d_res_low="6.24"> <VRPTx:delta_phi_final>29.2</VRPTx:delta_phi_final> <VRPTx:fom>0.838</VRPTx:fom> <VRPTx:reflns>504</VRPTx:reflns> </VRPTx:pdbx_phasing_dm_shell> <VRPTx:pdbx_phasing_dm_shell d_res_high="5.02" d_res_low="5.50"> <VRPTx:delta_phi_final>25.3</VRPTx:delta_phi_final> <VRPTx:fom>0.851</VRPTx:fom> <VRPTx:reflns>502</VRPTx:reflns> </VRPTx:pdbx_phasing_dm_shell> <VRPTx:pdbx_phasing_dm_shell d_res_high="4.67" d_res_low="5.02"> <VRPTx:delta_phi_final>22.7</VRPTx:delta_phi_final> <VRPTx:fom>0.831</VRPTx:fom> <VRPTx:reflns>503</VRPTx:reflns> </VRPTx:pdbx_phasing_dm_shell> </VRPTx:pdbx_phasing_dm_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_phasing_dm_shellCategory This property indicates that datablock has a category holder pdbx_phasing_dm_shellCategory. pdbx_phasing_dm_shellCategory This property indicates that pdbx_phasing_dm_shellCategory. has a category pdbx_phasing_dm_shell. pdbx_phasing_dm_shellItem Abstract datatype property for pdbx_phasing_dm_shell items. reference_to_pdbx_phasing_dm_shell cross-reference to pdbx_phasing_dm_shell. referenced_by_pdbx_phasing_dm_shell cross-reference from pdbx_phasing_dm_shell. pdbx_phasing_dm_shell.delta_phi_final The value of attribute delta_phi_final in category pdbx_phasing_dm_shell identifies phase difference after density modification with resolution shells. pdbx_phasing_dm_shell.delta_phi_initial The value of attribute delta_phi_initial in category pdbx_phasing_dm_shell identifies phase difference before density modification with resolution shells. pdbx_phasing_dm_shell.fom The value of attribute fom in category pdbx_phasing_dm_shell identifies the figure of merit for all the data with resolution shells. pdbx_phasing_dm_shell.fom_acentric The value of attribute fom_acentric in category pdbx_phasing_dm_shell identifies the figure of merit for acentric data with resolution shells pdbx_phasing_dm_shell.fom_centric The value of attribute fom_centric in category pdbx_phasing_dm_shell identifies the figure of merit for centric data with resolution shells. pdbx_phasing_dm_shell.reflns The value of attribute reflns in category pdbx_phasing_dm_shell identifies the number of centric and acentric reflections with resolution shells. pdbx_phasing_dm_shell.reflns_acentric The value of attribute reflns_acentric in category pdbx_phasing_dm_shell identifies the number of acentric reflections with resolution shells. pdbx_phasing_dm_shell.reflns_centric The value of attribute reflns_centric in category pdbx_phasing_dm_shell identifies the number of centric reflections with resolution shells. pdbx_phasing_dm_shell.d_res_high The value of attribute d_res_high in category pdbx_phasing_dm_shell identifies high resolution pdbx_phasing_dm_shell.d_res_low The value of attribute d_res_low in category pdbx_phasing_dm_shell identifies low resolution 0 pdbx_point_symmetry Data items in the PDBX_POINT_SYMMETRY category record details about the point symmetry group associated with this entry. Example 1 - <VRPTx:pdbx_point_symmetryCategory> <VRPTx:pdbx_point_symmetry entry_id="1ABC"> <VRPTx:H-M_notation>532</VRPTx:H-M_notation> <VRPTx:Schoenflies_symbol>I</VRPTx:Schoenflies_symbol> </VRPTx:pdbx_point_symmetry> </VRPTx:pdbx_point_symmetryCategory> 0 1 1 1 0 1 1 pdbx_point_symmetryCategory This property indicates that datablock has a category holder pdbx_point_symmetryCategory. pdbx_point_symmetryCategory This property indicates that pdbx_point_symmetryCategory. has a category pdbx_point_symmetry. pdbx_point_symmetryItem Abstract datatype property for pdbx_point_symmetry items. reference_to_pdbx_point_symmetry cross-reference to pdbx_point_symmetry. referenced_by_pdbx_point_symmetry cross-reference from pdbx_point_symmetry. pdbx_point_symmetry.H-M_notation The Hermann-Mauguin notation for this point symmetry group. I -> 532 O -> 432 T -> 23 Cn -> n (e.g. C5 -> 5) Dn -> n22 (n even) Dn -> n2 (n odd) I O T C D The Schoenflies point symmetry symbol. pdbx_point_symmetry.circular_symmetry Rotational n-fold C and D point symmetry. pdbx_point_symmetry.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_poly_seq_scheme The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities. Example 1 - based on NDB entry DDFB25 <VRPTx:pdbx_poly_seq_schemeCategory> <VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="1"> <VRPTx:auth_mon_id>DC</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>1</VRPTx:auth_seq_num> <VRPTx:ndb_seq_num>1</VRPTx:ndb_seq_num> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>DC</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>1</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id> </VRPTx:pdbx_poly_seq_scheme> <VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="2"> <VRPTx:auth_mon_id>DG</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>2</VRPTx:auth_seq_num> <VRPTx:ndb_seq_num>2</VRPTx:ndb_seq_num> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>DG</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>2</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id> </VRPTx:pdbx_poly_seq_scheme> <VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DT" seq_id="3"> <VRPTx:auth_mon_id>DT</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>3</VRPTx:auth_seq_num> <VRPTx:ndb_seq_num>3</VRPTx:ndb_seq_num> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>DT</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>3</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id> </VRPTx:pdbx_poly_seq_scheme> <VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DA" seq_id="4"> <VRPTx:auth_mon_id>DA</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>4</VRPTx:auth_seq_num> <VRPTx:ndb_seq_num>4</VRPTx:ndb_seq_num> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>DA</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>4</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id> </VRPTx:pdbx_poly_seq_scheme> <VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="5"> <VRPTx:auth_mon_id>DC</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>5</VRPTx:auth_seq_num> <VRPTx:ndb_seq_num>5</VRPTx:ndb_seq_num> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>DC</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>5</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id> </VRPTx:pdbx_poly_seq_scheme> <VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="6"> <VRPTx:auth_mon_id>DG</VRPTx:auth_mon_id> <VRPTx:auth_seq_num>6</VRPTx:auth_seq_num> <VRPTx:ndb_seq_num>6</VRPTx:ndb_seq_num> <VRPTx:pdb_ins_code xsi:nil="true" /> <VRPTx:pdb_mon_id>DG</VRPTx:pdb_mon_id> <VRPTx:pdb_seq_num>6</VRPTx:pdb_seq_num> <VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id> </VRPTx:pdbx_poly_seq_scheme> </VRPTx:pdbx_poly_seq_schemeCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 pdbx_poly_seq_schemeCategory This property indicates that datablock has a category holder pdbx_poly_seq_schemeCategory. pdbx_poly_seq_schemeCategory This property indicates that pdbx_poly_seq_schemeCategory. has a category pdbx_poly_seq_scheme. pdbx_poly_seq_schemeItem Abstract datatype property for pdbx_poly_seq_scheme items. reference_to_pdbx_poly_seq_scheme cross-reference to pdbx_poly_seq_scheme. referenced_by_pdbx_poly_seq_scheme cross-reference from pdbx_poly_seq_scheme. pdbx_poly_seq_scheme.auth_mon_id Author provided residue identifier. This value may differ from the PDB residue identifier and may not correspond to residue identifier within the coordinate records. pdbx_poly_seq_scheme.auth_seq_num Author provided residue number. This value may differ from the PDB residue number and may not correspond to residue numbering within the coordinate records. no n yes y Pointer to attribute hetero in category entity_poly_seq pdbx_poly_seq_scheme.ndb_seq_num NDB residue number. pdbx_poly_seq_scheme.pdb_ins_code PDB insertion code. pdbx_poly_seq_scheme.pdb_mon_id PDB residue identifier. pdbx_poly_seq_scheme.pdb_seq_num PDB residue number. pdbx_poly_seq_scheme.pdb_strand_id PDB strand/chain id. pdbx_poly_seq_scheme.asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 pdbx_poly_seq_scheme.entity_id Pointer to attribute id in category entity. pdbx_poly_seq_scheme.mon_id Pointer to attribute mon_id in category entity_poly_seq. pdbx_poly_seq_scheme.seq_id Pointer to attribute num in category entity_poly_seq 0 pdbx_re_refinement Describes the origin of the experimental data used in this entry. Example 1 - <VRPTx:pdbx_re_refinementCategory> <VRPTx:pdbx_re_refinement entry_id="1ABC"> <VRPTx:citation_id>2</VRPTx:citation_id> <VRPTx:details>Re-refinement of data from entry 1ABC</VRPTx:details> </VRPTx:pdbx_re_refinement> </VRPTx:pdbx_re_refinementCategory> 1 1 1 1 1 pdbx_re_refinementCategory This property indicates that datablock has a category holder pdbx_re_refinementCategory. pdbx_re_refinementCategory This property indicates that pdbx_re_refinementCategory. has a category pdbx_re_refinement. pdbx_re_refinementItem Abstract datatype property for pdbx_re_refinement items. reference_to_pdbx_re_refinement cross-reference to pdbx_re_refinement. referenced_by_pdbx_re_refinement cross-reference from pdbx_re_refinement. pdbx_re_refinement.citation_id A pointer to attribute id in category citation in category CITATION describing the citation of the entry from from which the experimental data were obtained. pdbx_re_refinement.details Additional details about this re-refinement. pdbx_re_refinement.entry_id The identifier for entry where the experimental data was obtained. 0 pdbx_refine Data items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files. Example 1 - PDB placeholders for refinement program SHELX <VRPTx:pdbx_refineCategory> <VRPTx:pdbx_refine entry_id="ABC001" pdbx_refine_id="x-ray"> <VRPTx:R_factor_all_4sig_cutoff>0.174</VRPTx:R_factor_all_4sig_cutoff> <VRPTx:R_factor_obs_4sig_cutoff>0.169</VRPTx:R_factor_obs_4sig_cutoff> <VRPTx:free_R_factor_4sig_cutoff>0.216</VRPTx:free_R_factor_4sig_cutoff> <VRPTx:free_R_val_test_set_ct_4sig_cutoff>164</VRPTx:free_R_val_test_set_ct_4sig_cutoff> <VRPTx:free_R_val_test_set_size_perc_4sig_cutoff>1.29</VRPTx:free_R_val_test_set_size_perc_4sig_cutoff> <VRPTx:number_reflns_obs_4sig_cutoff>1263</VRPTx:number_reflns_obs_4sig_cutoff> </VRPTx:pdbx_refine> </VRPTx:pdbx_refineCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_refineCategory This property indicates that datablock has a category holder pdbx_refineCategory. pdbx_refineCategory This property indicates that pdbx_refineCategory. has a category pdbx_refine. pdbx_refineItem Abstract datatype property for pdbx_refine items. reference_to_pdbx_refine cross-reference to pdbx_refine. referenced_by_pdbx_refine cross-reference from pdbx_refine. pdbx_refine.R_factor_all_4sig_cutoff R-value (all reflections, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 0.174 pdbx_refine.R_factor_all_no_cutoff R-value (all reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.R_factor_obs_4sig_cutoff R-value (working set, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 0.169 pdbx_refine.R_factor_obs_no_cutoff R-value (working set reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.free_R_error_no_cutoff Free R-value error(no cutoff) pdbx_refine.free_R_factor_4sig_cutoff R free value (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. 0.216 pdbx_refine.free_R_factor_no_cutoff Free R-value (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.free_R_val_4sig_cutoff Free R-value (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.free_R_val_test_set_ct_4sig_cutoff Free R-value test set count (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 164 pdbx_refine.free_R_val_test_set_ct_no_cutoff Free R-value test set count (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff Free R-value test set size (in percent, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 1.29 pdbx_refine.free_R_val_test_set_size_perc_no_cutoff Free R-value test set size (in percent, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.number_reflns_obs_4sig_cutoff Total number of reflections (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. 1263 pdbx_refine.number_reflns_obs_no_cutoff Total number of reflections (no cutoff). Placeholder for PDB mapping of SHELXL refinement data. pdbx_refine.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. pdbx_refine.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine can be used to distinguish the results of joint refinements. 0 pdbx_refine_component Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map. Example 1 - 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 pdbx_refine_componentCategory This property indicates that datablock has a category holder pdbx_refine_componentCategory. pdbx_refine_componentCategory This property indicates that pdbx_refine_componentCategory. has a category pdbx_refine_component. pdbx_refine_componentItem Abstract datatype property for pdbx_refine_component items. reference_to_pdbx_refine_component cross-reference to pdbx_refine_component. referenced_by_pdbx_refine_component cross-reference from pdbx_refine_component. pdbx_refine_component.B_iso The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site pdbx_refine_component.B_iso_main_chain The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site pdbx_refine_component.B_iso_side_chain The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site pdbx_refine_component.PDB_ins_code A component of the identifier for the component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site ATOM_SITE category. pdbx_refine_component.auth_asym_id A component of the identifier for the component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_refine_component.auth_comp_id A component of the identifier for the component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_refine_component.auth_seq_id A component of the identifier for the component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_refine_component.connect The index of connectivity is the product of the (2Fobs-Fcal) electron density values for the backbone atoms (N, CA and C) divided by the average value for the structure. Low values (less than 1.0) of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing. connect = [(D(xi)...D(xi))^(1/N)] /<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.correlation Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.correlation_main_chain Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.correlation_side_chain Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.density_index The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.density_index_main_chain The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.density_index_side_chain The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.density_ratio The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group. pdbx_refine_component.density_ratio_main_chain The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group. pdbx_refine_component.density_ratio_side_chain The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group. pdbx_refine_component.real_space_R Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 pdbx_refine_component.real_space_R_main_chain Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 pdbx_refine_component.real_space_R_side_chain Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 pdbx_refine_component.shift The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.shift_main_chain The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.shift_side_chain The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 pdbx_refine_component.label_alt_id A component of the identifier for the component. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. pdbx_refine_component.label_asym_id A component of the identifier for the component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_refine_component.label_comp_id A component of the identifier for the component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_refine_component.label_seq_id A component of the identifier for the component. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 0 pdbx_refine_tls Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item attribute method in category pdbx_refine_tls 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_refine_tlsCategory This property indicates that datablock has a category holder pdbx_refine_tlsCategory. pdbx_refine_tlsCategory This property indicates that pdbx_refine_tlsCategory. has a category pdbx_refine_tls. pdbx_refine_tlsItem Abstract datatype property for pdbx_refine_tls items. reference_to_pdbx_refine_tls cross-reference to pdbx_refine_tls. referenced_by_pdbx_refine_tls cross-reference from pdbx_refine_tls. pdbx_refine_tls.L11 The [1][1] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. pdbx_refine_tls.L11_esd The estimated standard deviation of attribute L[1][1] in category pdbx_refine_tls. pdbx_refine_tls.L12 The [1][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. pdbx_refine_tls.L12_esd The estimated standard deviation of attribute L[1][2] in category pdbx_refine_tls. pdbx_refine_tls.L13 The [1][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. pdbx_refine_tls.L13_esd The estimated standard deviation of attribute L[1][3] in category pdbx_refine_tls. pdbx_refine_tls.L22 The [2][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. pdbx_refine_tls.L22_esd The estimated standard deviation of attribute L[2][2] in category pdbx_refine_tls. pdbx_refine_tls.L23 The [2][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. pdbx_refine_tls.L23_esd The estimated standard deviation of attribute L[2][3] in category pdbx_refine_tls. pdbx_refine_tls.L33 The [3][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. pdbx_refine_tls.L33_esd The estimated standard deviation of attribute L[3][3] in category pdbx_refine_tls. pdbx_refine_tls.S11 The [1][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. pdbx_refine_tls.S11_esd The estimated standard deviation of attribute S[1][1] in category pdbx_refine_tls. pdbx_refine_tls.S12 The [1][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.S12_esd The estimated standard deviation of attribute S[1][2] in category pdbx_refine_tls. pdbx_refine_tls.S13 The [1][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.S13_esd The estimated standard deviation of attribute S[1][3] in category pdbx_refine_tls. pdbx_refine_tls.S21 The [2][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.S21_esd The estimated standard deviation of attribute S[2][1] in category pdbx_refine_tls. pdbx_refine_tls.S22 The [2][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. pdbx_refine_tls.S22_esd The estimated standard deviation of attribute S[2][2] in category pdbx_refine_tls. pdbx_refine_tls.S23 The [2][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.S23_esd The estimated standard deviation of attribute S[2][3] in category pdbx_refine_tls. pdbx_refine_tls.S31 The [3][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.S31_esd The estimated standard deviation of attribute S[3][1] in category pdbx_refine_tls. pdbx_refine_tls.S32 The [3][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.S32_esd The estimated standard deviation of attribute S[3][2] in category pdbx_refine_tls. pdbx_refine_tls.S33 The [3][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. pdbx_refine_tls.S33_esd The estimated standard deviation of attribute S[3][3] in category pdbx_refine_tls. pdbx_refine_tls.T11 The [1][1] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. pdbx_refine_tls.T11_esd The estimated standard deviation of attribute T[1][1] in category pdbx_refine_tls. pdbx_refine_tls.T12 The [1][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. pdbx_refine_tls.T12_esd The estimated standard deviation of attribute T[1][2] in category pdbx_refine_tls. pdbx_refine_tls.T13 The [1][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. pdbx_refine_tls.T13_esd The estimated standard deviation of attribute T[1][3] in category pdbx_refine_tls. pdbx_refine_tls.T22 The [2][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. pdbx_refine_tls.T22_esd The estimated standard deviation of attribute T[2][2] in category pdbx_refine_tls. pdbx_refine_tls.T23 The [2][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. pdbx_refine_tls.T23_esd The estimated standard deviation of attribute T[2][3] in category pdbx_refine_tls. pdbx_refine_tls.T33 The [3][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. pdbx_refine_tls.T33_esd The estimated standard deviation of attribute T[3][3] in category pdbx_refine_tls. pdbx_refine_tls.details A description of the TLS group, such as a domain name or a chemical group name. Chain A catalytic domain Chain A Tyr 56 side chain refined fitted The method by which the TLS parameters were obtained. pdbx_refine_tls.origin_x The x coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.origin_y The y coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.origin_z The z coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric pdbx_refine_tls.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine_tls can be used to distinguish the results of joint refinements. pdbx_refine_tls.id The value of attribute id in category pdbx_refine_tls must uniquely identify a record in the PDBX_REFINE_TLS list. Note that this item need not be a number; it can be any unique identifier. 1 A 0 pdbx_refine_tls_group Data items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in PDBX_REFINE_TLS 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 1 pdbx_refine_tls_groupCategory This property indicates that datablock has a category holder pdbx_refine_tls_groupCategory. pdbx_refine_tls_groupCategory This property indicates that pdbx_refine_tls_groupCategory. has a category pdbx_refine_tls_group. pdbx_refine_tls_groupItem Abstract datatype property for pdbx_refine_tls_group items. reference_to_pdbx_refine_tls_group cross-reference to pdbx_refine_tls_group. referenced_by_pdbx_refine_tls_group cross-reference from pdbx_refine_tls_group. pdbx_refine_tls_group.beg_PDB_ins_code A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_refine_tls_group.beg_auth_asym_id A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. O 2B3 pdbx_refine_tls_group.beg_auth_seq_id A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 1 5A pdbx_refine_tls_group.beg_label_asym_id A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. O 2B3 pdbx_refine_tls_group.beg_label_seq_id A component of the identifier for the residue at which the TLS fragment range begins. 1 303 pdbx_refine_tls_group.end_PDB_ins_code A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_refine_tls_group.end_auth_asym_id A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. O 2B3 pdbx_refine_tls_group.end_auth_seq_id A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 1 5A pdbx_refine_tls_group.end_label_asym_id A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. O 2B3 pdbx_refine_tls_group.end_label_seq_id A component of the identifier for the residue at which the TLS fragment range ends. 1 303 pdbx_refine_tls_group.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine_tls_group can be used to distinguish the results of joint refinements. pdbx_refine_tls_group.refine_tls_id This data item is a pointer to attribute id in category pdbx_refine_tls in the REFINE_TLS category. pdbx_refine_tls_group.selection A qualification of the subset of atoms in the specified range included in the TLS fragment. all atoms in specified range all main chain atoms only mnc side chain atoms only sdc pdbx_refine_tls_group.selection_details A text description of subset of atoms included included in the TLS fragment. pdbx_refine_tls_group.id The value of attribute id in category pdbx_refine_tls_group must uniquely identify a record in the REFINE_TLS_GROUP list for a particular refinement. Note that this item need not be a number; it can be any unique identifier. 1 A 0 pdbx_refln_signal_binning The binning of the per-reflection signal generated by the software specified by attribute pdbx_signal_software_id. in category reflns If any reflections have a signal >= to the highest threshold specified, an additional bin should be inferred to hold them. Examples 1 - based on an internal STARANISO run <VRPTx:pdbx_refln_signal_binningCategory> <VRPTx:pdbx_refln_signal_binning ordinal="1"> <VRPTx:upper_threshold>1.20</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> <VRPTx:pdbx_refln_signal_binning ordinal="2"> <VRPTx:upper_threshold>7.22</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> <VRPTx:pdbx_refln_signal_binning ordinal="3"> <VRPTx:upper_threshold>19.00</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> <VRPTx:pdbx_refln_signal_binning ordinal="4"> <VRPTx:upper_threshold>36.81</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> <VRPTx:pdbx_refln_signal_binning ordinal="5"> <VRPTx:upper_threshold>48.87</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> <VRPTx:pdbx_refln_signal_binning ordinal="6"> <VRPTx:upper_threshold>53.84</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> <VRPTx:pdbx_refln_signal_binning ordinal="7"> <VRPTx:upper_threshold>57.69</VRPTx:upper_threshold> </VRPTx:pdbx_refln_signal_binning> </VRPTx:pdbx_refln_signal_binningCategory> 1 1 1 pdbx_refln_signal_binningCategory This property indicates that datablock has a category holder pdbx_refln_signal_binningCategory. pdbx_refln_signal_binningCategory This property indicates that pdbx_refln_signal_binningCategory. has a category pdbx_refln_signal_binning. pdbx_refln_signal_binningItem Abstract datatype property for pdbx_refln_signal_binning items. reference_to_pdbx_refln_signal_binning cross-reference to pdbx_refln_signal_binning. referenced_by_pdbx_refln_signal_binning cross-reference from pdbx_refln_signal_binning. pdbx_refln_signal_binning.upper_threshold The upper (exclusive) threshold of the bin. pdbx_refln_signal_binning.ordinal The ordinal number of the bin, ordered from lowest signal to highest. 0 pdbx_reflns_twin Details decribing crystallographic twinning. Example 1 - <VRPTx:pdbx_reflns_twinCategory> <VRPTx:pdbx_reflns_twin crystal_id="1" diffrn_id="1" operator="h,-h-k,-l"> <VRPTx:fraction>.43</VRPTx:fraction> <VRPTx:mean_F_square_over_mean_F2>.84</VRPTx:mean_F_square_over_mean_F2> <VRPTx:mean_I2_over_mean_I_square>1.3</VRPTx:mean_I2_over_mean_I_square> <VRPTx:type>merohedral</VRPTx:type> </VRPTx:pdbx_reflns_twin> </VRPTx:pdbx_reflns_twinCategory> 0 1 1 1 0 1 0 1 0 1 1 1 1 pdbx_reflns_twinCategory This property indicates that datablock has a category holder pdbx_reflns_twinCategory. pdbx_reflns_twinCategory This property indicates that pdbx_reflns_twinCategory. has a category pdbx_reflns_twin. pdbx_reflns_twinItem Abstract datatype property for pdbx_reflns_twin items. reference_to_pdbx_reflns_twin cross-reference to pdbx_reflns_twin. referenced_by_pdbx_reflns_twin cross-reference from pdbx_reflns_twin. pdbx_reflns_twin.domain_id An identifier for the twin domain. pdbx_reflns_twin.fraction The twin fraction or twin factor represents a quantitative parameter for the crystal twinning. The value 0 represents no twinning, < 0.5 partial twinning, = 0.5 for perfect twinning. pdbx_reflns_twin.mean_F_square_over_mean_F2 The ideal statistics for twinned crystals. The values calculated with the acentric data are given below. Statistic Untwinned data Perfect twinned data <I^2>/<I>^2 2.0 1.5 <F>^2/<F^2> 0.785 0.865 References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html pdbx_reflns_twin.mean_I2_over_mean_I_square The ideal statistics for twinned crystals. The values calculated with the acentric data are given below. Statistic Untwinned data Perfect twinned data <I^2>/<I>^2 2.0 1.5 <F>^2/<F^2> 0.785 0.865 References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html merohedral hemihedral non-merohedral pseudo-merohedral epitaxial tetartohedral There are two types of twinning: merohedral or hemihedral or non-merohedral or epitaxial For merohedral twinning the diffraction patterns from the different domains are completely superimposable. Hemihedral twinning is a special case of merohedral twinning. It only involves two distinct domains. Pseudo-merohedral twinning is a subclass merohedral twinning in which lattice is coincidentally superimposable. In the case of non-merohedral or epitaxial twinning the reciprocal lattices do not superimpose exactly. In this case the diffraction pattern consists of two (or more) interpenetrating lattices, which can in principle be separated. pdbx_reflns_twin.crystal_id The crystal identifier. A reference to attribute id in category exptl_crystal in category EXPTL_CRYSTAL. pdbx_reflns_twin.diffrn_id The diffraction data set identifier. A reference to attribute id in category diffrn in category DIFFRN. pdbx_reflns_twin.operator The possible merohedral or hemihedral twinning operators for different point groups are: True point group Twin operation hkl related to 3 2 along a,b h,-h-k,-l 2 along a*,b* h+k,-k,-l 2 along c -h,-k,l 4 2 along a,b,a*,b* h,-k,-l 6 2 along a,b,a*,b* h,-h-k,-l 321 2 along a*,b*,c -h,-k,l 312 2 along a,b,c -h,-k,l 23 4 along a,b,c k,-h,l References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html h,-h-k,-l h+k,-k,-l -h,-k,l h,-k,-l k,-h,l 0 pdbx_related_exp_data_set Data items in the PDBX_RELATED_DATA_SET category record references to experimental data sets related to the entry. Example 1 - <VRPTx:pdbx_related_exp_data_setCategory> <VRPTx:pdbx_related_exp_data_set ordinal="1"> <VRPTx:data_reference>10.000/10002/image_data/cif</VRPTx:data_reference> <VRPTx:data_set_type>diffraction image data</VRPTx:data_set_type> <VRPTx:details>imgCIF data set containing 500 frames</VRPTx:details> <VRPTx:metadata_reference>10.000/10002/image_data/txt</VRPTx:metadata_reference> </VRPTx:pdbx_related_exp_data_set> <VRPTx:pdbx_related_exp_data_set ordinal="2"> <VRPTx:data_reference>10.6019/EMPIAR-11866</VRPTx:data_reference> <VRPTx:data_set_type>EMPIAR</VRPTx:data_set_type> <VRPTx:metadata_reference>10.6019/EMPIAR-11866</VRPTx:metadata_reference> </VRPTx:pdbx_related_exp_data_set> </VRPTx:pdbx_related_exp_data_setCategory> 1 1 1 1 0 1 0 1 1 pdbx_related_exp_data_setCategory This property indicates that datablock has a category holder pdbx_related_exp_data_setCategory. pdbx_related_exp_data_setCategory This property indicates that pdbx_related_exp_data_setCategory. has a category pdbx_related_exp_data_set. pdbx_related_exp_data_setItem Abstract datatype property for pdbx_related_exp_data_set items. reference_to_pdbx_related_exp_data_set cross-reference to pdbx_related_exp_data_set. referenced_by_pdbx_related_exp_data_set cross-reference from pdbx_related_exp_data_set. pdbx_related_exp_data_set.data_reference A DOI reference to the related data set. 10.000/10002/image_data/cif pdbx_related_exp_data_set.data_set_type The type of the experimenatal data set. diffraction image data NMR free induction decay data pdbx_related_exp_data_set.details Additional details describing the content of the related data set and its application to the current investigation. pdbx_related_exp_data_set.metadata_reference A DOI reference to the metadata decribing the related data set. 10.000/10002/image_data/txt pdbx_related_exp_data_set.ordinal Ordinal identifier for each related experimental data set. 0 pdbx_sequence_range Data items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments. Example 1 - <VRPTx:pdbx_sequence_rangeCategory> <VRPTx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29" seq_range_id="s1"></VRPTx:pdbx_sequence_range> <VRPTx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119" seq_range_id="s2"></VRPTx:pdbx_sequence_range> </VRPTx:pdbx_sequence_rangeCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 pdbx_sequence_rangeCategory This property indicates that datablock has a category holder pdbx_sequence_rangeCategory. pdbx_sequence_rangeCategory This property indicates that pdbx_sequence_rangeCategory. has a category pdbx_sequence_range. pdbx_sequence_rangeItem Abstract datatype property for pdbx_sequence_range items. reference_to_pdbx_sequence_range cross-reference to pdbx_sequence_range. referenced_by_pdbx_sequence_range cross-reference from pdbx_sequence_range. pdbx_sequence_range.beg_auth_asym_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.beg_auth_comp_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.beg_auth_seq_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.end_auth_asym_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.end_auth_comp_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.end_auth_seq_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.beg_label_alt_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. pdbx_sequence_range.beg_label_asym_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.beg_label_comp_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.beg_label_seq_id A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.end_label_alt_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. pdbx_sequence_range.end_label_asym_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.end_label_comp_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.end_label_seq_id A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_sequence_range.seq_range_id This data item is an identifier for a sequence range. 0 pdbx_sifts_unp_segments pdbx_sifts_unp_segments describes residue-range based cross-references specific to UniProt. Example 1 - <VRPTx:pdbx_sifts_unp_segmentsCategory> <VRPTx:pdbx_sifts_unp_segments asym_id="A" entity_id="1" instance_id="1" segment_id="1" unp_acc="A0A5J6CYR6"> <VRPTx:best_mapping>Y</VRPTx:best_mapping> <VRPTx:identity>0.95</VRPTx:identity> <VRPTx:seq_id_end>260</VRPTx:seq_id_end> <VRPTx:seq_id_start>26</VRPTx:seq_id_start> <VRPTx:unp_end>238</VRPTx:unp_end> <VRPTx:unp_start>2</VRPTx:unp_start> </VRPTx:pdbx_sifts_unp_segments> </VRPTx:pdbx_sifts_unp_segmentsCategory> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 pdbx_sifts_unp_segmentsCategory This property indicates that datablock has a category holder pdbx_sifts_unp_segmentsCategory. pdbx_sifts_unp_segmentsCategory This property indicates that pdbx_sifts_unp_segmentsCategory. has a category pdbx_sifts_unp_segments. pdbx_sifts_unp_segmentsItem Abstract datatype property for pdbx_sifts_unp_segments items. reference_to_pdbx_sifts_unp_segments cross-reference to pdbx_sifts_unp_segments. referenced_by_pdbx_sifts_unp_segments cross-reference from pdbx_sifts_unp_segments. Y N This code indicates whether the SIFTS UniProt accession and residue range was the best-scoring sequence match. pdbx_sifts_unp_segments.identity The identity score reports on the sequence identity for the sequence defined by the entity start and end range compared to the sequence defined by start and end range of the related UniProt accession. pdbx_sifts_unp_segments.seq_id_end The sequence position in the entity or biological unit described in the data block at which the UniProt alignment ends. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_sifts_unp_segments.seq_id_start The sequence position in the entity or biological unit described in the data block at which the UniProt alignment begins. pdbx_sifts_unp_segments.unp_end The sequence position in the related UniProt entry at which the mapping alignment ends. pdbx_sifts_unp_segments.unp_start The sequence position in the related UniProt entry at which the mapping alignment begins. pdbx_sifts_unp_segments.asym_id This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. 1 A 2B3 pdbx_sifts_unp_segments.entity_id This data item is a pointer to attribute entity_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_sifts_unp_segments.instance_id The UniProt instance identifier. pdbx_sifts_unp_segments.segment_id The UniProt segment defined by the external database. pdbx_sifts_unp_segments.unp_acc The UniProt accession code related to the SIFTS segment mapping. 0 pdbx_sifts_xref_db pdbx_sifts_xref_db describes residue-level cross-references to external databases. Example 1 - <VRPTx:pdbx_sifts_xref_dbCategory> <VRPTx:pdbx_sifts_xref_db asym_id="A" entity_id="1" seq_id="254" seq_id_ordinal="1"> <VRPTx:mh_id>1</VRPTx:mh_id> <VRPTx:mon_id>ILE</VRPTx:mon_id> <VRPTx:mon_id_one_letter_code>I</VRPTx:mon_id_one_letter_code> <VRPTx:observed>1</VRPTx:observed> <VRPTx:res_type xsi:nil="true" /> <VRPTx:unp_acc>P00720</VRPTx:unp_acc> <VRPTx:unp_instance_id>1</VRPTx:unp_instance_id> <VRPTx:unp_num>50</VRPTx:unp_num> <VRPTx:unp_res>I</VRPTx:unp_res> <VRPTx:unp_segment_id>1</VRPTx:unp_segment_id> <VRPTx:xref_db_acc>PF14843</VRPTx:xref_db_acc> <VRPTx:xref_db_instance_id>1</VRPTx:xref_db_instance_id> <VRPTx:xref_db_name>Pfam</VRPTx:xref_db_name> <VRPTx:xref_db_segment_id>1</VRPTx:xref_db_segment_id> <VRPTx:xref_domain_name xsi:nil="true" /> </VRPTx:pdbx_sifts_xref_db> </VRPTx:pdbx_sifts_xref_dbCategory> 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 pdbx_sifts_xref_dbCategory This property indicates that datablock has a category holder pdbx_sifts_xref_dbCategory. pdbx_sifts_xref_dbCategory This property indicates that pdbx_sifts_xref_dbCategory. has a category pdbx_sifts_xref_db. pdbx_sifts_xref_dbItem Abstract datatype property for pdbx_sifts_xref_db items. reference_to_pdbx_sifts_xref_db cross-reference to pdbx_sifts_xref_db. referenced_by_pdbx_sifts_xref_db cross-reference from pdbx_sifts_xref_db. pdbx_sifts_xref_db.mh_id An index value corresponding to the instance of microheterogeneity per residue pdbx_sifts_xref_db.mon_id This data item is an effective pointer to attribute mon_id in category entity_poly_seq. pdbx_sifts_xref_db.mon_id_one_letter_code Describes the standard polymer component of attribute mon_id in category pdbx_sifts_xref_db as one-letter code alanine A arginine R asparagine N aspartic acid D cysteine C glutamine Q glutamic acid E glycine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P pyrrolysine O selenocysteine U serine S threonine T tryptophan W tyrosine Y valine V other X Y N Describes whether or not a reside has atomic coordinates in the corresponding model. pdbx_sifts_xref_db.res_type A description of the difference between the entity sequence position residue type and that in the mapped UniProt entry. engineered mutation cloning artifact variant expression tag insertion deletion chromophore linker conflict acetylation amidation initiating methionine modified residue microheterogeneity microheterogeneity/modified residue pdbx_sifts_xref_db.unp_acc The UniProt accession code for the mapped entry pdbx_sifts_xref_db.unp_instance_id The pdbx_sifts_xref_db UniProt instance ID refers to distinct UniProt residue mappings for a given position (i.e. the same segment, residue, asym, & entity). pdbx_sifts_xref_db.unp_num The sequence position of the UniProt entry that corresponds to the residue mapping. pdbx_sifts_xref_db.unp_res Describes the residue type, in one-letter code, at the corresponding residue position of the related UniProt match alanine A arginine R asparagine N aspartic acid D cysteine C glutamine Q glutamic acid E glycine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P selenocysteine U serine S threonine T tryptophan W tyrosine Y valine V other X pdbx_sifts_xref_db.unp_segment_id The pdbx_sifts_xref_db UniProt segment ID refers to the distinct contiguous residue-range segments with a UniProt residue mapping. pdbx_sifts_xref_db.xref_db_acc The accession code related to the additional external database entry. pdbx_sifts_xref_db.xref_db_instance_id The instance identifier defined by the external database. pdbx_sifts_xref_db.xref_db_name The name of additional external databases with residue level mapping. pdbx_sifts_xref_db.xref_db_segment_id The pdbx_sifts_xref_db xref segment ID refers to a distinct contiguous residue-range segment for a mapping to a specific external database. pdbx_sifts_xref_db.xref_domain_name The domain name defined by the external database. pdbx_sifts_xref_db.asym_id This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. 1 A 2B3 pdbx_sifts_xref_db.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. pdbx_sifts_xref_db.seq_id This data item is an effective pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_sifts_xref_db.seq_id_ordinal The value of pdbx_sifts_xref_db.seq_id_ordinal identifies a distinct residue specific cross-reference record in the _pdbx_sifts_xref_db category. 0 pdbx_sifts_xref_db_segments pdbx_sifts_xref_db_segments describes residue-range based cross-references to external databases. Example 1 - <VRPTx:pdbx_sifts_xref_db_segmentsCategory> <VRPTx:pdbx_sifts_xref_db_segments asym_id="A" entity_id="1" instance_id="1" segment_id="1" seq_id_end="252" seq_id_start="26" xref_db="SCOP2B" xref_db_acc="8102030"> <VRPTx:domain_name>SF</VRPTx:domain_name> </VRPTx:pdbx_sifts_xref_db_segments> </VRPTx:pdbx_sifts_xref_db_segmentsCategory> 0 1 1 1 1 1 1 1 1 1 pdbx_sifts_xref_db_segmentsCategory This property indicates that datablock has a category holder pdbx_sifts_xref_db_segmentsCategory. pdbx_sifts_xref_db_segmentsCategory This property indicates that pdbx_sifts_xref_db_segmentsCategory. has a category pdbx_sifts_xref_db_segments. pdbx_sifts_xref_db_segmentsItem Abstract datatype property for pdbx_sifts_xref_db_segments items. reference_to_pdbx_sifts_xref_db_segments cross-reference to pdbx_sifts_xref_db_segments. referenced_by_pdbx_sifts_xref_db_segments cross-reference from pdbx_sifts_xref_db_segments. pdbx_sifts_xref_db_segments.domain_name The domain name defined by the external database. pdbx_sifts_xref_db_segments.asym_id This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. 1 A 2B3 pdbx_sifts_xref_db_segments.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. pdbx_sifts_xref_db_segments.instance_id The instance identifier defined by the external database. pdbx_sifts_xref_db_segments.segment_id The segment identifier defined by the external database. pdbx_sifts_xref_db_segments.seq_id_end The sequence position in the entity or biological unit described in the data block at which the segment alignment ends. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_sifts_xref_db_segments.seq_id_start The sequence position in the entity or biological unit described in the data block at which the segment alignment begins. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. pdbx_sifts_xref_db_segments.xref_db The name of additional external databases with range level mapping. pdbx_sifts_xref_db_segments.xref_db_acc The accession code related to the external database entry. 0 pdbx_soln_scatter Data items in the PDBX_SOLN_SCATTER category record details about a solution scattering experiment Example 1 - based on PDB entry 1HAQ <VRPTx:pdbx_soln_scatterCategory> <VRPTx:pdbx_soln_scatter entry_id="1HAQ" id="1"> <VRPTx:buffer_name>tris</VRPTx:buffer_name> <VRPTx:concentration_range>0.7 - 14</VRPTx:concentration_range> <VRPTx:detector_specific xsi:nil="true" /> <VRPTx:detector_type>500-channel quadrant</VRPTx:detector_type> <VRPTx:max_mean_cross_sectional_radii_gyration>1.7</VRPTx:max_mean_cross_sectional_radii_gyration> <VRPTx:max_mean_cross_sectional_radii_gyration_esd>0.1</VRPTx:max_mean_cross_sectional_radii_gyration_esd> <VRPTx:mean_guiner_radius>11.1</VRPTx:mean_guiner_radius> <VRPTx:mean_guiner_radius_esd>0.4</VRPTx:mean_guiner_radius_esd> <VRPTx:min_mean_cross_sectional_radii_gyration>4.4</VRPTx:min_mean_cross_sectional_radii_gyration> <VRPTx:min_mean_cross_sectional_radii_gyration_esd>0.2</VRPTx:min_mean_cross_sectional_radii_gyration_esd> <VRPTx:num_time_frames>10</VRPTx:num_time_frames> <VRPTx:protein_length>40</VRPTx:protein_length> <VRPTx:sample_pH xsi:nil="true" /> <VRPTx:source_beamline>2.1</VRPTx:source_beamline> <VRPTx:source_beamline_instrument xsi:nil="true" /> <VRPTx:source_class>synchrotron</VRPTx:source_class> <VRPTx:source_type>SRS BEAMLINE 2.1</VRPTx:source_type> <VRPTx:temperature>288</VRPTx:temperature> <VRPTx:type>x-ray</VRPTx:type> </VRPTx:pdbx_soln_scatter> <VRPTx:pdbx_soln_scatter entry_id="1HAQ" id="2"> <VRPTx:buffer_name>PBS in 99.9&#37; D2O</VRPTx:buffer_name> <VRPTx:concentration_range>0.4 - 9.6</VRPTx:concentration_range> <VRPTx:detector_specific xsi:nil="true" /> <VRPTx:detector_type>area</VRPTx:detector_type> <VRPTx:max_mean_cross_sectional_radii_gyration>1.51</VRPTx:max_mean_cross_sectional_radii_gyration> <VRPTx:max_mean_cross_sectional_radii_gyration_esd>0.06</VRPTx:max_mean_cross_sectional_radii_gyration_esd> <VRPTx:mean_guiner_radius>11.3</VRPTx:mean_guiner_radius> <VRPTx:mean_guiner_radius_esd>0.4</VRPTx:mean_guiner_radius_esd> <VRPTx:min_mean_cross_sectional_radii_gyration>3.9</VRPTx:min_mean_cross_sectional_radii_gyration> <VRPTx:min_mean_cross_sectional_radii_gyration_esd>0.2</VRPTx:min_mean_cross_sectional_radii_gyration_esd> <VRPTx:num_time_frames xsi:nil="true" /> <VRPTx:protein_length>37.0 - 39.0</VRPTx:protein_length> <VRPTx:sample_pH xsi:nil="true" /> <VRPTx:source_beamline xsi:nil="true" /> <VRPTx:source_beamline_instrument>D11, D22</VRPTx:source_beamline_instrument> <VRPTx:source_class>neutron source</VRPTx:source_class> <VRPTx:source_type>ILL</VRPTx:source_type> <VRPTx:temperature xsi:nil="true" /> <VRPTx:type>neutron</VRPTx:type> </VRPTx:pdbx_soln_scatter> <VRPTx:pdbx_soln_scatter entry_id="1HAQ" id="3"> <VRPTx:buffer_name>PBS in 99.9&#37; D2O</VRPTx:buffer_name> <VRPTx:concentration_range>3.7, 6.1</VRPTx:concentration_range> <VRPTx:detector_specific xsi:nil="true" /> <VRPTx:detector_type>AREA (TIME-OF-FLIGHT)</VRPTx:detector_type> <VRPTx:max_mean_cross_sectional_radii_gyration xsi:nil="true" /> <VRPTx:max_mean_cross_sectional_radii_gyration_esd xsi:nil="true" /> <VRPTx:mean_guiner_radius>11.7</VRPTx:mean_guiner_radius> <VRPTx:mean_guiner_radius_esd>0.5</VRPTx:mean_guiner_radius_esd> <VRPTx:min_mean_cross_sectional_radii_gyration xsi:nil="true" /> <VRPTx:min_mean_cross_sectional_radii_gyration_esd xsi:nil="true" /> <VRPTx:num_time_frames xsi:nil="true" /> <VRPTx:protein_length>40.0</VRPTx:protein_length> <VRPTx:sample_pH xsi:nil="true" /> <VRPTx:source_beamline>Pulsed Neutron</VRPTx:source_beamline> <VRPTx:source_beamline_instrument>LOQ</VRPTx:source_beamline_instrument> <VRPTx:source_class>neutron source</VRPTx:source_class> <VRPTx:source_type>ISIS</VRPTx:source_type> <VRPTx:temperature xsi:nil="true" /> <VRPTx:type>neutron</VRPTx:type> </VRPTx:pdbx_soln_scatter> </VRPTx:pdbx_soln_scatterCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 pdbx_soln_scatterCategory This property indicates that datablock has a category holder pdbx_soln_scatterCategory. pdbx_soln_scatterCategory This property indicates that pdbx_soln_scatterCategory. has a category pdbx_soln_scatter. pdbx_soln_scatterItem Abstract datatype property for pdbx_soln_scatter items. reference_to_pdbx_soln_scatter cross-reference to pdbx_soln_scatter. referenced_by_pdbx_soln_scatter cross-reference from pdbx_soln_scatter. pdbx_soln_scatter.buffer_name The name of the buffer used for the sample in the solution scattering experiment. acetic acid pdbx_soln_scatter.concentration_range The concentration range (mg/mL) of the complex in the sample used in the solution scattering experiment to determine the mean radius of structural elongation. 0.7 - 14 pdbx_soln_scatter.data_analysis_software_list A list of the software used in the data analysis SCTPL5 GNOM pdbx_soln_scatter.data_reduction_software_list A list of the software used in the data reduction OTOKO pdbx_soln_scatter.detector_specific The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. pdbx_soln_scatter.detector_type The general class of the radiation detector. pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration The maximum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 pdbx_soln_scatter.mean_guiner_radius The mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q gives the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 pdbx_soln_scatter.mean_guiner_radius_esd The estimated standard deviation for the mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration The minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 pdbx_soln_scatter.num_time_frames The number of time frame solution scattering images used. pdbx_soln_scatter.protein_length The length (or range) of the protein sample under study. If the solution structure is approximated as an elongated elliptical cyclinder the length L is determined from, L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ] The length should also be given by L = pi I(0) / [ I(Q).Q]_Q->0 pdbx_soln_scatter.sample_pH The pH value of the buffered sample. pdbx_soln_scatter.source_beamline The beamline name used for the experiment pdbx_soln_scatter.source_beamline_instrument The instrumentation used on the beamline pdbx_soln_scatter.source_class The general class of the radiation source. neutron source synchrotron pdbx_soln_scatter.source_type The make, model, name or beamline of the source of radiation. pdbx_soln_scatter.temperature The temperature in kelvins at which the experiment was conducted x-ray neutron modelling The type of solution scattering experiment carried out pdbx_soln_scatter.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. pdbx_soln_scatter.id The value of attribute id in category pdbx_soln_scatter must uniquely identify the sample in the category PDBX_SOLN_SCATTER 0 pdbx_soln_scatter_model Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_soln_scatter_modelCategory This property indicates that datablock has a category holder pdbx_soln_scatter_modelCategory. pdbx_soln_scatter_modelCategory This property indicates that pdbx_soln_scatter_modelCategory. has a category pdbx_soln_scatter_model. pdbx_soln_scatter_modelItem Abstract datatype property for pdbx_soln_scatter_model items. reference_to_pdbx_soln_scatter_model cross-reference to pdbx_soln_scatter_model. referenced_by_pdbx_soln_scatter_model cross-reference from pdbx_soln_scatter_model. pdbx_soln_scatter_model.conformer_selection_criteria A description of the conformer selection criteria used. The modelled scattering curves were assessed by calculation of the RG, RSX-1 and RXS-2 values in the same Q ranges used in the experimental Guinier fits. models were then ranked using a goodness-of-fit R-factor defined by analogy with protein crystallography and based on the experimental curves in the Q range extending to 1.4 nm-1. pdbx_soln_scatter_model.details A description of any additional details concerning the experiment. Homology models were built for the 17 SCR domains and energy minimisations were performed to improve the connectivity in the fh model. triantennary complex-type carbohydrate structures (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the N-linked glycosylation sites. a library of linker peptide conformations was used in domain modelling constrained by the solution scattering fits. modelling with the scattering data was also carried out by rotational search methods. the x-ray and neutron scattering curve I(Q) was calculated assuming a uniform scattering density for the spheres using the debye equation as adapted to spheres. x-ray curves were calculated from the hydrated sphere models without corrections for wavelength spread or beam divergence, while these corrections were applied for the neutron curves but now using unhydrated models. pdbx_soln_scatter_model.entry_fitting_list A list of the entries used to fit the model to the scattering data PDB CODE 1HFI, 1HCC, 1HFH, 1VCC pdbx_soln_scatter_model.method A description of the methods used in the modelling Constrained scattering fitting of homology models pdbx_soln_scatter_model.num_conformers_calculated The number of model conformers calculated. pdbx_soln_scatter_model.num_conformers_submitted The number of model conformers submitted in the entry pdbx_soln_scatter_model.representative_conformer The index of the representative conformer among the submitted conformers for the entry pdbx_soln_scatter_model.software_author_list A list of the software authors MSI pdbx_soln_scatter_model.software_list A list of the software used in the modeeling INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI pdbx_soln_scatter_model.id The value of attribute id in category pdbx_soln_scatter_model must uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL pdbx_soln_scatter_model.scatter_id This data item is a pointer to attribute id in category pdbx_soln_scatter in the PDBX_SOLN_SCATTER category. 0 pdbx_struct_assembly Data items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies. Example 1 - <VRPTx:pdbx_struct_assemblyCategory> <VRPTx:pdbx_struct_assembly id="1"> <VRPTx:details> The icosahedral virus particle.</VRPTx:details> </VRPTx:pdbx_struct_assembly> </VRPTx:pdbx_struct_assemblyCategory> 1 1 0 1 0 1 0 1 1 pdbx_struct_assemblyCategory This property indicates that datablock has a category holder pdbx_struct_assemblyCategory. pdbx_struct_assemblyCategory This property indicates that pdbx_struct_assemblyCategory. has a category pdbx_struct_assembly. pdbx_struct_assemblyItem Abstract datatype property for pdbx_struct_assembly items. reference_to_pdbx_struct_assembly cross-reference to pdbx_struct_assembly. referenced_by_pdbx_struct_assembly cross-reference from pdbx_struct_assembly. pdbx_struct_assembly.details A description of special aspects of the macromolecular assembly. In the PDB, 'representative helical assembly', 'complete point assembly', 'complete icosahedral assembly', 'software_defined_assembly', 'author_defined_assembly', and 'author_and_software_defined_assembly' are considered "biologically relevant assemblies. The icosahedral virus particle. pdbx_struct_assembly.method_details Provides details of the method used to determine or compute the assembly. pdbx_struct_assembly.oligomeric_count The number of polymer molecules in the assembly. pdbx_struct_assembly.oligomeric_details Provides the details of the oligomeric state of the assembly. monomer octameric tetradecameric eicosameric 21-meric 60-meric 180-meric helical pdbx_struct_assembly.id The value of attribute id in category pdbx_struct_assembly must uniquely identify a record in the PDBX_STRUCT_ASSEMBLY list. 0 pdbx_struct_assembly_gen Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN data items provide the specifications of the components that constitute that assembly in terms of cartesian transformations. Example 1 - <VRPTx:pdbx_struct_assembly_genCategory> <VRPTx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A" oper_expression="1"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="B" oper_expression="1"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="B" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="C" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="B" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="D" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen> </VRPTx:pdbx_struct_assembly_genCategory> Example 2 - <VRPTx:pdbx_struct_assembly_genCategory> <VRPTx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A,B" oper_expression="1"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A,B,C" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen> <VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A,B,D" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen> </VRPTx:pdbx_struct_assembly_genCategory> 0 1 0 1 1 1 1 pdbx_struct_assembly_genCategory This property indicates that datablock has a category holder pdbx_struct_assembly_genCategory. pdbx_struct_assembly_genCategory This property indicates that pdbx_struct_assembly_genCategory. has a category pdbx_struct_assembly_gen. pdbx_struct_assembly_genItem Abstract datatype property for pdbx_struct_assembly_gen items. reference_to_pdbx_struct_assembly_gen cross-reference to pdbx_struct_assembly_gen. referenced_by_pdbx_struct_assembly_gen cross-reference from pdbx_struct_assembly_gen. pdbx_struct_assembly_gen.auth_asym_id_list This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This item may be expressed as a comma separated list of identifiers. pdbx_struct_assembly_gen.entity_inst_id This data item is a pointer to attribute id in category pdbx_struct_entity_inst in the PDBX_STRUCT_ENTITY_INST category. This item may be expressed as a comma separated list of instance identifiers. pdbx_struct_assembly_gen.assembly_id This data item is a pointer to attribute id in category pdbx_struct_assembly in the PDBX_STRUCT_ASSEMBLY category. pdbx_struct_assembly_gen.asym_id_list This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. This item may be expressed as a comma separated list of identifiers. pdbx_struct_assembly_gen.oper_expression Identifies the operation of collection of operations from category PDBX_STRUCT_OPER_LIST. Operation expressions may have the forms: (1) the single operation 1 (1,2,5) the operations 1, 2, 5 (1-4) the operations 1,2,3 and 4 (1,2)(3,4) the combinations of operations 3 and 4 followed by 1 and 2 (i.e. the cartesian product of parenthetical groups applied from right to left) (1) (1,2,5) (1-60) (1-60)(61) 0 pdbx_struct_assembly_prop Properties and features of structural assemblies. Example 1 - <VRPTx:pdbx_struct_assembly_propCategory> <VRPTx:pdbx_struct_assembly_prop biol_id="1" type="ABSA"> <VRPTx:details> </VRPTx:details> <VRPTx:value>1456.7</VRPTx:value> </VRPTx:pdbx_struct_assembly_prop> </VRPTx:pdbx_struct_assembly_propCategory> 0 1 1 1 1 1 pdbx_struct_assembly_propCategory This property indicates that datablock has a category holder pdbx_struct_assembly_propCategory. pdbx_struct_assembly_propCategory This property indicates that pdbx_struct_assembly_propCategory. has a category pdbx_struct_assembly_prop. pdbx_struct_assembly_propItem Abstract datatype property for pdbx_struct_assembly_prop items. reference_to_pdbx_struct_assembly_prop cross-reference to pdbx_struct_assembly_prop. referenced_by_pdbx_struct_assembly_prop cross-reference from pdbx_struct_assembly_prop. pdbx_struct_assembly_prop.details Additional details about this assembly property. pdbx_struct_assembly_prop.value The value of the assembly property. pdbx_struct_assembly_prop.biol_id The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY. ABSA (A^2) SSA (A^2) MORE The property type for the assembly. 0 pdbx_struct_asym_gen Data items in the PDBX_STRUCT_ASYM_GEN category record details about the generation of the crystallographic asymmetric unit. The PDBX_STRUCT_ASYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates. Example 1 - <VRPTx:pdbx_struct_asym_genCategory> <VRPTx:pdbx_struct_asym_gen entity_inst_id="A" oper_expression="1"> <VRPTx:asym_id>A</VRPTx:asym_id> </VRPTx:pdbx_struct_asym_gen> <VRPTx:pdbx_struct_asym_gen entity_inst_id="B" oper_expression="1"> <VRPTx:asym_id>B</VRPTx:asym_id> </VRPTx:pdbx_struct_asym_gen> </VRPTx:pdbx_struct_asym_genCategory> 0 1 1 1 pdbx_struct_asym_genCategory This property indicates that datablock has a category holder pdbx_struct_asym_genCategory. pdbx_struct_asym_genCategory This property indicates that pdbx_struct_asym_genCategory. has a category pdbx_struct_asym_gen. pdbx_struct_asym_genItem Abstract datatype property for pdbx_struct_asym_gen items. reference_to_pdbx_struct_asym_gen cross-reference to pdbx_struct_asym_gen. referenced_by_pdbx_struct_asym_gen cross-reference from pdbx_struct_asym_gen. pdbx_struct_asym_gen.asym_id This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. pdbx_struct_asym_gen.entity_inst_id This data item is a pointer to attribute id in category pdbx_struct_entity_inst in the PDBX_STRUCT_ENTITY_INST category. pdbx_struct_asym_gen.oper_expression Identifies the operation from category PDBX_STRUCT_OPER_LIST. (1) (1-2) 0 pdbx_struct_chem_comp_diagnostics Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides structural diagnostics in chemical components instances. Example 1 - <VRPTx:pdbx_struct_chem_comp_diagnosticsCategory> <VRPTx:pdbx_struct_chem_comp_diagnostics ordinal="1"> <VRPTx:asym_id>Q</VRPTx:asym_id> <VRPTx:auth_comp_id>Q20</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>10</VRPTx:auth_seq_id> <VRPTx:details>Strained geometry. Long carbonyl bond at C10.</VRPTx:details> <VRPTx:pdb_strand_id>Q</VRPTx:pdb_strand_id> <VRPTx:seq_num xsi:nil="true" /> <VRPTx:type>GEOMETRY</VRPTx:type> </VRPTx:pdbx_struct_chem_comp_diagnostics> </VRPTx:pdbx_struct_chem_comp_diagnosticsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_struct_chem_comp_diagnosticsCategory This property indicates that datablock has a category holder pdbx_struct_chem_comp_diagnosticsCategory. pdbx_struct_chem_comp_diagnosticsCategory This property indicates that pdbx_struct_chem_comp_diagnosticsCategory. has a category pdbx_struct_chem_comp_diagnostics. pdbx_struct_chem_comp_diagnosticsItem Abstract datatype property for pdbx_struct_chem_comp_diagnostics items. reference_to_pdbx_struct_chem_comp_diagnostics cross-reference to pdbx_struct_chem_comp_diagnostics. referenced_by_pdbx_struct_chem_comp_diagnostics cross-reference from pdbx_struct_chem_comp_diagnostics. pdbx_struct_chem_comp_diagnostics.asym_id Instance identifier for the polymer molecule. A B pdbx_struct_chem_comp_diagnostics.auth_comp_id PDB component ID NAG ATP pdbx_struct_chem_comp_diagnostics.auth_seq_id PDB position in the sequence. 1 2 pdbx_struct_chem_comp_diagnostics.details Special structural details about this chemical component. pdbx_struct_chem_comp_diagnostics.pdb_ins_code Insertion code of the monomer or ligand . A B pdbx_struct_chem_comp_diagnostics.pdb_strand_id PDB strand/chain id. A B pdbx_struct_chem_comp_diagnostics.seq_num Position in the sequence. 1 2 MISSING_ATOM STEREOCHEMISTRY VALENCE GEOMETRY LABELING OTHER A classification of the diagnostic for the chemical component instance pdbx_struct_chem_comp_diagnostics.ordinal An ordinal index for this category 1 2 0 pdbx_struct_conn_angle Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles in connections between portions of the structure. Example 1 - PDB entry 2v8d <VRPTx:pdbx_struct_conn_angleCategory> <VRPTx:pdbx_struct_conn_angle id="1"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>114</VRPTx:ptnr3_label_seq_id> <VRPTx:value>104.7</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="2"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id> <VRPTx:value>91.3</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="3"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id> <VRPTx:value>120.6</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="4"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>2041</VRPTx:ptnr3_label_seq_id> <VRPTx:value>172.5</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="5"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>2041</VRPTx:ptnr3_label_seq_id> <VRPTx:value>80.0</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="6"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>226</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>2041</VRPTx:ptnr3_label_seq_id> <VRPTx:value>91.3</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="7"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id> <VRPTx:value>76.9</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="8"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id> <VRPTx:value>112.3</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="9"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>226</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id> <VRPTx:value>127.0</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="10"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>2041</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id> <VRPTx:value>95.9</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="11"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>OE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>GLU</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>160</VRPTx:ptnr3_label_seq_id> <VRPTx:value>89.8</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="12"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id> <VRPTx:value>95.5</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="13"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>GLU</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>160</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id> <VRPTx:value>109.4</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="14"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>421</VRPTx:ptnr3_label_seq_id> <VRPTx:value>90.4</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="15"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>GLU</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>160</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>421</VRPTx:ptnr3_label_seq_id> <VRPTx:value>111.3</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="16"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>421</VRPTx:ptnr3_label_seq_id> <VRPTx:value>138.9</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="17"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>114</VRPTx:ptnr3_label_seq_id> <VRPTx:value>106.4</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="18"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>OD</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>ASP</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>125</VRPTx:ptnr3_label_seq_id> <VRPTx:value>100.5</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="19"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>OD</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>ASP</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>125</VRPTx:ptnr3_label_seq_id> <VRPTx:value>115.6</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="20"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id> <VRPTx:value>123.2</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="21"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id> <VRPTx:value>123.2</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="22"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id> <VRPTx:value>82.7</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> <VRPTx:pdbx_struct_conn_angle id="23"> <VRPTx:ptnr1_PDB_ins_code xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>OE</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>GLU</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>160</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id xsi:nil="true" /> <VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr3_PDB_ins_code>OD</VRPTx:ptnr3_PDB_ins_code> <VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id> <VRPTx:ptnr3_label_atom_id xsi:nil="true" /> <VRPTx:ptnr3_label_comp_id>ASP</VRPTx:ptnr3_label_comp_id> <VRPTx:ptnr3_label_seq_id>125</VRPTx:ptnr3_label_seq_id> <VRPTx:value>148.6</VRPTx:value> </VRPTx:pdbx_struct_conn_angle> </VRPTx:pdbx_struct_conn_angleCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_struct_conn_angleCategory This property indicates that datablock has a category holder pdbx_struct_conn_angleCategory. pdbx_struct_conn_angleCategory This property indicates that pdbx_struct_conn_angleCategory. has a category pdbx_struct_conn_angle. pdbx_struct_conn_angleItem Abstract datatype property for pdbx_struct_conn_angle items. reference_to_pdbx_struct_conn_angle cross-reference to pdbx_struct_conn_angle. referenced_by_pdbx_struct_conn_angle cross-reference from pdbx_struct_conn_angle. pdbx_struct_conn_angle.ptnr1_PDB_ins_code A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_auth_alt_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_auth_asym_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_auth_atom_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_auth_comp_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_auth_seq_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_label_alt_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_label_asym_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_label_atom_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_label_comp_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_label_seq_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr1_symmetry Describes the symmetry operation that should be applied to the atom specified by attribute ptnr1_label* in category pdbx_struct_conn_angle to generate the first partner in the structure angle. 7th symm. posn.; +a on x; -b on y 7_645 pdbx_struct_conn_angle.ptnr2_PDB_ins_code A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_auth_alt_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_auth_asym_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_auth_atom_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_auth_comp_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_auth_seq_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_label_alt_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_label_asym_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_label_atom_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_label_comp_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_label_seq_id A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr2_symmetry Describes the symmetry operation that should be applied to the atom specified by attribute ptnr2_label* in category pdbx_struct_conn_angle to generate the second partner in the structure angle. pdbx_struct_conn_angle.ptnr3_PDB_ins_code A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_auth_alt_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_auth_asym_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_auth_atom_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_auth_comp_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_auth_seq_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_label_alt_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_label_asym_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_label_atom_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_label_comp_id A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_label_seq_id A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_conn_angle.ptnr3_symmetry Describes the symmetry operation that should be applied to the atom specified by attribute ptnr3_label* in category pdbx_struct_conn_angle to generate the first partner in the structure angle. 7th symm. posn.; +a on x; -b on y 7_645 pdbx_struct_conn_angle.value Angle in degrees defined by the three sites attribute ptnr1_label_atom_id, in category pdbx_struct_conn_angle attribute ptnr2_label_atom_id, in category pdbx_struct_conn_angle attribute ptnr3_label_atom_id in category pdbx_struct_conn_angle pdbx_struct_conn_angle.value_esd The standard uncertainty (estimated standard deviation) of attribute value in category pdbx_struct_conn_angle pdbx_struct_conn_angle.id The value of attribute id in category pdbx_struct_conn_angle must uniquely identify a record in the PDBX_STRUCT_CONN_ANGLE list. Note that this item need not be a number; it can be any unique identifier. 0 pdbx_struct_entity_inst Data items in the PDBX_STRUCT_ENTITY_INST category record details about the structural elements in the deposited entry. The entity instance is a method neutral identifier for the observed molecular entities in the deposited coordinate set. Example 1 - <VRPTx:pdbx_struct_entity_instCategory> <VRPTx:pdbx_struct_entity_inst id="A"> <VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details> <VRPTx:entity_id>1</VRPTx:entity_id> </VRPTx:pdbx_struct_entity_inst> <VRPTx:pdbx_struct_entity_inst id="B"> <VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details> <VRPTx:entity_id>1</VRPTx:entity_id> </VRPTx:pdbx_struct_entity_inst> </VRPTx:pdbx_struct_entity_instCategory> 0 1 0 1 1 pdbx_struct_entity_instCategory This property indicates that datablock has a category holder pdbx_struct_entity_instCategory. pdbx_struct_entity_instCategory This property indicates that pdbx_struct_entity_instCategory. has a category pdbx_struct_entity_inst. pdbx_struct_entity_instItem Abstract datatype property for pdbx_struct_entity_inst items. reference_to_pdbx_struct_entity_inst cross-reference to pdbx_struct_entity_inst. referenced_by_pdbx_struct_entity_inst cross-reference from pdbx_struct_entity_inst. pdbx_struct_entity_inst.details A description of special aspects of this portion of the contents of the deposited unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. pdbx_struct_entity_inst.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. pdbx_struct_entity_inst.id The value of attribute id in category pdbx_struct_entity_inst must uniquely identify a record in the PDBX_STRUCT_ENTITY_INST list. The entity instance is a method neutral identifier for the observed molecular entities in the deposited coordinate set. 1 A 2B3 0 pdbx_struct_group_component_range Data items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural group as a continuous span chemical components. Example 1 - <VRPTx:pdbx_struct_group_component_rangeCategory> <VRPTx:pdbx_struct_group_component_range ordinal="1"> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:beg_PDB_ins_code xsi:nil="true" /> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>MLU</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>1</VRPTx:beg_auth_seq_id> <VRPTx:end_PDB_ins_code xsi:nil="true" /> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>RAM</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>10</VRPTx:end_auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_component_range> </VRPTx:pdbx_struct_group_component_rangeCategory> 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_struct_group_component_rangeCategory This property indicates that datablock has a category holder pdbx_struct_group_component_rangeCategory. pdbx_struct_group_component_rangeCategory This property indicates that pdbx_struct_group_component_rangeCategory. has a category pdbx_struct_group_component_range. pdbx_struct_group_component_rangeItem Abstract datatype property for pdbx_struct_group_component_range items. reference_to_pdbx_struct_group_component_range cross-reference to pdbx_struct_group_component_range. referenced_by_pdbx_struct_group_component_range cross-reference from pdbx_struct_group_component_range. pdbx_struct_group_component_range.PDB_model_num Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_PDB_ins_code Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_auth_asym_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_auth_comp_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_auth_seq_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_label_alt_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_label_asym_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_label_comp_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.beg_label_seq_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_PDB_ins_code Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_auth_asym_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_auth_comp_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_auth_seq_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_label_alt_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_label_asym_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_label_comp_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.end_label_seq_id Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_component_range.struct_group_id This data item is a pointer to attribute struct_group_id in category pdbx_struct_group_list in the PDBX_STRUCT_GROUP_LIST category. pdbx_struct_group_component_range.ordinal The value of attribute id in category pdbx_struct_group_component_range must uniquely identify a record in the PDBX_STRUCT_GROUP_COMPONENT_RANGE list. 0 pdbx_struct_group_components Data items in the PDBX_STRUCT_GROUP_COMPONENTS category list component-level group assignments within the entry. Groups are defined and described in category PDBX_STRUCT_GROUP_LIST. Example 1 - <VRPTx:pdbx_struct_group_componentsCategory> <VRPTx:pdbx_struct_group_components ordinal="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>MLU</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>1</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>OMZ</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>2</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>ASN</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="4"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>GHP</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>4</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="5"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>GHP</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>5</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="6"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>OMX</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>6</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="7"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>3FG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>7</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="8"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>ERE</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>8</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="9"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BGC</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>9</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> <VRPTx:pdbx_struct_group_components ordinal="10"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>RAM</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>10</VRPTx:auth_seq_id> <VRPTx:struct_group_id>1</VRPTx:struct_group_id> </VRPTx:pdbx_struct_group_components> </VRPTx:pdbx_struct_group_componentsCategory> 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 pdbx_struct_group_componentsCategory This property indicates that datablock has a category holder pdbx_struct_group_componentsCategory. pdbx_struct_group_componentsCategory This property indicates that pdbx_struct_group_componentsCategory. has a category pdbx_struct_group_components. pdbx_struct_group_componentsItem Abstract datatype property for pdbx_struct_group_components items. reference_to_pdbx_struct_group_components cross-reference to pdbx_struct_group_components. referenced_by_pdbx_struct_group_components cross-reference from pdbx_struct_group_components. pdbx_struct_group_components.PDB_ins_code Part of the identifier for the component in this group assignment. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.PDB_model_num Part of the identifier for the component in this group assignment. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.auth_asym_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.auth_comp_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.auth_seq_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.label_alt_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.label_asym_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.label_comp_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.label_seq_id Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_group_components.struct_group_id The value of attribute group_id in category pdbx_struct_group_components identifies the group assignment for the component. This is a reference to the identifier for group definition in category PDBX_STRUCT_GROUP_LIST. pdbx_struct_group_components.ordinal The value of attribute ordinal in category pdbx_struct_group_components must uniquely identify each item in the PDBX_STRUCT_GROUP_COMPONENTS list. This is an integer serial number. 0 pdbx_struct_group_list Data items in the PDBX_STRUCT_GROUP_LIST define groups of related components or atoms. Example 1 - <VRPTx:pdbx_struct_group_listCategory> <VRPTx:pdbx_struct_group_list struct_group_id="1"> <VRPTx:description> Decaplanin is a tricyclic glycopeptide. The scaffold is a heptapeptide with the configuration D-D-L-D-D-L-L, glycosylated by a monosaccharide and a disaccharide</VRPTx:description> <VRPTx:group_enumeration_type>component</VRPTx:group_enumeration_type> <VRPTx:name>DECAPLANIN</VRPTx:name> <VRPTx:type>MolecularComplex</VRPTx:type> </VRPTx:pdbx_struct_group_list> </VRPTx:pdbx_struct_group_listCategory> 1 1 1 1 1 1 0 1 0 1 1 1 1 pdbx_struct_group_listCategory This property indicates that datablock has a category holder pdbx_struct_group_listCategory. pdbx_struct_group_listCategory This property indicates that pdbx_struct_group_listCategory. has a category pdbx_struct_group_list. pdbx_struct_group_listItem Abstract datatype property for pdbx_struct_group_list items. reference_to_pdbx_struct_group_list cross-reference to pdbx_struct_group_list. referenced_by_pdbx_struct_group_list cross-reference from pdbx_struct_group_list. pdbx_struct_group_list.description The description of the group. atom component component_range The manner in which the group is defined. Groups consist of collections within the set of deposited coordinates which can be defined in terms of a list of chemical components in category PDBX_STRUCT_GROUP_COMPONENTS, ranges of chemical components in PDBX_STRUCT_GROUP_COMPONENT_RANGE, or as individual atoms using attribute pdbx_group_id. in category atom_site Groups can be composed of selections from multiple categories in which case the enumeration types are separated by commas. a list of components component a selection of listed components and component range selections component,component_range pdbx_struct_group_list.name The name of the group. pdbx_struct_group_list.selection A qualification of the subset of atoms in the group. all atoms in specified range all main chain atoms only mnc side chain atoms only sdc pdbx_struct_group_list.selection_details A text description of subset of the atom selection in the group. Molecular Complex Heterogen Complex TLS group NCS group A selected list of group types. pdbx_struct_group_list.struct_group_id The unique identifier for the group. 0 pdbx_struct_info Special features of this structural entry. Example 1 - <VRPTx:pdbx_struct_infoCategory> <VRPTx:pdbx_struct_info type="nonpolymer_zero_occupancy_flag" value="Y"></VRPTx:pdbx_struct_info> <VRPTx:pdbx_struct_info type="polymer_zero_occupancy_flag" value="Y"></VRPTx:pdbx_struct_info> <VRPTx:pdbx_struct_info type="multiple_model_flag" value="Y"></VRPTx:pdbx_struct_info> <VRPTx:pdbx_struct_info type="multiple_model_details" value="Model 3 missing ligand ACX"></VRPTx:pdbx_struct_info> <VRPTx:pdbx_struct_info type="nonpolymer_details" value="Disordered ligand geometry for C34 with missing pyridine ring"></VRPTx:pdbx_struct_info> <VRPTx:pdbx_struct_info type="missing atoms in alternate conformations" value="Y"></VRPTx:pdbx_struct_info> </VRPTx:pdbx_struct_infoCategory> 0 1 1 1 pdbx_struct_infoCategory This property indicates that datablock has a category holder pdbx_struct_infoCategory. pdbx_struct_infoCategory This property indicates that pdbx_struct_infoCategory. has a category pdbx_struct_info. pdbx_struct_infoItem Abstract datatype property for pdbx_struct_info items. reference_to_pdbx_struct_info cross-reference to pdbx_struct_info. referenced_by_pdbx_struct_info cross-reference from pdbx_struct_info. pdbx_struct_info.details Additional details about this information item. nonpolymer_zero_occupancy_flag polymer_zero_occupancy_flag multiple_model_flag multiple_model_details nonpolymer_details missing atoms in alternate conformations The information category/type for this item. pdbx_struct_info.value The value of this information item. 0 pdbx_struct_legacy_oper_list Data items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry. This category provides a container for matrices used to construct icosahedral assemblies in legacy entries. Example 1 - <VRPTx:pdbx_struct_legacy_oper_listCategory> <VRPTx:pdbx_struct_legacy_oper_list id="2"> <VRPTx:matrix11>0.247</VRPTx:matrix11> <VRPTx:matrix12>0.935</VRPTx:matrix12> <VRPTx:matrix13>0.256</VRPTx:matrix13> <VRPTx:matrix21>0.929</VRPTx:matrix21> <VRPTx:matrix22>0.153</VRPTx:matrix22> <VRPTx:matrix23>0.337</VRPTx:matrix23> <VRPTx:matrix31>0.276</VRPTx:matrix31> <VRPTx:matrix32>0.321</VRPTx:matrix32> <VRPTx:matrix33>-0.906</VRPTx:matrix33> <VRPTx:vector1>-8.253</VRPTx:vector1> <VRPTx:vector2>-11.743</VRPTx:vector2> <VRPTx:vector3>-1.782</VRPTx:vector3> </VRPTx:pdbx_struct_legacy_oper_list> </VRPTx:pdbx_struct_legacy_oper_listCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_struct_legacy_oper_listCategory This property indicates that datablock has a category holder pdbx_struct_legacy_oper_listCategory. pdbx_struct_legacy_oper_listCategory This property indicates that pdbx_struct_legacy_oper_listCategory. has a category pdbx_struct_legacy_oper_list. pdbx_struct_legacy_oper_listItem Abstract datatype property for pdbx_struct_legacy_oper_list items. reference_to_pdbx_struct_legacy_oper_list cross-reference to pdbx_struct_legacy_oper_list. referenced_by_pdbx_struct_legacy_oper_list cross-reference from pdbx_struct_legacy_oper_list. pdbx_struct_legacy_oper_list.matrix11 The [1][1] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix12 The [1][2] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix13 The [1][3] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix21 The [2][1] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix22 The [2][2] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix23 The [2][3] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix31 The [3][1] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix32 The [3][2] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.matrix33 The [3][3] element of the 3x3 matrix component of the transformation operation. pdbx_struct_legacy_oper_list.name A descriptive name for the transformation operation. identity matrix two-fold rotation pdbx_struct_legacy_oper_list.vector1 The [1] element of the three-element vector component of the transformation operation. pdbx_struct_legacy_oper_list.vector2 The [2] element of the three-element vector component of the transformation operation. pdbx_struct_legacy_oper_list.vector3 The [3] element of the three-element vector component of the transformation operation. pdbx_struct_legacy_oper_list.id This integer value must uniquely identify a record in the PDBX_STRUCT_LEGACY_OPER_LIST list. 0 pdbx_struct_mod_residue Data items in the PDBX_STRUCT_MOD_RESIDUE category list the modified polymer components in the entry and provide some details describing the nature of the modification. Example 1 - <VRPTx:pdbx_struct_mod_residueCategory> <VRPTx:pdbx_struct_mod_residue id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>CRW</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>66</VRPTx:auth_seq_id> <VRPTx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</VRPTx:details> <VRPTx:parent_comp_id>ALA</VRPTx:parent_comp_id> </VRPTx:pdbx_struct_mod_residue> <VRPTx:pdbx_struct_mod_residue id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>CRW</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>66</VRPTx:auth_seq_id> <VRPTx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</VRPTx:details> <VRPTx:parent_comp_id>SER</VRPTx:parent_comp_id> </VRPTx:pdbx_struct_mod_residue> <VRPTx:pdbx_struct_mod_residue id="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>CRW</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>66</VRPTx:auth_seq_id> <VRPTx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</VRPTx:details> <VRPTx:parent_comp_id>GLY</VRPTx:parent_comp_id> </VRPTx:pdbx_struct_mod_residue> </VRPTx:pdbx_struct_mod_residueCategory> 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_struct_mod_residueCategory This property indicates that datablock has a category holder pdbx_struct_mod_residueCategory. pdbx_struct_mod_residueCategory This property indicates that pdbx_struct_mod_residueCategory. has a category pdbx_struct_mod_residue. pdbx_struct_mod_residueItem Abstract datatype property for pdbx_struct_mod_residue items. reference_to_pdbx_struct_mod_residue cross-reference to pdbx_struct_mod_residue. referenced_by_pdbx_struct_mod_residue cross-reference from pdbx_struct_mod_residue. pdbx_struct_mod_residue.PDB_ins_code Part of the identifier for the modified polymer component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.PDB_model_num Part of the identifier for the modified polymer component. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.auth_asym_id Part of the identifier for the modified polymer component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.auth_comp_id Part of the identifier for the modified polymer component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.auth_seq_id Part of the identifier for the modified polymer component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.details Details of the modification for this polymer component. pdbx_struct_mod_residue.label_asym_id Part of the identifier for the modified polymer component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.label_comp_id Part of the identifier for the modified polymer component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.label_seq_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_mod_residue.parent_comp_id The parent component identifier for this modified polymer component. pdbx_struct_mod_residue.id The value of attribute id in category pdbx_struct_mod_residue must uniquely identify each item in the PDBX_STRUCT_MOD_RESIDUE list. This is an integer serial number. 0 pdbx_struct_msym_gen Data items in the PDBX_STRUCT_MSYM_GEN category record details about the generation of the minimal asymmetric unit. For instance, this category can be used to provide this information for helical and point symmetry systems. The PDBX_STRUCT_MSYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates. Example 1 - <VRPTx:pdbx_struct_msym_genCategory> <VRPTx:pdbx_struct_msym_gen entity_inst_id="A" msym_id="A" oper_expression="3"></VRPTx:pdbx_struct_msym_gen> <VRPTx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="B" oper_expression="4"></VRPTx:pdbx_struct_msym_gen> <VRPTx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="C" oper_expression="5"></VRPTx:pdbx_struct_msym_gen> </VRPTx:pdbx_struct_msym_genCategory> 1 1 1 pdbx_struct_msym_genCategory This property indicates that datablock has a category holder pdbx_struct_msym_genCategory. pdbx_struct_msym_genCategory This property indicates that pdbx_struct_msym_genCategory. has a category pdbx_struct_msym_gen. pdbx_struct_msym_genItem Abstract datatype property for pdbx_struct_msym_gen items. reference_to_pdbx_struct_msym_gen cross-reference to pdbx_struct_msym_gen. referenced_by_pdbx_struct_msym_gen cross-reference from pdbx_struct_msym_gen. pdbx_struct_msym_gen.entity_inst_id This data item is a pointer to attribute id in category pdbx_struct_entity_inst in the PDBX_STRUCT_ENTITY_INST category. pdbx_struct_msym_gen.msym_id Uniquely identifies the this structure instance in point symmetry unit. pdbx_struct_msym_gen.oper_expression Identifies the operation from category PDBX_STRUCT_OPER_LIST. (1) (1-3) 0 pdbx_struct_nmr_ens_clust Data items in the PDBX_STRUCT_NMR_ENS_CLUST category record information about cluster analysis of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_clustCategory> <VRPTx:pdbx_struct_nmr_ens_clust entry_id="5UB9"> <VRPTx:clusters_total_number>4</VRPTx:clusters_total_number> <VRPTx:conformers_total_number>20</VRPTx:conformers_total_number> <VRPTx:error>success</VRPTx:error> <VRPTx:outliers_total_number>2</VRPTx:outliers_total_number> </VRPTx:pdbx_struct_nmr_ens_clust> </VRPTx:pdbx_struct_nmr_ens_clustCategory> 0 1 0 1 0 1 0 1 1 pdbx_struct_nmr_ens_clustCategory This property indicates that datablock has a category holder pdbx_struct_nmr_ens_clustCategory. pdbx_struct_nmr_ens_clustCategory This property indicates that pdbx_struct_nmr_ens_clustCategory. has a category pdbx_struct_nmr_ens_clust. pdbx_struct_nmr_ens_clustItem Abstract datatype property for pdbx_struct_nmr_ens_clust items. reference_to_pdbx_struct_nmr_ens_clust cross-reference to pdbx_struct_nmr_ens_clust. referenced_by_pdbx_struct_nmr_ens_clust cross-reference from pdbx_struct_nmr_ens_clust. pdbx_struct_nmr_ens_clust.clusters_total_number The number of clusters (group of conformers) that are identified by the cluster analysis of the NMR ensemble structure. 1 pdbx_struct_nmr_ens_clust.conformers_total_number The number of conformer (models) that are used for the cluster analysis of the NMR ensemble structure. 20 pdbx_struct_nmr_ens_clust.error Details of any error or warning messages. pdbx_struct_nmr_ens_clust.outliers_total_number The number of conformers (models) that are not belong any group of conformers in the cluster analysis of the NMR ensemble structure. 0 pdbx_struct_nmr_ens_clust.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 pdbx_struct_nmr_ens_clust_gen Data items in the PDBX_STRUCT_NMR_ENS_CLUST_GEN category records generation of clusters (group of conformers) by cluster analysis of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_clust_genCategory> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="1"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="2"> <VRPTx:cluster_id>3</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="3"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="4"> <VRPTx:cluster_id>3</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="5"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="6"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="7"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="8"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="9"> <VRPTx:cluster_id>outlier</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="10"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="11"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="12"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="13"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="14"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="15"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="16"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="17"> <VRPTx:cluster_id>4</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="18"> <VRPTx:cluster_id>3</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="19"> <VRPTx:cluster_id>outlier</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="20"> <VRPTx:cluster_id>4</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> </VRPTx:pdbx_struct_nmr_ens_clust_genCategory> 1 1 0 1 1 pdbx_struct_nmr_ens_clust_genCategory This property indicates that datablock has a category holder pdbx_struct_nmr_ens_clust_genCategory. pdbx_struct_nmr_ens_clust_genCategory This property indicates that pdbx_struct_nmr_ens_clust_genCategory. has a category pdbx_struct_nmr_ens_clust_gen. pdbx_struct_nmr_ens_clust_genItem Abstract datatype property for pdbx_struct_nmr_ens_clust_gen items. reference_to_pdbx_struct_nmr_ens_clust_gen cross-reference to pdbx_struct_nmr_ens_clust_gen. referenced_by_pdbx_struct_nmr_ens_clust_gen cross-reference from pdbx_struct_nmr_ens_clust_gen. pdbx_struct_nmr_ens_clust_gen.cluster_id The identifier of the group of conformers (clusters) identified by the cluster analysis of the NMR ensemble structure. Y N Whether the conformer represents medoid conformer of a cluster by cluster analysis of the NMR ensemble structure (Y) or not (N). pdbx_struct_nmr_ens_clust_gen.PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site. 0 pdbx_struct_nmr_ens_dom Data items in the PDBX_STRUCT_NMR_ENS_DOM category records generation of domains (polypeptide chain segments) by domain identification of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_domCategory> <VRPTx:pdbx_struct_nmr_ens_dom id="1"> <VRPTx:distance_rms_dev>0.800</VRPTx:distance_rms_dev> <VRPTx:distance_rms_dev_medoid>0.652</VRPTx:distance_rms_dev_medoid> <VRPTx:error>success</VRPTx:error> <VRPTx:medoid_model_number>3</VRPTx:medoid_model_number> <VRPTx:number_of_gaps>2</VRPTx:number_of_gaps> <VRPTx:number_of_monomers>96</VRPTx:number_of_monomers> </VRPTx:pdbx_struct_nmr_ens_dom> </VRPTx:pdbx_struct_nmr_ens_domCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_struct_nmr_ens_domCategory This property indicates that datablock has a category holder pdbx_struct_nmr_ens_domCategory. pdbx_struct_nmr_ens_domCategory This property indicates that pdbx_struct_nmr_ens_domCategory. has a category pdbx_struct_nmr_ens_dom. pdbx_struct_nmr_ens_domItem Abstract datatype property for pdbx_struct_nmr_ens_dom items. reference_to_pdbx_struct_nmr_ens_dom cross-reference to pdbx_struct_nmr_ens_dom. referenced_by_pdbx_struct_nmr_ens_dom cross-reference from pdbx_struct_nmr_ens_dom. pdbx_struct_nmr_ens_dom.distance_rms_dev The average backbone distance rmsd of the each well formed domain regions over the NMR ensemble structures. 0.800 pdbx_struct_nmr_ens_dom.distance_rms_dev_medoid The average backbone distance rmsd to the medoid domain model of the other models in the NMR ensemble structures. 0.652 pdbx_struct_nmr_ens_dom.error Details of any error or warning messages. pdbx_struct_nmr_ens_dom.medoid_model_number Describes the medoid model number of the domain. pdbx_struct_nmr_ens_dom.number_of_gaps The number of dropout residues from continuous polypeptide chain within the each well formed domain. 2 pdbx_struct_nmr_ens_dom.number_of_monomers The number of residues constituting the each well formed domain. 96 pdbx_struct_nmr_ens_dom.percent_of_core The percentage of the individual well formed domain in the entire well formed regions. pdbx_struct_nmr_ens_dom.id The value of attribute id in category pdbx_struct_nmr_ens_dom must uniquely identify a record in the PDBX_STRUCT_NMR_ENS_DOM list. 0 pdbx_struct_nmr_ens_dom_lim Data items in the PDBX_STRUCT_NMR_ENS_DOM_LIM category identify the start and end points of generated polypeptide chain segments (domains) of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_dom_limCategory> <VRPTx:pdbx_struct_nmr_ens_dom_lim component_id="1" dom_id="1"> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>THR</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>515</VRPTx:beg_auth_seq_id> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>THR</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>525</VRPTx:end_auth_seq_id> </VRPTx:pdbx_struct_nmr_ens_dom_lim> <VRPTx:pdbx_struct_nmr_ens_dom_lim component_id="2" dom_id="1"> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>ASN</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>530</VRPTx:beg_auth_seq_id> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>LYS</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>555</VRPTx:end_auth_seq_id> </VRPTx:pdbx_struct_nmr_ens_dom_lim> <VRPTx:pdbx_struct_nmr_ens_dom_lim component_id="3" dom_id="1"> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>ASP</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>560</VRPTx:beg_auth_seq_id> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>ARG</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>616</VRPTx:end_auth_seq_id> </VRPTx:pdbx_struct_nmr_ens_dom_lim> </VRPTx:pdbx_struct_nmr_ens_dom_limCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_struct_nmr_ens_dom_limCategory This property indicates that datablock has a category holder pdbx_struct_nmr_ens_dom_limCategory. pdbx_struct_nmr_ens_dom_limCategory This property indicates that pdbx_struct_nmr_ens_dom_limCategory. has a category pdbx_struct_nmr_ens_dom_lim. pdbx_struct_nmr_ens_dom_limItem Abstract datatype property for pdbx_struct_nmr_ens_dom_lim items. reference_to_pdbx_struct_nmr_ens_dom_lim cross-reference to pdbx_struct_nmr_ens_dom_lim. referenced_by_pdbx_struct_nmr_ens_dom_lim cross-reference from pdbx_struct_nmr_ens_dom_lim. pdbx_struct_nmr_ens_dom_lim.beg_auth_asym_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_nmr_ens_dom_lim.beg_auth_comp_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_nmr_ens_dom_lim.beg_auth_seq_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_nmr_ens_dom_lim.end_auth_asym_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_nmr_ens_dom_lim.end_auth_comp_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_nmr_ens_dom_lim.end_auth_seq_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_nmr_ens_dom_lim.component_id Record number of the NMR domain limit assignment. pdbx_struct_nmr_ens_dom_lim.dom_id This data item is a pointer to attribute id in category pdbx_struct_nmr_ens_dom in the PDBX_STRUCT_NMR_ENS_DOM_LIM category. 0 pdbx_struct_oper_list Data items in the PDBX_STRUCT_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry. Example 1 - <VRPTx:pdbx_struct_oper_listCategory> <VRPTx:pdbx_struct_oper_list id="2"> <VRPTx:matrix11>0.247</VRPTx:matrix11> <VRPTx:matrix12>0.935</VRPTx:matrix12> <VRPTx:matrix13>0.256</VRPTx:matrix13> <VRPTx:matrix21>0.929</VRPTx:matrix21> <VRPTx:matrix22>0.153</VRPTx:matrix22> <VRPTx:matrix23>0.337</VRPTx:matrix23> <VRPTx:matrix31>0.276</VRPTx:matrix31> <VRPTx:matrix32>0.321</VRPTx:matrix32> <VRPTx:matrix33>-0.906</VRPTx:matrix33> <VRPTx:type>point symmetry operation</VRPTx:type> <VRPTx:vector1>-8.253</VRPTx:vector1> <VRPTx:vector2>-11.743</VRPTx:vector2> <VRPTx:vector3>-1.782</VRPTx:vector3> </VRPTx:pdbx_struct_oper_list> </VRPTx:pdbx_struct_oper_listCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 pdbx_struct_oper_listCategory This property indicates that datablock has a category holder pdbx_struct_oper_listCategory. pdbx_struct_oper_listCategory This property indicates that pdbx_struct_oper_listCategory. has a category pdbx_struct_oper_list. pdbx_struct_oper_listItem Abstract datatype property for pdbx_struct_oper_list items. reference_to_pdbx_struct_oper_list cross-reference to pdbx_struct_oper_list. referenced_by_pdbx_struct_oper_list cross-reference from pdbx_struct_oper_list. pdbx_struct_oper_list.matrix11 The [1][1] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix12 The [1][2] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix13 The [1][3] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix21 The [2][1] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix22 The [2][2] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix23 The [2][3] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix31 The [3][1] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix32 The [3][2] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.matrix33 The [3][3] element of the 3x3 matrix component of the transformation operation. pdbx_struct_oper_list.name A descriptive name for the transformation operation. 1_555 two-fold rotation pdbx_struct_oper_list.symmetry_operation The symmetry operation corresponding to the transformation operation. x,y,z x+1/2,y,-z identity operation point symmetry operation helical symmetry operation crystal symmetry operation 3D crystal symmetry operation 2D crystal symmetry operation transform to point frame transform to helical frame transform to crystal frame transform to 2D crystal frame transform to 3D crystal frame build point asymmetric unit build helical asymmetric unit build 2D crystal asymmetric unit build 3D crystal asymmetric unit A code to indicate the type of operator. pdbx_struct_oper_list.vector1 The [1] element of the three-element vector component of the transformation operation. pdbx_struct_oper_list.vector2 The [2] element of the three-element vector component of the transformation operation. pdbx_struct_oper_list.vector3 The [3] element of the three-element vector component of the transformation operation. pdbx_struct_oper_list.id This identifier code must uniquely identify a record in the PDBX_STRUCT_OPER_LIST list. 0 pdbx_struct_ref_seq_deletion Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate deletions in the sequence of the entity described in the referenced database entry. Example 1 - <VRPTx:pdbx_struct_ref_seq_deletionCategory> <VRPTx:pdbx_struct_ref_seq_deletion id="1"> <VRPTx:asym_id>A</VRPTx:asym_id> <VRPTx:comp_id>LEU</VRPTx:comp_id> <VRPTx:db_code>P15456</VRPTx:db_code> <VRPTx:db_name>UNP</VRPTx:db_name> <VRPTx:db_seq_id>23</VRPTx:db_seq_id> <VRPTx:details xsi:nil="true" /> </VRPTx:pdbx_struct_ref_seq_deletion> <VRPTx:pdbx_struct_ref_seq_deletion id="1"> <VRPTx:asym_id>A</VRPTx:asym_id> <VRPTx:comp_id>THR</VRPTx:comp_id> <VRPTx:db_code>P15456</VRPTx:db_code> <VRPTx:db_name>UNP</VRPTx:db_name> <VRPTx:db_seq_id>24</VRPTx:db_seq_id> <VRPTx:details xsi:nil="true" /> </VRPTx:pdbx_struct_ref_seq_deletion> <VRPTx:pdbx_struct_ref_seq_deletion id="1"> <VRPTx:asym_id>A</VRPTx:asym_id> <VRPTx:comp_id>GLN</VRPTx:comp_id> <VRPTx:db_code>P15456</VRPTx:db_code> <VRPTx:db_name>UNP</VRPTx:db_name> <VRPTx:db_seq_id>25</VRPTx:db_seq_id> <VRPTx:details xsi:nil="true" /> </VRPTx:pdbx_struct_ref_seq_deletion> </VRPTx:pdbx_struct_ref_seq_deletionCategory> 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_struct_ref_seq_deletionCategory This property indicates that datablock has a category holder pdbx_struct_ref_seq_deletionCategory. pdbx_struct_ref_seq_deletionCategory This property indicates that pdbx_struct_ref_seq_deletionCategory. has a category pdbx_struct_ref_seq_deletion. pdbx_struct_ref_seq_deletionItem Abstract datatype property for pdbx_struct_ref_seq_deletion items. reference_to_pdbx_struct_ref_seq_deletion cross-reference to pdbx_struct_ref_seq_deletion. referenced_by_pdbx_struct_ref_seq_deletion cross-reference from pdbx_struct_ref_seq_deletion. pdbx_struct_ref_seq_deletion.asym_id Identifies the polymer entity instance in this entry corresponding to the reference sequence in which the deletion is specified. This data item is a pointer to attribute asym_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_deletion.comp_id The monomer name found at this position in the referenced database entry. pdbx_struct_ref_seq_deletion.db_code The code for this entity or biological unit or for a closely related entity or biological unit in the named database. pdbx_struct_ref_seq_deletion.db_name The name of the database containing reference information about this entity or biological unit. pdbx_struct_ref_seq_deletion.db_seq_id This data item is the database sequence numbering of the deleted residue pdbx_struct_ref_seq_deletion.details A description of any special aspects of the deletion pdbx_struct_ref_seq_deletion.id The value of attribute id in category pdbx_struct_ref_seq_deletion must uniquely identify a record in the PDBX_STRUCT_REF_SEQ_DELETION list. 0 pdbx_struct_ref_seq_insertion Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate insertions in the sequence of the entity described in the referenced database entry. Example 1 - <VRPTx:pdbx_struct_ref_seq_insertionCategory> <VRPTx:pdbx_struct_ref_seq_insertion id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:asym_id>A</VRPTx:asym_id> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_seq_id>104</VRPTx:auth_seq_id> <VRPTx:comp_id>GLY</VRPTx:comp_id> <VRPTx:db_code>P00752</VRPTx:db_code> <VRPTx:db_name>UNP</VRPTx:db_name> <VRPTx:details>INSERTION</VRPTx:details> <VRPTx:seq_id>102</VRPTx:seq_id> </VRPTx:pdbx_struct_ref_seq_insertion> <VRPTx:pdbx_struct_ref_seq_insertion id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:asym_id>A</VRPTx:asym_id> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_seq_id>105</VRPTx:auth_seq_id> <VRPTx:comp_id>TRP</VRPTx:comp_id> <VRPTx:db_code>P00752</VRPTx:db_code> <VRPTx:db_name>UNP</VRPTx:db_name> <VRPTx:details>INSERTION</VRPTx:details> <VRPTx:seq_id>103</VRPTx:seq_id> </VRPTx:pdbx_struct_ref_seq_insertion> </VRPTx:pdbx_struct_ref_seq_insertionCategory> 0 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 pdbx_struct_ref_seq_insertionCategory This property indicates that datablock has a category holder pdbx_struct_ref_seq_insertionCategory. pdbx_struct_ref_seq_insertionCategory This property indicates that pdbx_struct_ref_seq_insertionCategory. has a category pdbx_struct_ref_seq_insertion. pdbx_struct_ref_seq_insertionItem Abstract datatype property for pdbx_struct_ref_seq_insertion items. reference_to_pdbx_struct_ref_seq_insertion cross-reference to pdbx_struct_ref_seq_insertion. referenced_by_pdbx_struct_ref_seq_insertion cross-reference from pdbx_struct_ref_seq_insertion. pdbx_struct_ref_seq_insertion.PDB_ins_code Part of the author identifier of the inserted residue. This data item is a pointer to attribute pdb_ins_code in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_insertion.asym_id Part of the identifier of the inserted residue. This data item is a pointer to attribute asym_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_insertion.auth_asym_id Part of the author identifier of the inserted residue. This data item is a pointer to attribute pdb_strand_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_insertion.auth_seq_id Part of the author identifier of the inserted residue. This data item is a pointer to attribute auth_seq_num in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_insertion.comp_id Part of the identifier of the inserted residue. This data item is a pointer to attribute mon_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_insertion.db_code The code for this entity or biological unit or for a closely related entity or biological unit in the named database. pdbx_struct_ref_seq_insertion.db_name The name of the database containing reference information about this entity or biological unit. pdbx_struct_ref_seq_insertion.details A description of any special aspects of the insertion pdbx_struct_ref_seq_insertion.seq_id Part of the author identifier of the inserted residue. This data item is a pointer to attribute seq_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. pdbx_struct_ref_seq_insertion.id The value of attribute id in category pdbx_struct_ref_seq_insertion must uniquely identify a record in the PDBX_STRUCT_REF_SEQ_INSERTION list. 0 pdbx_struct_sheet_hbond Data items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet. This category is provided for cases where only a single hydrogen bond is used to register the two residue ranges. Category STRUCT_SHEET_HBOND should be used when the initial and terminal hydrogen bonds for strand pair are known. 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 1 1 pdbx_struct_sheet_hbondCategory This property indicates that datablock has a category holder pdbx_struct_sheet_hbondCategory. pdbx_struct_sheet_hbondCategory This property indicates that pdbx_struct_sheet_hbondCategory. has a category pdbx_struct_sheet_hbond. pdbx_struct_sheet_hbondItem Abstract datatype property for pdbx_struct_sheet_hbond items. reference_to_pdbx_struct_sheet_hbond cross-reference to pdbx_struct_sheet_hbond. referenced_by_pdbx_struct_sheet_hbond cross-reference from pdbx_struct_sheet_hbond. pdbx_struct_sheet_hbond.range_1_PDB_ins_code A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_auth_asym_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_auth_atom_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_auth_comp_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_auth_seq_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_label_asym_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_label_atom_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_label_comp_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_1_label_seq_id A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_PDB_ins_code A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_auth_asym_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_auth_atom_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_auth_comp_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_auth_seq_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_label_asym_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_label_atom_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_label_comp_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_2_label_seq_id A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_sheet_hbond.range_id_1 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. pdbx_struct_sheet_hbond.range_id_2 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. pdbx_struct_sheet_hbond.sheet_id This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. 0 pdbx_struct_special_symmetry Data items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the molecular components that lie on special symmetry positions. Example 1 - <VRPTx:pdbx_struct_special_symmetryCategory> <VRPTx:pdbx_struct_special_symmetry id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>Q</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>ATP</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> </VRPTx:pdbx_struct_special_symmetry> </VRPTx:pdbx_struct_special_symmetryCategory> 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 pdbx_struct_special_symmetryCategory This property indicates that datablock has a category holder pdbx_struct_special_symmetryCategory. pdbx_struct_special_symmetryCategory This property indicates that pdbx_struct_special_symmetryCategory. has a category pdbx_struct_special_symmetry. pdbx_struct_special_symmetryItem Abstract datatype property for pdbx_struct_special_symmetry items. reference_to_pdbx_struct_special_symmetry cross-reference to pdbx_struct_special_symmetry. referenced_by_pdbx_struct_special_symmetry cross-reference from pdbx_struct_special_symmetry. pdbx_struct_special_symmetry.PDB_ins_code Part of the identifier for the molecular component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.PDB_model_num Part of the identifier for the molecular component. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.auth_asym_id Part of the identifier for the molecular component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.auth_comp_id Part of the identifier for the molecular component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.auth_seq_id Part of the identifier for the molecular component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.label_alt_id Part of the identifier for the molecular component. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.label_asym_id Part of the identifier for the molecular component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.label_comp_id Part of the identifier for the molecular component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.label_seq_id Part of the identifier for the molecular component. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_struct_special_symmetry.id The value of attribute id in category pdbx_struct_special_symmetry must uniquely identify each item in the PDBX_STRUCT_SPECIAL_SYMMETRY list. This is an integer serial number. 0 pdbx_unobs_or_zero_occ_atoms Data items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the atoms within the entry that are either unobserved or have zero occupancy/ Example 1 - <VRPTx:pdbx_unobs_or_zero_occ_atomsCategory> <VRPTx:pdbx_unobs_or_zero_occ_atoms id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>CG</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_atoms> <VRPTx:pdbx_unobs_or_zero_occ_atoms id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>CD</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_atoms> <VRPTx:pdbx_unobs_or_zero_occ_atoms id="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>NE</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_atoms> <VRPTx:pdbx_unobs_or_zero_occ_atoms id="4"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>CZ</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_atoms> <VRPTx:pdbx_unobs_or_zero_occ_atoms id="5"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>NH1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_atoms> <VRPTx:pdbx_unobs_or_zero_occ_atoms id="6"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>NH2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>412</VRPTx:auth_seq_id> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_atoms> </VRPTx:pdbx_unobs_or_zero_occ_atomsCategory> 0 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 pdbx_unobs_or_zero_occ_atomsCategory This property indicates that datablock has a category holder pdbx_unobs_or_zero_occ_atomsCategory. pdbx_unobs_or_zero_occ_atomsCategory This property indicates that pdbx_unobs_or_zero_occ_atomsCategory. has a category pdbx_unobs_or_zero_occ_atoms. pdbx_unobs_or_zero_occ_atomsItem Abstract datatype property for pdbx_unobs_or_zero_occ_atoms items. reference_to_pdbx_unobs_or_zero_occ_atoms cross-reference to pdbx_unobs_or_zero_occ_atoms. referenced_by_pdbx_unobs_or_zero_occ_atoms cross-reference from pdbx_unobs_or_zero_occ_atoms. pdbx_unobs_or_zero_occ_atoms.PDB_ins_code Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.PDB_model_num Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.auth_asym_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.auth_atom_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.auth_comp_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.auth_seq_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.label_alt_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.label_asym_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.label_atom_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.label_comp_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_atoms.label_seq_id Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 1 0 The value of occupancy flag indicates whether the atom is either unobserved (=1) or has zero occupancy (=0) Y N The value of polymer flag indicates whether the unobserved or zero occupancy atom is part of a polymer chain pdbx_unobs_or_zero_occ_atoms.id The value of attribute id in category pdbx_unobs_or_zero_occ_atoms must uniquely identify each item in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS list. This is an integer serial number. 0 pdbx_unobs_or_zero_occ_residues Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the residues within the entry that are not observed or have zero occupancy. Example 1 - <VRPTx:pdbx_unobs_or_zero_occ_residuesCategory> <VRPTx:pdbx_unobs_or_zero_occ_residues id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>VAL</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>36</VRPTx:auth_seq_id> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_residues> <VRPTx:pdbx_unobs_or_zero_occ_residues id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>108</VRPTx:auth_seq_id> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>Y</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_residues> <VRPTx:pdbx_unobs_or_zero_occ_residues id="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>D</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>PPI</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>438</VRPTx:auth_seq_id> <VRPTx:occupancy_flag>1</VRPTx:occupancy_flag> <VRPTx:polymer_flag>N</VRPTx:polymer_flag> </VRPTx:pdbx_unobs_or_zero_occ_residues> </VRPTx:pdbx_unobs_or_zero_occ_residuesCategory> 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 1 pdbx_unobs_or_zero_occ_residuesCategory This property indicates that datablock has a category holder pdbx_unobs_or_zero_occ_residuesCategory. pdbx_unobs_or_zero_occ_residuesCategory This property indicates that pdbx_unobs_or_zero_occ_residuesCategory. has a category pdbx_unobs_or_zero_occ_residues. pdbx_unobs_or_zero_occ_residuesItem Abstract datatype property for pdbx_unobs_or_zero_occ_residues items. reference_to_pdbx_unobs_or_zero_occ_residues cross-reference to pdbx_unobs_or_zero_occ_residues. referenced_by_pdbx_unobs_or_zero_occ_residues cross-reference from pdbx_unobs_or_zero_occ_residues. pdbx_unobs_or_zero_occ_residues.PDB_ins_code Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.PDB_model_num Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.auth_asym_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.auth_comp_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.auth_seq_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.label_asym_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.label_comp_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_unobs_or_zero_occ_residues.label_seq_id Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 1 0 The value of occupancy flag indicates whether the residue is unobserved (= 1) or the coordinates have an occupancy of zero (=0) Y N The value of polymer flag indicates whether the unobserved or zero occupancy residue is part of a polymer chain or not pdbx_unobs_or_zero_occ_residues.id The value of attribute id in category pdbx_unobs_or_zero_occ_residues must uniquely identify each item in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES list. This is an integer serial number. 0 pdbx_validate_chiral Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0 Example 1 - <VRPTx:pdbx_validate_chiralCategory> <VRPTx:pdbx_validate_chiral id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>ASP</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>B</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>405</VRPTx:auth_seq_id> <VRPTx:details>ALPHA-CARBON</VRPTx:details> <VRPTx:omega>150.48</VRPTx:omega> </VRPTx:pdbx_validate_chiral> </VRPTx:pdbx_validate_chiralCategory> 0 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 0 1 1 pdbx_validate_chiralCategory This property indicates that datablock has a category holder pdbx_validate_chiralCategory. pdbx_validate_chiralCategory This property indicates that pdbx_validate_chiralCategory. has a category pdbx_validate_chiral. pdbx_validate_chiralItem Abstract datatype property for pdbx_validate_chiral items. reference_to_pdbx_validate_chiral cross-reference to pdbx_validate_chiral. referenced_by_pdbx_validate_chiral cross-reference from pdbx_validate_chiral. pdbx_validate_chiral.PDB_ins_code Optional identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.PDB_model_num The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.auth_asym_id Part of the identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.auth_atom_id Part of the identifier of the residue This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.auth_comp_id Part of the identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.auth_seq_id Part of the identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.details A description of the outlier angle e.g. ALPHA-CARBON pdbx_validate_chiral.label_alt_id Part of the identifier of the residue This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_chiral.omega The value of the OMEGA angle for the peptide linkage between the two defined residues pdbx_validate_chiral.id The value of attribute id in category pdbx_validate_chiral must uniquely identify each item in the PDBX_VALIDATE_CHIRAL list. This is an integer serial number. 0 pdbx_validate_close_contact Data items in the PDBX_VALIDATE_CLOSE_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts within the asymmetric unit are considered. For those contacts not involving hydrogen a limit of 2.2 angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 angstroms is used. Example 1 - <VRPTx:pdbx_validate_close_contactCategory> <VRPTx:pdbx_validate_close_contact id="1"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2> <VRPTx:auth_atom_id_1 xsi:nil="true" /> <VRPTx:auth_atom_id_2 xsi:nil="true" /> <VRPTx:auth_comp_id_1>VAL</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>ARG</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>36</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>108</VRPTx:auth_seq_id_2> <VRPTx:dist>2.16</VRPTx:dist> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> </VRPTx:pdbx_validate_close_contact> <VRPTx:pdbx_validate_close_contact id="2"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2> <VRPTx:auth_atom_id_1 xsi:nil="true" /> <VRPTx:auth_atom_id_2 xsi:nil="true" /> <VRPTx:auth_comp_id_1>ARG</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>VAL</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>108</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>36</VRPTx:auth_seq_id_2> <VRPTx:dist>2.16</VRPTx:dist> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> </VRPTx:pdbx_validate_close_contact> </VRPTx:pdbx_validate_close_contactCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 1 pdbx_validate_close_contactCategory This property indicates that datablock has a category holder pdbx_validate_close_contactCategory. pdbx_validate_close_contactCategory This property indicates that pdbx_validate_close_contactCategory. has a category pdbx_validate_close_contact. pdbx_validate_close_contactItem Abstract datatype property for pdbx_validate_close_contact items. reference_to_pdbx_validate_close_contact cross-reference to pdbx_validate_close_contact. referenced_by_pdbx_validate_close_contact cross-reference from pdbx_validate_close_contact. pdbx_validate_close_contact.PDB_ins_code_1 Optional identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.PDB_ins_code_2 Optional identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.PDB_model_num The model number for the given contact pdbx_validate_close_contact.auth_asym_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_asym_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_atom_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_atom_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_comp_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_comp_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_seq_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.auth_seq_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.clash_magnitude The difference in angstroms between the observed interatomic distance and the sum of the van der Waals radii of the atoms involved. pdbx_validate_close_contact.dist The value of the close contact for the two atoms defined. pdbx_validate_close_contact.label_alt_id_1 An optional identifier of the first of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.label_alt_id_2 An optional identifier of the second of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_close_contact.symm_as_xyz_1 The symmetry of the first of the two atoms define the close contact. The symmetry equivalent position is given in the 'xyz' representation. pdbx_validate_close_contact.symm_as_xyz_2 The symmetry of the second of the two atoms define the close contact. The symmetry equivalent position is given in the 'xyz' representation. pdbx_validate_close_contact.id The value of attribute id in category pdbx_validate_close_contact must uniquely identify each item in the PDBX_VALIDATE_CLOSE_CONTACT list. This is an integer serial number. 0 pdbx_validate_main_chain_plane Data items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the residues that contain unexpected deviations from planes for main chain atoms as defined by the improper torsion angle describing planarity: PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5 as a pseudo torsion Example 1 - <VRPTx:pdbx_validate_main_chain_planeCategory> <VRPTx:pdbx_validate_main_chain_plane id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>G</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>TRP</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>20</VRPTx:auth_seq_id> <VRPTx:improper_torsion_angle>29.901</VRPTx:improper_torsion_angle> </VRPTx:pdbx_validate_main_chain_plane> <VRPTx:pdbx_validate_main_chain_plane id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>G</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>TRP</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>21</VRPTx:auth_seq_id> <VRPTx:improper_torsion_angle>-42.450</VRPTx:improper_torsion_angle> </VRPTx:pdbx_validate_main_chain_plane> </VRPTx:pdbx_validate_main_chain_planeCategory> 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 pdbx_validate_main_chain_planeCategory This property indicates that datablock has a category holder pdbx_validate_main_chain_planeCategory. pdbx_validate_main_chain_planeCategory This property indicates that pdbx_validate_main_chain_planeCategory. has a category pdbx_validate_main_chain_plane. pdbx_validate_main_chain_planeItem Abstract datatype property for pdbx_validate_main_chain_plane items. reference_to_pdbx_validate_main_chain_plane cross-reference to pdbx_validate_main_chain_plane. referenced_by_pdbx_validate_main_chain_plane cross-reference from pdbx_validate_main_chain_plane. pdbx_validate_main_chain_plane.PDB_ins_code Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_main_chain_plane.PDB_model_num The model number for the residue in which the plane is calculated This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_main_chain_plane.auth_asym_id Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_main_chain_plane.auth_comp_id Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_main_chain_plane.auth_seq_id Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_main_chain_plane.improper_torsion_angle The value for the torsion angle C(i-1) - CA(i-1) - N(i) - O(i-1) pdbx_validate_main_chain_plane.label_alt_id Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_main_chain_plane.id The value of attribute id in category pdbx_validate_main_chain_plane must uniquely identify each item in the PDBX_VALIDATE_MAIN_CHAIN_PLANE list. This is an integer serial number. 0 pdbx_validate_nmr_chem_shift Items in the PDBX_VALIDATE_NMR_CHEM_SHIFT category provide information about assigned chemical shifts that deviate from expected BMRB standards by 5 * the expected RMSD. 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_validate_nmr_chem_shiftCategory This property indicates that datablock has a category holder pdbx_validate_nmr_chem_shiftCategory. pdbx_validate_nmr_chem_shiftCategory This property indicates that pdbx_validate_nmr_chem_shiftCategory. has a category pdbx_validate_nmr_chem_shift. pdbx_validate_nmr_chem_shiftItem Abstract datatype property for pdbx_validate_nmr_chem_shift items. reference_to_pdbx_validate_nmr_chem_shift cross-reference to pdbx_validate_nmr_chem_shift. referenced_by_pdbx_validate_nmr_chem_shift cross-reference from pdbx_validate_nmr_chem_shift. pdbx_validate_nmr_chem_shift.Zscore Z score of the assigned chemical shift expected from the BMRB statistics. pdbx_validate_nmr_chem_shift.auth_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_nmr_chem_shift.auth_atom_id Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_nmr_chem_shift.auth_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_nmr_chem_shift.auth_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_nmr_chem_shift.method Method used to detect chemical shift outliers. pdbx_validate_nmr_chem_shift.target_val The target value of the assigned chemical shift expected from the BMRB statistics. pdbx_validate_nmr_chem_shift.val Assigned chemical shift value in ppm. pdbx_validate_nmr_chem_shift.id The value of attribute id in category pdbx_validate_nmr_chem_shift must uniquely identify each item in the PDBX_VALIDATE_NMR_CHEM_SHIFT list. This is an integer serial number. pdbx_validate_nmr_chem_shift.list_id Pointer to attribute id in category pdbx_nmr_assigned_chem_shift_list. 0 pdbx_validate_peptide_omega Data items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the residues that contain peptide bonds deviate significantly from both cis and trans conformation. cis bonds, if any, are listed on cispep records. trans is defined as 180 +/- 30 and cis is defined as 0 +/- 30 degrees. Example 1 - <VRPTx:pdbx_validate_peptide_omegaCategory> <VRPTx:pdbx_validate_peptide_omega id="1"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>ASP</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>ARG</VRPTx:auth_asym_id_2> <VRPTx:auth_comp_id_1>A</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>A</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>414</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>413</VRPTx:auth_seq_id_2> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:omega>147.84</VRPTx:omega> </VRPTx:pdbx_validate_peptide_omega> <VRPTx:pdbx_validate_peptide_omega id="2"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>ASN</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>ALA</VRPTx:auth_asym_id_2> <VRPTx:auth_comp_id_1>B</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>B</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>289</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>288</VRPTx:auth_seq_id_2> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:omega>-39.12</VRPTx:omega> </VRPTx:pdbx_validate_peptide_omega> </VRPTx:pdbx_validate_peptide_omegaCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 pdbx_validate_peptide_omegaCategory This property indicates that datablock has a category holder pdbx_validate_peptide_omegaCategory. pdbx_validate_peptide_omegaCategory This property indicates that pdbx_validate_peptide_omegaCategory. has a category pdbx_validate_peptide_omega. pdbx_validate_peptide_omegaItem Abstract datatype property for pdbx_validate_peptide_omega items. reference_to_pdbx_validate_peptide_omega cross-reference to pdbx_validate_peptide_omega. referenced_by_pdbx_validate_peptide_omega cross-reference from pdbx_validate_peptide_omega. pdbx_validate_peptide_omega.PDB_ins_code_1 Optional identifier of the first residue in the bond This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.PDB_ins_code_2 Optional identifier of the second residue in the bond This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.PDB_model_num The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.auth_asym_id_1 Part of the identifier of the first residue in the bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.auth_asym_id_2 Part of the identifier of the second residue in the bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.auth_comp_id_1 Part of the identifier of the first residue in the bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.auth_comp_id_2 Part of the identifier of the second residue in the bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.auth_seq_id_1 Part of the identifier of the first residue in the bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.auth_seq_id_2 Part of the identifier of the second residue in the bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.label_alt_id_1 Optional identifier of the first residue in the torsion angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.label_alt_id_2 Optional identifier of the second residue in the torsion angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_peptide_omega.omega The value of the OMEGA angle for the peptide linkage between the two defined residues pdbx_validate_peptide_omega.id The value of attribute id in category pdbx_validate_peptide_omega must uniquely identify each item in the PDBX_VALIDATE_PEPTIDE_OMEGA list. This is an integer serial number. 0 pdbx_validate_planes Data items in the PDBX_VALIDATE_PLANES category list the residues that contain unexpected deviations from planes centers. Example 1 - <VRPTx:pdbx_validate_planesCategory> <VRPTx:pdbx_validate_planes id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>DG</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:rmsd>0.068</VRPTx:rmsd> <VRPTx:type>SIDE CHAIN</VRPTx:type> </VRPTx:pdbx_validate_planes> <VRPTx:pdbx_validate_planes id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>DT</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>4</VRPTx:auth_seq_id> <VRPTx:rmsd>0.198</VRPTx:rmsd> <VRPTx:type>SIDE CHAIN</VRPTx:type> </VRPTx:pdbx_validate_planes> <VRPTx:pdbx_validate_planes id="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>DC</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>8</VRPTx:auth_seq_id> <VRPTx:rmsd>0.090</VRPTx:rmsd> <VRPTx:type>SIDE CHAIN</VRPTx:type> </VRPTx:pdbx_validate_planes> </VRPTx:pdbx_validate_planesCategory> 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 pdbx_validate_planesCategory This property indicates that datablock has a category holder pdbx_validate_planesCategory. pdbx_validate_planesCategory This property indicates that pdbx_validate_planesCategory. has a category pdbx_validate_planes. pdbx_validate_planesItem Abstract datatype property for pdbx_validate_planes items. reference_to_pdbx_validate_planes cross-reference to pdbx_validate_planes. referenced_by_pdbx_validate_planes cross-reference from pdbx_validate_planes. pdbx_validate_planes.PDB_ins_code Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_planes.PDB_model_num The model number for the given angle This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_planes.auth_asym_id Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes.auth_comp_id Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes.auth_seq_id Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes.label_alt_id Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes.rmsd The value of the overall deviation from ideal plane for the atoms defining the plane. MAIN_CHAIN SIDE_CHAIN MAIN CHAIN SIDE CHAIN The type of plane - MAIN CHAIN or SIDE CHAIN atoms pdbx_validate_planes.id The value of attribute id in category pdbx_validate_planes must uniquely identify each item in the PDBX_VALIDATE_PLANES list. This is an integer serial number. 0 pdbx_validate_planes_atom Data items in the PDBX_VALIDATE_PLANES_ATOM category list the residues that contain unexpected deviations from planes centers. Example 1 - <VRPTx:pdbx_validate_planes_atomCategory> <VRPTx:pdbx_validate_planes_atom id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.003</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>N1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.011</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="3"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.074</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>N2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="4"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.005</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>N3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="5"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.010</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C4</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="6"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.029</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="7"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.039</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="8"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.074</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>O6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="9"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.050</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>N7</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="10"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.129</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C8</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="11"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.033</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>N9</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="12"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.147</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1&apos;</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>3</VRPTx:auth_seq_id> <VRPTx:plane_id>1</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> <VRPTx:pdbx_validate_planes_atom id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:atom_deviation>0.069</VRPTx:atom_deviation> <VRPTx:auth_asym_id>DT</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>N1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>A</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>4</VRPTx:auth_seq_id> <VRPTx:plane_id>2</VRPTx:plane_id> </VRPTx:pdbx_validate_planes_atom> </VRPTx:pdbx_validate_planes_atomCategory> 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 pdbx_validate_planes_atomCategory This property indicates that datablock has a category holder pdbx_validate_planes_atomCategory. pdbx_validate_planes_atomCategory This property indicates that pdbx_validate_planes_atomCategory. has a category pdbx_validate_planes_atom. pdbx_validate_planes_atomItem Abstract datatype property for pdbx_validate_planes_atom items. reference_to_pdbx_validate_planes_atom cross-reference to pdbx_validate_planes_atom. referenced_by_pdbx_validate_planes_atom cross-reference from pdbx_validate_planes_atom. pdbx_validate_planes_atom.PDB_ins_code Optional identifier of an atom site that defines the plane pdbx_validate_planes_atom.PDB_model_num The model number for an atom site defining the plane This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_planes_atom.atom_deviation The deviation from the plane per atom pdbx_validate_planes_atom.auth_asym_id Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes_atom.auth_atom_id Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes_atom.auth_comp_id Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes_atom.auth_seq_id Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_planes_atom.plane_id A pointer to attribute id in category pdbx_validate_planes This is an integer serial number. pdbx_validate_planes_atom.id The value of attribute id in category pdbx_validate_planes_atom must uniquely identify each item in the PDBX_VALIDATE_PLANES_ATOM list. This is an integer serial number. 0 pdbx_validate_polymer_linkage Data items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the polymer linkages within the entry that are outside of typical covalent distances. Example 1 - <VRPTx:pdbx_validate_polymer_linkageCategory> <VRPTx:pdbx_validate_polymer_linkage id="1"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2> <VRPTx:auth_atom_id_1 xsi:nil="true" /> <VRPTx:auth_atom_id_2 xsi:nil="true" /> <VRPTx:auth_comp_id_1>VAL</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>ARG</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>107</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>108</VRPTx:auth_seq_id_2> <VRPTx:dist>3.16</VRPTx:dist> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> </VRPTx:pdbx_validate_polymer_linkage> <VRPTx:pdbx_validate_polymer_linkage id="2"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2> <VRPTx:auth_atom_id_1 xsi:nil="true" /> <VRPTx:auth_atom_id_2 xsi:nil="true" /> <VRPTx:auth_comp_id_1>ARG</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>LYS</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>110</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>110</VRPTx:auth_seq_id_2> <VRPTx:dist>2.95</VRPTx:dist> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> </VRPTx:pdbx_validate_polymer_linkage> </VRPTx:pdbx_validate_polymer_linkageCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 pdbx_validate_polymer_linkageCategory This property indicates that datablock has a category holder pdbx_validate_polymer_linkageCategory. pdbx_validate_polymer_linkageCategory This property indicates that pdbx_validate_polymer_linkageCategory. has a category pdbx_validate_polymer_linkage. pdbx_validate_polymer_linkageItem Abstract datatype property for pdbx_validate_polymer_linkage items. reference_to_pdbx_validate_polymer_linkage cross-reference to pdbx_validate_polymer_linkage. referenced_by_pdbx_validate_polymer_linkage cross-reference from pdbx_validate_polymer_linkage. pdbx_validate_polymer_linkage.PDB_ins_code_1 Optional identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.PDB_ins_code_2 Optional identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.PDB_model_num The model number for the given linkage pdbx_validate_polymer_linkage.auth_asym_id_1 Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_asym_id_2 Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_atom_id_1 Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_atom_id_2 Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_comp_id_1 Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_comp_id_2 Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_seq_id_1 Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.auth_seq_id_2 Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.dist The value of the polymer linkage for the two atoms defined. pdbx_validate_polymer_linkage.label_alt_id_1 An optional identifier of the first of the two atoms that define the linkage. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.label_alt_id_2 An optional identifier of the second of the two atoms that define the linkage. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_polymer_linkage.id The value of attribute id in category pdbx_validate_polymer_linkage must uniquely identify each item in the PDBX_VALIDATE_POLYMER_LINKAGE list. This is an integer serial number. 0 pdbx_validate_rmsd_angle Data items in the PDBX_VALIDATE_RMSD_ANGLE category list the covalent bond angles found in an entry that have values which deviate from expected values by more than 6*rmsd for the particular entry from the expected standard value Example 1 - <VRPTx:pdbx_validate_rmsd_angleCategory> <VRPTx:pdbx_validate_rmsd_angle id="1"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_ins_code_3 xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:angle_deviation>-3.14</VRPTx:angle_deviation> <VRPTx:angle_value>117.16</VRPTx:angle_value> <VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2> <VRPTx:auth_asym_id_3>A</VRPTx:auth_asym_id_3> <VRPTx:auth_atom_id_1>NE</VRPTx:auth_atom_id_1> <VRPTx:auth_atom_id_2>CZ</VRPTx:auth_atom_id_2> <VRPTx:auth_atom_id_3>NH2</VRPTx:auth_atom_id_3> <VRPTx:auth_comp_id_1>ARG</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>ARG</VRPTx:auth_comp_id_2> <VRPTx:auth_comp_id_3>ARG</VRPTx:auth_comp_id_3> <VRPTx:auth_seq_id_1>35</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>35</VRPTx:auth_seq_id_2> <VRPTx:auth_seq_id_3>35</VRPTx:auth_seq_id_3> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:label_alt_id_3 xsi:nil="true" /> <VRPTx:linker_flag>N</VRPTx:linker_flag> </VRPTx:pdbx_validate_rmsd_angle> <VRPTx:pdbx_validate_rmsd_angle id="2"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_ins_code_3 xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:angle_deviation>34.68</VRPTx:angle_deviation> <VRPTx:angle_value>148.88</VRPTx:angle_value> <VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2> <VRPTx:auth_asym_id_3>A</VRPTx:auth_asym_id_3> <VRPTx:auth_atom_id_1>CB</VRPTx:auth_atom_id_1> <VRPTx:auth_atom_id_2>CG</VRPTx:auth_atom_id_2> <VRPTx:auth_atom_id_3>CD</VRPTx:auth_atom_id_3> <VRPTx:auth_comp_id_1>GLU</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>GLU</VRPTx:auth_comp_id_2> <VRPTx:auth_comp_id_3>GLU</VRPTx:auth_comp_id_3> <VRPTx:auth_seq_id_1>166</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>166</VRPTx:auth_seq_id_2> <VRPTx:auth_seq_id_3>166</VRPTx:auth_seq_id_3> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:label_alt_id_3 xsi:nil="true" /> <VRPTx:linker_flag>N</VRPTx:linker_flag> </VRPTx:pdbx_validate_rmsd_angle> </VRPTx:pdbx_validate_rmsd_angleCategory> 0 1 0 1 0 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_validate_rmsd_angleCategory This property indicates that datablock has a category holder pdbx_validate_rmsd_angleCategory. pdbx_validate_rmsd_angleCategory This property indicates that pdbx_validate_rmsd_angleCategory. has a category pdbx_validate_rmsd_angle. pdbx_validate_rmsd_angleItem Abstract datatype property for pdbx_validate_rmsd_angle items. reference_to_pdbx_validate_rmsd_angle cross-reference to pdbx_validate_rmsd_angle. referenced_by_pdbx_validate_rmsd_angle cross-reference from pdbx_validate_rmsd_angle. pdbx_validate_rmsd_angle.PDB_ins_code_1 Optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.PDB_ins_code_2 Optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.PDB_ins_code_3 Optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.PDB_model_num The model number for the given angle pdbx_validate_rmsd_angle.Zscore Z score of the bond angle expected by knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_angle.angle_deviation Value of the deviation (in degrees) from 6*REBI for the angle bounded by the three sites from the expected dictionary value. pdbx_validate_rmsd_angle.angle_minimum_diff_to_kb The minimum difference to the known bond angles in similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_angle.angle_standard_deviation The uncertainty in the target value of the bond angle expressed as a standard deviation. pdbx_validate_rmsd_angle.angle_target_value The target value of the bond angle pdbx_validate_rmsd_angle.angle_value The value of the bond angle pdbx_validate_rmsd_angle.auth_asym_id_1 Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_asym_id_2 Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_asym_id_3 Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_atom_id_1 Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_atom_id_2 Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_atom_id_3 Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_comp_id_1 Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_comp_id_2 Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_comp_id_3 Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_seq_id_1 Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_seq_id_2 Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.auth_seq_id_3 Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.label_alt_id_1 An optional identifier of the first of the three atoms that define the covalent angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.label_alt_id_2 An optional identifier of the second of the three atoms that define the covalent angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.label_alt_id_3 An optional identifier of the third of the three atoms that define the covalent angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_angle.linker_flag A flag to indicate if the angle is between two residues pdbx_validate_rmsd_angle.number_angles_in_kb The number of bond angles in similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_angle.id The value of attribute id in category pdbx_validate_rmsd_angle must uniquely identify each item in the PDBX_VALIDATE_RMSD_ANGLE list. This is an integer serial number. 0 pdbx_validate_rmsd_bond Data items in the PDBX_VALIDATE_RMSD_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd. Example 1 - <VRPTx:pdbx_validate_rmsd_bondCategory> <VRPTx:pdbx_validate_rmsd_bond id="1"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2> <VRPTx:auth_atom_id_1>CD</VRPTx:auth_atom_id_1> <VRPTx:auth_atom_id_2>CE</VRPTx:auth_atom_id_2> <VRPTx:auth_comp_id_1>LYS</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>LYS</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>152</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>152</VRPTx:auth_seq_id_2> <VRPTx:bond_deviation>-0.372</VRPTx:bond_deviation> <VRPTx:bond_value>1.136</VRPTx:bond_value> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:linker_flag>N</VRPTx:linker_flag> </VRPTx:pdbx_validate_rmsd_bond> <VRPTx:pdbx_validate_rmsd_bond id="2"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>0</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1> <VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2> <VRPTx:auth_atom_id_1>CG</VRPTx:auth_atom_id_1> <VRPTx:auth_atom_id_2>CD</VRPTx:auth_atom_id_2> <VRPTx:auth_comp_id_1>GLU</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>GLU</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>166</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>166</VRPTx:auth_seq_id_2> <VRPTx:bond_deviation>-0.622</VRPTx:bond_deviation> <VRPTx:bond_value>0.893</VRPTx:bond_value> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:linker_flag>N</VRPTx:linker_flag> </VRPTx:pdbx_validate_rmsd_bond> </VRPTx:pdbx_validate_rmsd_bondCategory> 0 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_validate_rmsd_bondCategory This property indicates that datablock has a category holder pdbx_validate_rmsd_bondCategory. pdbx_validate_rmsd_bondCategory This property indicates that pdbx_validate_rmsd_bondCategory. has a category pdbx_validate_rmsd_bond. pdbx_validate_rmsd_bondItem Abstract datatype property for pdbx_validate_rmsd_bond items. reference_to_pdbx_validate_rmsd_bond cross-reference to pdbx_validate_rmsd_bond. referenced_by_pdbx_validate_rmsd_bond cross-reference from pdbx_validate_rmsd_bond. pdbx_validate_rmsd_bond.PDB_ins_code_1 Optional identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.PDB_ins_code_2 Optional identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.PDB_model_num The model number for the given bond pdbx_validate_rmsd_bond.Zscore Z score of the bond length expected by knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_bond.auth_asym_id_1 Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_asym_id_2 Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_atom_id_1 Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_atom_id_2 Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_comp_id_1 Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_comp_id_2 Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_seq_id_1 Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.auth_seq_id_2 Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.bond_deviation The value of the deviation from ideal for the defined covalent bond for the two atoms defined. pdbx_validate_rmsd_bond.bond_minimum_diff_to_kb The minimum difference to the known bond lengths in similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_bond.bond_standard_deviation The uncertainty in target value of the bond length expressed as a standard deviation. pdbx_validate_rmsd_bond.bond_target_value The target value of the bond length pdbx_validate_rmsd_bond.bond_value The value of the bond length pdbx_validate_rmsd_bond.label_alt_id_1 An optional identifier of the first of the two atoms that define the covalent bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.label_alt_id_2 An optional identifier of the second of the two atoms that define the covalent bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_bond.linker_flag A flag to indicate if the bond is between two residues pdbx_validate_rmsd_bond.number_bonds_in_kb The number of bonds in similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_bond.id The value of attribute id in category pdbx_validate_rmsd_bond must uniquely identify each item in the PDBX_VALIDATE_RMSD_BOND list. This is an integer serial number. 0 pdbx_validate_rmsd_ring Data items in the PDBX_VALIDATE_RMSD_RING category list the residues that contain unexpected deviations of dihedral angles in a ring conformation. The values are computed by Mogul. Mogul finds the similar ring conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_ringCategory> <VRPTx:pdbx_validate_rmsd_ring id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>5.62</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>73.11</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_ring> <VRPTx:pdbx_validate_rmsd_ring id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>6.08</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>74.52</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_ring> </VRPTx:pdbx_validate_rmsd_ringCategory> 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_validate_rmsd_ringCategory This property indicates that datablock has a category holder pdbx_validate_rmsd_ringCategory. pdbx_validate_rmsd_ringCategory This property indicates that pdbx_validate_rmsd_ringCategory. has a category pdbx_validate_rmsd_ring. pdbx_validate_rmsd_ringItem Abstract datatype property for pdbx_validate_rmsd_ring items. reference_to_pdbx_validate_rmsd_ring cross-reference to pdbx_validate_rmsd_ring. referenced_by_pdbx_validate_rmsd_ring cross-reference from pdbx_validate_rmsd_ring. pdbx_validate_rmsd_ring.PDB_ins_code Optional identifier of the residue in which the ring is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_ring.PDB_model_num The model number for the given ring conformation. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_ring.auth_asym_id Part of the identifier of the residue in which the ring is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_ring.auth_comp_id Part of the identifier of the residue in which the ring is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_ring.auth_seq_id Part of the identifier of the residue in which the ring is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_ring.dihedral_angle_minimum_diff_to_kb The minimum difference to the known dihedral angles in similar ring conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_ring.dihedral_angle_standard_deviation The uncertainty in the target value of the ring conformation expressed as a standard deviation. pdbx_validate_rmsd_ring.dihedral_angle_target_value The target value of the dihedral angle in similar ring conformations. pdbx_validate_rmsd_ring.label_alt_id Optional identifier of the residue in which the ring is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_ring.number_dihedral_angles_in_kb The number of dihedral angles in similar ring conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_ring.id The value of attribute id in category pdbx_validate_rmsd_ring must uniquely identify each item in the PDBX_VALIDATE_RMSD_RING list. This is an integer serial number. 0 pdbx_validate_rmsd_rings_atom Data items in the PDBX_VALIDATE_RMSD_RINGS_ATOM category list the atoms involved in outlier ring conformations instanced in the PDBX_VALIDATE_RMSD_RING category. The values are computed by Mogul. Mogul finds the similar ring conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_rings_atomCategory> <VRPTx:pdbx_validate_rmsd_rings_atom id="1" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="2" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="3" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="4" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="5" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="6" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="1" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="2" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="3" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="4" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="5" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="6" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> </VRPTx:pdbx_validate_rmsd_rings_atomCategory> 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 pdbx_validate_rmsd_rings_atomCategory This property indicates that datablock has a category holder pdbx_validate_rmsd_rings_atomCategory. pdbx_validate_rmsd_rings_atomCategory This property indicates that pdbx_validate_rmsd_rings_atomCategory. has a category pdbx_validate_rmsd_rings_atom. pdbx_validate_rmsd_rings_atomItem Abstract datatype property for pdbx_validate_rmsd_rings_atom items. reference_to_pdbx_validate_rmsd_rings_atom cross-reference to pdbx_validate_rmsd_rings_atom. referenced_by_pdbx_validate_rmsd_rings_atom cross-reference from pdbx_validate_rmsd_rings_atom. pdbx_validate_rmsd_rings_atom.PDB_ins_code Optional identifier of the residue in which the ring is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.PDB_model_num The model number for the given ring conformation. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.auth_asym_id Part of the identifier of the residue in which the ring is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.auth_atom_id Part of the identifier of the atom sites that involved in the outlier ring conformation. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.auth_comp_id Part of the identifier of the residue in which the ring is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.auth_seq_id Part of the identifier of the residue in which the ring is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.label_alt_id Optional identifier of the residue in which the ring is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_rings_atom.id The value of attribute id in category pdbx_validate_rmsd_rings_atom must uniquely identify each item in the PDBX_VALIDATE_RMSD_RINGS_ATOM list. This is an integer serial number. pdbx_validate_rmsd_rings_atom.ring_id Pointer to attribute id in category pdbx_validate_rmsd_ring. 0 pdbx_validate_rmsd_torsion Data items in the PDBX_VALIDATE_RMSD_TORSION category list the residues that contain unexpected deviations of torsion angles. The values are computed by Mogul. Mogul finds the similar conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_torsionCategory> <VRPTx:pdbx_validate_rmsd_torsion id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>5.62</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>73.11</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_torsion> <VRPTx:pdbx_validate_rmsd_torsion id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>6.08</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>74.52</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_torsion> </VRPTx:pdbx_validate_rmsd_torsionCategory> 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_validate_rmsd_torsionCategory This property indicates that datablock has a category holder pdbx_validate_rmsd_torsionCategory. pdbx_validate_rmsd_torsionCategory This property indicates that pdbx_validate_rmsd_torsionCategory. has a category pdbx_validate_rmsd_torsion. pdbx_validate_rmsd_torsionItem Abstract datatype property for pdbx_validate_rmsd_torsion items. reference_to_pdbx_validate_rmsd_torsion cross-reference to pdbx_validate_rmsd_torsion. referenced_by_pdbx_validate_rmsd_torsion cross-reference from pdbx_validate_rmsd_torsion. pdbx_validate_rmsd_torsion.PDB_ins_code Optional identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsion.PDB_model_num The model number for the given torsion angle. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsion.auth_asym_id Part of the identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsion.auth_comp_id Part of the identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsion.auth_seq_id Part of the identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsion.dihedral_angle_minimum_diff_to_kb The minimum difference to the known torsion angles in similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_torsion.dihedral_angle_standard_deviation The uncertainty in the target value of the torsion angle expressed as a standard deviation. pdbx_validate_rmsd_torsion.dihedral_angle_target_value The target value of the dihedral angle in similar conformations. pdbx_validate_rmsd_torsion.dihedral_angle_value The value of the dihedral angle. pdbx_validate_rmsd_torsion.label_alt_id Optional identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsion.number_dihedral_angles_in_kb The number of torsion angles in similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_torsion.percent_dihedral_angles_fitted_to_kb The percent of torsion angles within certain range of the similar conformations archived in knowledge base such as the Cambridge Structural Database (CSD) pdbx_validate_rmsd_torsion.id The value of attribute id in category pdbx_validate_rmsd_torsion must uniquely identify each item in the PDBX_VALIDATE_RMSD_TORSION list. This is an integer serial number. 0 pdbx_validate_rmsd_torsions_atom Data items in the PDBX_VALIDATE_RMSD_TORSIONS_ATOM category list the atoms involved in outlier conformations instanced in the PDBX_VALIDATE_RMSD_TORSION category. The values are computed by Mogul. Mogul finds the similar conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_torsions_atomCategory> <VRPTx:pdbx_validate_rmsd_torsions_atom id="1" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="2" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="3" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="4" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="5" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="6" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="1" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="2" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="3" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="4" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="5" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="6" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> </VRPTx:pdbx_validate_rmsd_torsions_atomCategory> 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 pdbx_validate_rmsd_torsions_atomCategory This property indicates that datablock has a category holder pdbx_validate_rmsd_torsions_atomCategory. pdbx_validate_rmsd_torsions_atomCategory This property indicates that pdbx_validate_rmsd_torsions_atomCategory. has a category pdbx_validate_rmsd_torsions_atom. pdbx_validate_rmsd_torsions_atomItem Abstract datatype property for pdbx_validate_rmsd_torsions_atom items. reference_to_pdbx_validate_rmsd_torsions_atom cross-reference to pdbx_validate_rmsd_torsions_atom. referenced_by_pdbx_validate_rmsd_torsions_atom cross-reference from pdbx_validate_rmsd_torsions_atom. pdbx_validate_rmsd_torsions_atom.PDB_ins_code Optional identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.PDB_model_num The model number for the given conformation. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.auth_asym_id Part of the identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.auth_atom_id Part of the identifier of the atom sites that involved in the outlier conformation. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.auth_comp_id Part of the identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.auth_seq_id Part of the identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.label_alt_id Optional identifier of the residue in which the torsion angle is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_rmsd_torsions_atom.id The value of attribute id in category pdbx_validate_rmsd_torsions_atom must uniquely identify each item in the PDBX_VALIDATE_RMSD_TORSIONS_ATOM list. This is an integer serial number. pdbx_validate_rmsd_torsions_atom.torsion_id Pointer to attribute id in category pdbx_validate_rmsd_torsion. 0 pdbx_validate_symm_contact Data items in the PDBX_VALIDATE_SYMM_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts with for symmetry related contacts are considered. For those contacts not involving hydrogen a limit of 2.2 angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 angstrom is used. Example 1 - <VRPTx:pdbx_validate_symm_contactCategory> <VRPTx:pdbx_validate_symm_contact id="1"> <VRPTx:PDB_ins_code_1 xsi:nil="true" /> <VRPTx:PDB_ins_code_2 xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id_1 xsi:nil="true" /> <VRPTx:auth_asym_id_2 xsi:nil="true" /> <VRPTx:auth_atom_id_1>O</VRPTx:auth_atom_id_1> <VRPTx:auth_atom_id_2>O</VRPTx:auth_atom_id_2> <VRPTx:auth_comp_id_1>HOH</VRPTx:auth_comp_id_1> <VRPTx:auth_comp_id_2>HOH</VRPTx:auth_comp_id_2> <VRPTx:auth_seq_id_1>70</VRPTx:auth_seq_id_1> <VRPTx:auth_seq_id_2>70</VRPTx:auth_seq_id_2> <VRPTx:dist>2.05</VRPTx:dist> <VRPTx:label_alt_id_1 xsi:nil="true" /> <VRPTx:label_alt_id_2 xsi:nil="true" /> <VRPTx:site_symmetry_1>1555</VRPTx:site_symmetry_1> <VRPTx:site_symmetry_2>7555</VRPTx:site_symmetry_2> </VRPTx:pdbx_validate_symm_contact> </VRPTx:pdbx_validate_symm_contactCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 1 1 1 1 1 pdbx_validate_symm_contactCategory This property indicates that datablock has a category holder pdbx_validate_symm_contactCategory. pdbx_validate_symm_contactCategory This property indicates that pdbx_validate_symm_contactCategory. has a category pdbx_validate_symm_contact. pdbx_validate_symm_contactItem Abstract datatype property for pdbx_validate_symm_contact items. reference_to_pdbx_validate_symm_contact cross-reference to pdbx_validate_symm_contact. referenced_by_pdbx_validate_symm_contact cross-reference from pdbx_validate_symm_contact. pdbx_validate_symm_contact.PDB_ins_code_1 Optional identifier of the first of the two atom sites that define the close contact. pdbx_validate_symm_contact.PDB_ins_code_2 Optional identifier of the second of the two atom sites that define the close contact. pdbx_validate_symm_contact.PDB_model_num The model number for the given angle pdbx_validate_symm_contact.auth_asym_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_asym_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_atom_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_atom_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_comp_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_comp_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_seq_id_1 Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.auth_seq_id_2 Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.clash_magnitude The difference in angstroms between the observed interatomic distance and the sum of the van der Waals radii of the atoms involved. pdbx_validate_symm_contact.dist The value of the close contact for the two atoms defined. pdbx_validate_symm_contact.label_alt_id_1 An optional identifier of the first of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.label_alt_id_2 An optional identifier of the second of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_symm_contact.site_symmetry_1 The symmetry of the first of the two atoms define the close contact. Symmetry defined in ORTEP style of 555 equal to unit cell with translations +-1 from 555 as 000 pdbx_validate_symm_contact.site_symmetry_2 The symmetry of the second of the two atoms define the close contact. Symmetry defined in ORTEP style of 555 equal to unit cell with translations +-1 from 555 as 000 pdbx_validate_symm_contact.id The value of attribute id in category pdbx_validate_symm_contact must uniquely identify each item in the PDBX_VALIDATE_SYMM_CONTACT list. This is an integer serial number. 0 pdbx_validate_torsion Data items in the PDBX_VALIDATE_TORSION category list the residues with torsion angles outside the expected Ramachandran regions Example 1 - <VRPTx:pdbx_validate_torsionCategory> <VRPTx:pdbx_validate_torsion id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>SER</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>12</VRPTx:auth_seq_id> <VRPTx:phi>-64.75</VRPTx:phi> <VRPTx:psi>2.02</VRPTx:psi> </VRPTx:pdbx_validate_torsion> <VRPTx:pdbx_validate_torsion id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>THR</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>22</VRPTx:auth_seq_id> <VRPTx:phi>-116.30</VRPTx:phi> <VRPTx:psi>61.44</VRPTx:psi> </VRPTx:pdbx_validate_torsion> </VRPTx:pdbx_validate_torsionCategory> 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 pdbx_validate_torsionCategory This property indicates that datablock has a category holder pdbx_validate_torsionCategory. pdbx_validate_torsionCategory This property indicates that pdbx_validate_torsionCategory. has a category pdbx_validate_torsion. pdbx_validate_torsionItem Abstract datatype property for pdbx_validate_torsion items. reference_to_pdbx_validate_torsion cross-reference to pdbx_validate_torsion. referenced_by_pdbx_validate_torsion cross-reference from pdbx_validate_torsion. pdbx_validate_torsion.PDB_ins_code Optional identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_validate_torsion.PDB_model_num The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. pdbx_validate_torsion.auth_asym_id Part of the identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_validate_torsion.auth_comp_id Part of the identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_validate_torsion.auth_seq_id Part of the identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_validate_torsion.label_alt_id Optional identifier of the residue This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_validate_torsion.phi The Phi value that for the residue that lies outside normal limits (in combination with the Psi value) with regards to the Ramachandran plot pdbx_validate_torsion.psi The Psi value that for the residue that lies outside normal limits (in combination with the Phi value) with regards to the Ramachandran plot pdbx_validate_torsion.id The value of attribute id in category pdbx_validate_torsion must uniquely identify each item in the PDBX_VALIDATE_TORSION list. This is an integer serial number. 0 pdbx_validation_software Description of the software that was used for wwPDB validation pipeline. The description should include the name of the software and the version used. This example describes the software used in wwPDB validation pipeline. <VRPTx:pdbx_validation_softwareCategory> <VRPTx:pdbx_validation_software ordinal="1"> <VRPTx:classification>refinement package</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>EDS</VRPTx:name> <VRPTx:version>trunk28620</VRPTx:version> </VRPTx:pdbx_validation_software> <VRPTx:pdbx_validation_software ordinal="2"> <VRPTx:classification>refinement package</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>DCC</VRPTx:name> <VRPTx:version>2.18 (2016-06-28)</VRPTx:version> </VRPTx:pdbx_validation_software> <VRPTx:pdbx_validation_software ordinal="3"> <VRPTx:classification>geometric validation</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>Mogul</VRPTx:name> <VRPTx:version>1.7.2 (RC1), CSD as538be (2017)</VRPTx:version> </VRPTx:pdbx_validation_software> <VRPTx:pdbx_validation_software ordinal="4"> <VRPTx:classification>phasing,refinement</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>Xtriage</VRPTx:name> <VRPTx:version>1.9-1692</VRPTx:version> </VRPTx:pdbx_validation_software> </VRPTx:pdbx_validation_softwareCategory> 1 1 0 1 1 1 1 1 1 pdbx_validation_softwareCategory This property indicates that datablock has a category holder pdbx_validation_softwareCategory. pdbx_validation_softwareCategory This property indicates that pdbx_validation_softwareCategory. has a category pdbx_validation_software. pdbx_validation_softwareItem Abstract datatype property for pdbx_validation_software items. reference_to_pdbx_validation_software cross-reference to pdbx_validation_software. referenced_by_pdbx_validation_software cross-reference from pdbx_validation_software. pdbx_validation_software.classification The purpose of the software. processing data analysis phasing refinement refinement package model building geometric classification geometric validation pdbx_validation_software.details Text description of the software. This item is temporary used to record name list of information items of wwPDB validation information (XML). pdbx_validation_software.name The name of the software used for the task. CCP4 CNS CYRANGE DCC EDS MapMan Mogul MolProbity NMRClust PANAV Percentiles PHENIX RCI REFMAC ShiftChecker Validation-Pack Validation-Pipeline Xtriage pdbx_validation_software.version The version of the software. trunk28620 2.18 (2016-06-28) 1.7.2 (RC1), CSD as538be (2017) 1.9-1692 pdbx_validation_software.ordinal An ordinal index for this category 1 2 0 phasing Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories. Example 1 - hypothetical example. <VRPTx:phasingCategory> <VRPTx:phasing method="mir"></VRPTx:phasing> <VRPTx:phasing method="averaging"></VRPTx:phasing> </VRPTx:phasingCategory> 1 phasingCategory This property indicates that datablock has a category holder phasingCategory. phasingCategory This property indicates that phasingCategory. has a category phasing. phasingItem Abstract datatype property for phasing items. reference_to_phasing cross-reference to phasing. referenced_by_phasing cross-reference from phasing. phasing.method A listing of the method or methods used to phase this structure. phasing by ab initio methods abinitio phase improvement by averaging over multiple images of the structure averaging phasing by direct methods dm phasing by iterative single-wavelength anomalous scattering isas phasing by iterative single-wavelength isomorphous replacement isir phasing beginning with phases calculated from an isomorphous structure isomorphous phasing by multiple-wavelength anomalous dispersion mad phasing by multiple isomorphous replacement mir phasing by multiple isomorphous replacement with anomalous scattering miras phasing by molecular replacement mr phasing by single isomorphous replacement sir phasing by single isomorphous replacement with anomalous scattering siras 0 phasing_MAD Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <VRPTx:phasing_MADCategory> <VRPTx:phasing_MAD entry_id="NCAD"></VRPTx:phasing_MAD> </VRPTx:phasing_MADCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 phasing_MADCategory This property indicates that datablock has a category holder phasing_MADCategory. phasing_MADCategory This property indicates that phasing_MADCategory. has a category phasing_MAD. phasing_MADItem Abstract datatype property for phasing_MAD items. reference_to_phasing_MAD cross-reference to phasing_MAD. referenced_by_phasing_MAD cross-reference from phasing_MAD. phasing_MAD.details A description of special aspects of the MAD phasing. phasing_MAD.method A description of the MAD phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program. phasing_MAD.pdbx_R_cullis attribute pdbx_R_cullis in category phasing_MAD records R_cullis for MAD phasing. phasing_MAD.pdbx_R_cullis_acentric attribute pdbx_R_cullis_acentric in category phasing_MAD records R_cullis using acentric data for MAD phasing. phasing_MAD.pdbx_R_cullis_centric attribute pdbx_R_cullis_centric in category phasing_MAD records R_cullis using centric data for MAD phasing. phasing_MAD.pdbx_R_kraut attribute pdbx_R_kraut in category phasing_MAD records R_kraut for MAD phasing. phasing_MAD.pdbx_R_kraut_acentric attribute pdbx_R_kraut_acentric in category phasing_MAD records R_kraut using acentric data for MAD phasing. phasing_MAD.pdbx_R_kraut_centric attribute pdbx_R_kraut_centric in category phasing_MAD records R_kraut using centric data for MAD phasing. phasing_MAD.pdbx_anom_scat_method attribute pdbx_anom_scat_method in category phasing_MAD records the method used to locate anomalous scatterers for MAD phasing. phasing_MAD.pdbx_d_res_high attribute pdbx_d_res_high in category phasing_MAD records the highest resolution for MAD phasing. phasing_MAD.pdbx_d_res_low attribute pdbx_d_res_low in category phasing_MAD records the lowest resolution for MAD phasing. phasing_MAD.pdbx_fom attribute pdbx_fom in category phasing_MAD records the figure of merit for MAD phasing. phasing_MAD.pdbx_fom_acentric attribute pdbx_fom_acentric in category phasing_MAD records the figure of merit using acentric data for MAD phasing. phasing_MAD.pdbx_fom_centric attribute pdbx_fom_centric in category phasing_MAD records the figure of merit using centric data for MAD phasing. phasing_MAD.pdbx_loc attribute pdbx_loc in category phasing_MAD records lack of closure for MAD phasing. phasing_MAD.pdbx_loc_acentric attribute pdbx_loc_acentric in category phasing_MAD records lack of closure using acentric data for MAD phasing. phasing_MAD.pdbx_loc_centric attribute pdbx_loc_centric in category phasing_MAD records lack of closure using centric data for MAD phasing. phasing_MAD.pdbx_number_data_sets attribute pdbx_loc in category phasing_MAD records the number of data sets used for MAD phasing. phasing_MAD.pdbx_power attribute pdbx_power in category phasing_MAD records phasing power for MAD phasing. phasing_MAD.pdbx_power_acentric attribute pdbx_power_acentric in category phasing_MAD records phasing power using acentric data for MAD phasing. phasing_MAD.pdbx_power_centric attribute pdbx_power_centric in category phasing_MAD records phasing power using centric data for MAD phasing. phasing_MAD.pdbx_reflns attribute pdbx_reflns in category phasing_MAD records the number of reflections used for MAD phasing. phasing_MAD.pdbx_reflns_acentric attribute pdbx_reflns_acentric in category phasing_MAD records the number of acentric reflections for MAD phasing. phasing_MAD.pdbx_reflns_centric attribute pdbx_reflns_centric in category phasing_MAD records the number of centric reflections for MAD phasing. phasing_MAD.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 phasing_MAD_clust Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <VRPTx:phasing_MAD_clustCategory> <VRPTx:phasing_MAD_clust expt_id="1" id="4 wavelength"> <VRPTx:number_set>4</VRPTx:number_set> </VRPTx:phasing_MAD_clust> <VRPTx:phasing_MAD_clust expt_id="1" id="5 wavelength"> <VRPTx:number_set>5</VRPTx:number_set> </VRPTx:phasing_MAD_clust> <VRPTx:phasing_MAD_clust expt_id="2" id="5 wavelength"> <VRPTx:number_set>5</VRPTx:number_set> </VRPTx:phasing_MAD_clust> </VRPTx:phasing_MAD_clustCategory> 0 1 1 1 phasing_MAD_clustCategory This property indicates that datablock has a category holder phasing_MAD_clustCategory. phasing_MAD_clustCategory This property indicates that phasing_MAD_clustCategory. has a category phasing_MAD_clust. phasing_MAD_clustItem Abstract datatype property for phasing_MAD_clust items. reference_to_phasing_MAD_clust cross-reference to phasing_MAD_clust. referenced_by_phasing_MAD_clust cross-reference from phasing_MAD_clust. phasing_MAD_clust.number_set The number of data sets in this cluster of data sets. phasing_MAD_clust.expt_id This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. phasing_MAD_clust.id The value of attribute id in category phasing_MAD_clust must, together with attribute expt_id in category phasing_MAD_clust, uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier. 0 phasing_MAD_expt Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <VRPTx:phasing_MAD_exptCategory> <VRPTx:phasing_MAD_expt id="1"> <VRPTx:R_normal_all>0.063</VRPTx:R_normal_all> <VRPTx:R_normal_anom_scat>0.451</VRPTx:R_normal_anom_scat> <VRPTx:delta_delta_phi>58.5</VRPTx:delta_delta_phi> <VRPTx:delta_phi_sigma>20.3</VRPTx:delta_phi_sigma> <VRPTx:mean_fom>0.88</VRPTx:mean_fom> <VRPTx:number_clust>2</VRPTx:number_clust> </VRPTx:phasing_MAD_expt> <VRPTx:phasing_MAD_expt id="2"> <VRPTx:R_normal_all>0.051</VRPTx:R_normal_all> <VRPTx:R_normal_anom_scat>0.419</VRPTx:R_normal_anom_scat> <VRPTx:delta_delta_phi>36.8</VRPTx:delta_delta_phi> <VRPTx:delta_phi_sigma>18.2</VRPTx:delta_phi_sigma> <VRPTx:mean_fom>0.93</VRPTx:mean_fom> <VRPTx:number_clust>1</VRPTx:number_clust> </VRPTx:phasing_MAD_expt> </VRPTx:phasing_MAD_exptCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 phasing_MAD_exptCategory This property indicates that datablock has a category holder phasing_MAD_exptCategory. phasing_MAD_exptCategory This property indicates that phasing_MAD_exptCategory. has a category phasing_MAD_expt. phasing_MAD_exptItem Abstract datatype property for phasing_MAD_expt items. reference_to_phasing_MAD_expt cross-reference to phasing_MAD_expt. referenced_by_phasing_MAD_expt cross-reference from phasing_MAD_expt. phasing_MAD_expt.R_normal_all phasing_MAD_expt.R_normal_anom_scat phasing_MAD_expt.delta_delta_phi The difference between two independent determinations of attribute delta_phi in category phasing_MAD_expt. phasing_MAD_expt.delta_phi The phase difference between F~t~(h), the structure factor due to normal scattering from all atoms, and F~a~(h), the structure factor due to normal scattering from only the anomalous scatterers. phasing_MAD_expt.delta_phi_sigma The standard uncertainty (estimated standard deviation) of attribute delta_phi in category phasing_MAD_expt. phasing_MAD_expt.mean_fom The mean figure of merit. phasing_MAD_expt.number_clust The number of clusters of data sets in this phasing experiment. phasing_MAD_expt.id The value of attribute id in category phasing_MAD_expt must uniquely identify each record in the PHASING_MAD_EXPT list. 0 phasing_MAD_ratio Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <VRPTx:phasing_MAD_ratioCategory> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.084</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.076</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.067</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.051</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.044</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.110</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.049</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.049</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.067</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.149</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.072</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.039</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.102</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.071</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.114</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.111</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.089</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.086</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.077</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.140</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.127</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.085</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.089</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.155</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.119</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.082</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.124</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.120</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.075</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.027</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.041</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.060</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.057</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.072</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.105</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.032</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.036</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.044</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.065</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.072</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.031</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.040</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.059</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.059</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.032</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.059</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.3847"> <VRPTx:d_res_high>4.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.058</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.028</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.078</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.075</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.059</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.067</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.084</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.073</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.101</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.088</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.066</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.082</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.085</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.097</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.074</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.081</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.085</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.114</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.089</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.103</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.2862"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>4.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.062</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.060</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.035</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.026</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.028</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.023</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.025</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.026</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.060</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.026</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.029</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.031</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.035</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.075</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.030</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.023</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.027</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.069</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.026</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.024</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.060</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.028</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.060</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.050</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.056</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.055</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.053</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.056</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.089</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.050</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.054</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.058</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.063</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.104</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.057</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.052</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.057</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.098</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.052</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl xsi:nil="true" /> <VRPTx:ratio_one_wl_centric xsi:nil="true" /> <VRPTx:ratio_two_wl>0.054</VRPTx:ratio_two_wl> </VRPTx:phasing_MAD_ratio> <VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>3.00</VRPTx:d_res_low> <VRPTx:ratio_one_wl>0.089</VRPTx:ratio_one_wl> <VRPTx:ratio_one_wl_centric>0.060</VRPTx:ratio_one_wl_centric> <VRPTx:ratio_two_wl xsi:nil="true" /> </VRPTx:phasing_MAD_ratio> </VRPTx:phasing_MAD_ratioCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 1 phasing_MAD_ratioCategory This property indicates that datablock has a category holder phasing_MAD_ratioCategory. phasing_MAD_ratioCategory This property indicates that phasing_MAD_ratioCategory. has a category phasing_MAD_ratio. phasing_MAD_ratioItem Abstract datatype property for phasing_MAD_ratio items. reference_to_phasing_MAD_ratio cross-reference to phasing_MAD_ratio. referenced_by_phasing_MAD_ratio cross-reference from phasing_MAD_ratio. phasing_MAD_ratio.d_res_high The lowest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the highest resolution. phasing_MAD_ratio.d_res_low The highest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the lowest resolution. phasing_MAD_ratio.ratio_one_wl The root-mean-square Bijvoet difference at one wavelength for all reflections. phasing_MAD_ratio.ratio_one_wl_centric The root-mean-square Bijvoet difference at one wavelength for centric reflections. This would be equal to zero for perfect data and thus serves as an estimate of the noise in the anomalous signals. phasing_MAD_ratio.ratio_two_wl The root-mean-square dispersive Bijvoet difference between two wavelengths for all reflections. phasing_MAD_ratio.clust_id This data item is a pointer to attribute id in category phasing_MAD_clust in the PHASING_MAD_CLUST category. phasing_MAD_ratio.expt_id This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. phasing_MAD_ratio.wavelength_1 This data item is a pointer to attribute wavelength in category phasing_MAD_set in the PHASING_MAD_SET category. phasing_MAD_ratio.wavelength_2 This data item is a pointer to attribute wavelength in category phasing_MAD_set in the PHASING_MAD_SET category. 0 phasing_MAD_set Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <VRPTx:phasing_MAD_setCategory> <VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="aa" wavelength="1.4013"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>3.80</VRPTx:f_double_prime> <VRPTx:f_prime>-12.48</VRPTx:f_prime> <VRPTx:wavelength_details>pre-edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="bb" wavelength="1.3857"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>17.20</VRPTx:f_double_prime> <VRPTx:f_prime>-31.22</VRPTx:f_prime> <VRPTx:wavelength_details>peak</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="cc" wavelength="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>29.17</VRPTx:f_double_prime> <VRPTx:f_prime>-13.97</VRPTx:f_prime> <VRPTx:wavelength_details>edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="dd" wavelength="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>17.34</VRPTx:f_double_prime> <VRPTx:f_prime>-6.67</VRPTx:f_prime> <VRPTx:wavelength_details>remote</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ee" wavelength="1.3857"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>14.84</VRPTx:f_double_prime> <VRPTx:f_prime>-28.33</VRPTx:f_prime> <VRPTx:wavelength_details>ascending edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ff" wavelength="1.3852"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>30.23</VRPTx:f_double_prime> <VRPTx:f_prime>-21.50</VRPTx:f_prime> <VRPTx:wavelength_details>peak</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="gg" wavelength="1.3847"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>20.35</VRPTx:f_double_prime> <VRPTx:f_prime>-10.71</VRPTx:f_prime> <VRPTx:wavelength_details>descending edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="hh" wavelength="1.3784"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>11.84</VRPTx:f_double_prime> <VRPTx:f_prime>-14.45</VRPTx:f_prime> <VRPTx:wavelength_details>remote 1</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ii" wavelength="1.2862"> <VRPTx:d_res_high>3.00</VRPTx:d_res_high> <VRPTx:d_res_low>20.00</VRPTx:d_res_low> <VRPTx:f_double_prime>9.01</VRPTx:f_double_prime> <VRPTx:f_prime>-9.03</VRPTx:f_prime> <VRPTx:wavelength_details>remote 2</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="jj" wavelength="0.7263"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:f_double_prime>4.08</VRPTx:f_double_prime> <VRPTx:f_prime>-21.10</VRPTx:f_prime> <VRPTx:wavelength_details>pre-edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="kk" wavelength="0.7251"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:f_double_prime>7.92</VRPTx:f_double_prime> <VRPTx:f_prime>-34.72</VRPTx:f_prime> <VRPTx:wavelength_details>edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="ll" wavelength="0.7248"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:f_double_prime>10.30</VRPTx:f_double_prime> <VRPTx:f_prime>-24.87</VRPTx:f_prime> <VRPTx:wavelength_details>peak</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="mm" wavelength="0.7246"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:f_double_prime>9.62</VRPTx:f_double_prime> <VRPTx:f_prime>-17.43</VRPTx:f_prime> <VRPTx:wavelength_details>descending edge</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> <VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="nn" wavelength="0.7217"> <VRPTx:d_res_high>1.90</VRPTx:d_res_high> <VRPTx:d_res_low>15.00</VRPTx:d_res_low> <VRPTx:f_double_prime>8.40</VRPTx:f_double_prime> <VRPTx:f_prime>-13.26</VRPTx:f_prime> <VRPTx:wavelength_details>remote</VRPTx:wavelength_details> </VRPTx:phasing_MAD_set> </VRPTx:phasing_MAD_setCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 phasing_MAD_setCategory This property indicates that datablock has a category holder phasing_MAD_setCategory. phasing_MAD_setCategory This property indicates that phasing_MAD_setCategory. has a category phasing_MAD_set. phasing_MAD_setItem Abstract datatype property for phasing_MAD_set items. reference_to_phasing_MAD_set cross-reference to phasing_MAD_set. referenced_by_phasing_MAD_set cross-reference from phasing_MAD_set. phasing_MAD_set.d_res_high The lowest value for the interplanar spacings for the reflection data used for this set of data. This is called the highest resolution. phasing_MAD_set.d_res_low The highest value for the interplanar spacings for the reflection data used for this set of data. This is called the lowest resolution. phasing_MAD_set.f_double_prime The f'' component of the anomalous scattering factor for this wavelength. phasing_MAD_set.f_prime The f' component of the anomalous scattering factor for this wavelength. phasing_MAD_set.pdbx_atom_type Record the type of heavy atoms which produce anomolous singal. phasing_MAD_set.pdbx_f_double_prime_refined Record the refined f_double_prime (not from experiment). phasing_MAD_set.pdbx_f_prime_refined Record the refined f_prime (not from experiment). phasing_MAD_set.wavelength_details A descriptor for this wavelength in this cluster of data sets. peak remote ascending edge phasing_MAD_set.clust_id This data item is a pointer to attribute id in category phasing_MAD_clust in the PHASING_MAD_CLUST category. phasing_MAD_set.expt_id This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. phasing_MAD_set.set_id This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. phasing_MAD_set.wavelength The wavelength at which this data set was measured. 0 phasing_MIR Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS). Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. <VRPTx:phasing_MIRCategory> <VRPTx:phasing_MIR entry_id="1ABC"> <VRPTx:method> Standard phase refinement (Blow &amp; Crick, 1959)</VRPTx:method> </VRPTx:phasing_MIR> </VRPTx:phasing_MIRCategory> 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 phasing_MIRCategory This property indicates that datablock has a category holder phasing_MIRCategory. phasing_MIRCategory This property indicates that phasing_MIRCategory. has a category phasing_MIR. phasing_MIRItem Abstract datatype property for phasing_MIR items. reference_to_phasing_MIR cross-reference to phasing_MIR. referenced_by_phasing_MIR cross-reference from phasing_MIR. phasing_MIR.FOM The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. phasing_MIR.FOM_acentric The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. phasing_MIR.FOM_centric The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. phasing_MIR.d_res_high The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the highest resolution. phasing_MIR.d_res_low The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the lowest resolution. phasing_MIR.details A description of special aspects of the isomorphous-replacement phasing. phasing_MIR.method A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program. phasing_MIR.pdbx_number_derivatives The number of derivatives used in this phasing experiment. phasing_MIR.reflns The total number of reflections phased in the native data set. phasing_MIR.reflns_acentric The number of acentric reflections phased in the native data set. phasing_MIR.reflns_centric The number of centric reflections phased in the native data set. phasing_MIR.reflns_criterion Criterion used to limit the reflections used in the phasing calculations. > 4 \s(I) phasing_MIR.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 phasing_MIR_der Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via attribute der_set_id in category phasing_MIR_der and attribute native_set_id in category phasing_MIR_der. Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. <VRPTx:phasing_MIR_derCategory> <VRPTx:phasing_MIR_der id="KAu(CN)2"> <VRPTx:details>major site interpreted in difference Patterson</VRPTx:details> <VRPTx:number_of_sites>3</VRPTx:number_of_sites> </VRPTx:phasing_MIR_der> <VRPTx:phasing_MIR_der id="K2HgI4"> <VRPTx:details>sites found in cross-difference Fourier</VRPTx:details> <VRPTx:number_of_sites>6</VRPTx:number_of_sites> </VRPTx:phasing_MIR_der> <VRPTx:phasing_MIR_der id="K3IrCl6"> <VRPTx:details>sites found in cross-difference Fourier</VRPTx:details> <VRPTx:number_of_sites>2</VRPTx:number_of_sites> </VRPTx:phasing_MIR_der> <VRPTx:phasing_MIR_der id="All"> <VRPTx:details>data for all three derivatives combined</VRPTx:details> <VRPTx:number_of_sites>11</VRPTx:number_of_sites> </VRPTx:phasing_MIR_der> </VRPTx:phasing_MIR_derCategory> 0 1 0 1 0 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 phasing_MIR_derCategory This property indicates that datablock has a category holder phasing_MIR_derCategory. phasing_MIR_derCategory This property indicates that phasing_MIR_derCategory. has a category phasing_MIR_der. phasing_MIR_derItem Abstract datatype property for phasing_MIR_der items. reference_to_phasing_MIR_der cross-reference to phasing_MIR_der. referenced_by_phasing_MIR_der cross-reference from phasing_MIR_der. phasing_MIR_der.R_cullis_acentric Residual factor R~cullis,acen~ for acentric reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis,acen~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. phasing_MIR_der.R_cullis_anomalous Residual factor R~cullis,ano~ for anomalous reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. A value less than 1.0 means there is some contribution to the phasing from the anomalous data. sum |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| R~cullis,ano~ = ------------------------------------------------ sum|Fph+~obs~ - Fph-~obs~| Fph+~obs~ = the observed positive Friedel structure-factor amplitude for the derivative Fph-~obs~ = the observed negative Friedel structure-factor amplitude for the derivative Fh+~calc~ = the calculated positive Friedel structure-factor amplitude from the heavy-atom model Fh-~calc~ = the calculated negative Friedel structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. phasing_MIR_der.R_cullis_centric Residual factor R~cullis~ for centric reflections for this derivative. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. phasing_MIR_der.d_res_high The lowest value for the interplanar spacings for the reflection data used for this derivative. This is called the highest resolution. phasing_MIR_der.d_res_low The highest value for the interplanar spacings for the reflection data used for this derivative. This is called the lowest resolution. phasing_MIR_der.der_set_id The data set that was treated as the derivative in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. phasing_MIR_der.details A description of special aspects of this derivative, its data, its solution or its use in phasing. phasing_MIR_der.native_set_id The data set that was treated as the native in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. phasing_MIR_der.number_of_sites The number of heavy-atom sites in this derivative. phasing_MIR_der.pdbx_R_cullis Record R_cullis for each derivative. phasing_MIR_der.pdbx_R_kraut Record R_kraut obtained from all data data for each derivative. phasing_MIR_der.pdbx_R_kraut_acentric Record R_kraut obtained from acentric data for each derivative. phasing_MIR_der.pdbx_R_kraut_centric Record R_kraut obtained from centric data for each derivative. phasing_MIR_der.pdbx_fom Record figure of merit obtained from all data for each derivative. phasing_MIR_der.pdbx_fom_acentric Record figure of merit obtained from acentric data for each derivative. phasing_MIR_der.pdbx_fom_centric Record figure of merit obtained from centric data for each derivative. phasing_MIR_der.pdbx_loc Record lack of closure obtained from all data for each derivative. phasing_MIR_der.pdbx_loc_acentric Record lack of closure obtained from acentric data for each derivative. phasing_MIR_der.pdbx_loc_centric Record lack of closure obtained from centric data for each derivative. phasing_MIR_der.pdbx_power Record phasing power for each derivative. phasing_MIR_der.pdbx_reflns Record number of reflections used for each derivative. phasing_MIR_der.power_acentric The mean phasing power P for acentric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of this derivative Fph~calc~ = the calculated structure-factor amplitude of this derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections phasing_MIR_der.power_centric The mean phasing power P for centric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections phasing_MIR_der.reflns_acentric The number of acentric reflections used in phasing for this derivative. phasing_MIR_der.reflns_anomalous The number of anomalous reflections used in phasing for this derivative. phasing_MIR_der.reflns_centric The number of centric reflections used in phasing for this derivative. phasing_MIR_der.reflns_criteria Criteria used to limit the reflections used in the phasing calculations. > 4 \s(I) phasing_MIR_der.id The value of attribute id in category phasing_MIR_der must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. KAu(CN)2 K2HgI4_anom K2HgI4_iso 0 phasing_MIR_der_refln Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_refln indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness. Example 1 - based on laboratory records for the 6,1,25 reflection of an Hg/Pt derivative of protein NS1. <VRPTx:phasing_MIR_der_reflnCategory> <VRPTx:phasing_MIR_der_refln der_id="HGPT1" index_h="6" index_k="1" index_l="25" set_id="NS1-96"> <VRPTx:F_calc_au>106.66</VRPTx:F_calc_au> <VRPTx:F_meas_au>204.67</VRPTx:F_meas_au> <VRPTx:F_meas_sigma>6.21</VRPTx:F_meas_sigma> <VRPTx:HL_A_iso>-3.15</VRPTx:HL_A_iso> <VRPTx:HL_B_iso>-0.76</VRPTx:HL_B_iso> <VRPTx:HL_C_iso>0.65</VRPTx:HL_C_iso> <VRPTx:HL_D_iso>0.23</VRPTx:HL_D_iso> <VRPTx:phase_calc>194.48</VRPTx:phase_calc> </VRPTx:phasing_MIR_der_refln> </VRPTx:phasing_MIR_der_reflnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 phasing_MIR_der_reflnCategory This property indicates that datablock has a category holder phasing_MIR_der_reflnCategory. phasing_MIR_der_reflnCategory This property indicates that phasing_MIR_der_reflnCategory. has a category phasing_MIR_der_refln. phasing_MIR_der_reflnItem Abstract datatype property for phasing_MIR_der_refln items. reference_to_phasing_MIR_der_refln cross-reference to phasing_MIR_der_refln. referenced_by_phasing_MIR_der_refln cross-reference from phasing_MIR_der_refln. phasing_MIR_der_refln.F_calc The calculated value of the structure factor for this derivative, in electrons. phasing_MIR_der_refln.F_calc_au The calculated value of the structure factor for this derivative, in arbitrary units. phasing_MIR_der_refln.F_meas The measured value of the structure factor for this derivative, in electrons. phasing_MIR_der_refln.F_meas_au The measured value of the structure factor for this derivative, in arbitrary units. phasing_MIR_der_refln.F_meas_sigma The standard uncertainty (estimated standard deviation) of attribute F_meas in category phasing_MIR_der_refln, in electrons. phasing_MIR_der_refln.F_meas_sigma_au The standard uncertainty (estimated standard deviation) of attribute F_meas_au in category phasing_MIR_der_refln, in arbitrary units. phasing_MIR_der_refln.HL_A_iso The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the calculated phase from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. phasing_MIR_der_refln.HL_B_iso The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. phasing_MIR_der_refln.HL_C_iso The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)^2^ - cos(alphah~calc~)^2^] C~iso~ = ------------------------------------ E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. phasing_MIR_der_refln.HL_D_iso The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^ * cos(alphah~calc~)^2^ D~iso~ = ---------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. phasing_MIR_der_refln.phase_calc The calculated value of the structure-factor phase based on the heavy-atom model for this derivative in degrees. phasing_MIR_der_refln.der_id This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. phasing_MIR_der_refln.index_h Miller index h for this reflection for this derivative. phasing_MIR_der_refln.index_k Miller index k for this reflection for this derivative. phasing_MIR_der_refln.index_l Miller index l for this reflection for this derivative. phasing_MIR_der_refln.set_id This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. 0 phasing_MIR_der_shell Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_shell indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. <VRPTx:phasing_MIR_der_shellCategory> <VRPTx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="KAu(CN)2"> <VRPTx:ha_ampl>54</VRPTx:ha_ampl> <VRPTx:loc>26</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="KAu(CN)2"> <VRPTx:ha_ampl>54</VRPTx:ha_ampl> <VRPTx:loc>20</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="KAu(CN)2"> <VRPTx:ha_ampl>50</VRPTx:ha_ampl> <VRPTx:loc>20</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="KAu(CN)2"> <VRPTx:ha_ampl>44</VRPTx:ha_ampl> <VRPTx:loc>23</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="KAu(CN)2"> <VRPTx:ha_ampl>39</VRPTx:ha_ampl> <VRPTx:loc>23</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="KAu(CN)2"> <VRPTx:ha_ampl>33</VRPTx:ha_ampl> <VRPTx:loc>21</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="KAu(CN)2"> <VRPTx:ha_ampl>28</VRPTx:ha_ampl> <VRPTx:loc>17</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="KAu(CN)2"> <VRPTx:ha_ampl>38</VRPTx:ha_ampl> <VRPTx:loc>21</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K2HgI4"> <VRPTx:ha_ampl>149</VRPTx:ha_ampl> <VRPTx:loc>87</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K2HgI4"> <VRPTx:ha_ampl>121</VRPTx:ha_ampl> <VRPTx:loc>73</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K2HgI4"> <VRPTx:ha_ampl>95</VRPTx:ha_ampl> <VRPTx:loc>61</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K2HgI4"> <VRPTx:ha_ampl>80</VRPTx:ha_ampl> <VRPTx:loc>60</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K2HgI4"> <VRPTx:ha_ampl>73</VRPTx:ha_ampl> <VRPTx:loc>63</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K2HgI4"> <VRPTx:ha_ampl>68</VRPTx:ha_ampl> <VRPTx:loc>57</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K2HgI4"> <VRPTx:ha_ampl>63</VRPTx:ha_ampl> <VRPTx:loc>46</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K2HgI4"> <VRPTx:ha_ampl>79</VRPTx:ha_ampl> <VRPTx:loc>58</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K3IrCl6"> <VRPTx:ha_ampl>33</VRPTx:ha_ampl> <VRPTx:loc>27</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K3IrCl6"> <VRPTx:ha_ampl>40</VRPTx:ha_ampl> <VRPTx:loc>23</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K3IrCl6"> <VRPTx:ha_ampl>31</VRPTx:ha_ampl> <VRPTx:loc>22</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K3IrCl6"> <VRPTx:ha_ampl>27</VRPTx:ha_ampl> <VRPTx:loc>23</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K3IrCl6"> <VRPTx:ha_ampl>22</VRPTx:ha_ampl> <VRPTx:loc>23</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K3IrCl6"> <VRPTx:ha_ampl>19</VRPTx:ha_ampl> <VRPTx:loc>20</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K3IrCl6"> <VRPTx:ha_ampl>16</VRPTx:ha_ampl> <VRPTx:loc>20</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> <VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K3IrCl6"> <VRPTx:ha_ampl>23</VRPTx:ha_ampl> <VRPTx:loc>21</VRPTx:loc> </VRPTx:phasing_MIR_der_shell> </VRPTx:phasing_MIR_der_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 phasing_MIR_der_shellCategory This property indicates that datablock has a category holder phasing_MIR_der_shellCategory. phasing_MIR_der_shellCategory This property indicates that phasing_MIR_der_shellCategory. has a category phasing_MIR_der_shell. phasing_MIR_der_shellItem Abstract datatype property for phasing_MIR_der_shell items. reference_to_phasing_MIR_der_shell cross-reference to phasing_MIR_der_shell. referenced_by_phasing_MIR_der_shell cross-reference from phasing_MIR_der_shell. phasing_MIR_der_shell.R_cullis Residual factor R~cullis~ for centric reflections for this derivative in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. phasing_MIR_der_shell.R_kraut Residual factor R~kraut~ for general reflections for this derivative in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. phasing_MIR_der_shell.fom The mean value of the figure of merit m for reflections for this derivative in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi. phasing_MIR_der_shell.ha_ampl The mean heavy-atom amplitude for reflections for this derivative in this shell. phasing_MIR_der_shell.loc The mean lack-of-closure error loc for reflections for this derivative in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections phasing_MIR_der_shell.pdbx_R_cullis_acentric Record R Cullis obtained from acentric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_R_cullis_centric Record R Cullis obtained from centric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_R_kraut_acentric Record R Kraut obtained from acentric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_R_kraut_centric Record R Kraut obtained from centric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_fom_acentric Record figure of merit obtained from acentric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_fom_centric Record figure of merit obtained from centric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_loc_acentric Record lack of closure obtained from acentric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_loc_centric Record lack of closure obtained from centric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_power_acentric Record phasing power obtained from acentric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_power_centric Record phasing power obtained from centric data for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_reflns_acentric Record number of acentric reflections used for phasing for each derivative, but broken into resolution shells phasing_MIR_der_shell.pdbx_reflns_centric Record number of centric reflections used for phasing for each derivative, but broken into resolution shells phasing_MIR_der_shell.phase The mean of the phase values for reflections for this derivative in this shell. phasing_MIR_der_shell.power The mean phasing power P for reflections for this derivative in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections phasing_MIR_der_shell.reflns The number of reflections in this shell. phasing_MIR_der_shell.d_res_high The lowest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the highest resolution. phasing_MIR_der_shell.d_res_low The highest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the lowest resolution. phasing_MIR_der_shell.der_id This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. 0 phasing_MIR_der_site Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_site indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with occupancies converted from electrons to fractional. <VRPTx:phasing_MIR_der_siteCategory> <VRPTx:phasing_MIR_der_site der_id="KAu(CN)2" id="1"> <VRPTx:B_iso>33.0</VRPTx:B_iso> <VRPTx:atom_type_symbol>Au</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.082</VRPTx:fract_x> <VRPTx:fract_y>0.266</VRPTx:fract_y> <VRPTx:fract_z>0.615</VRPTx:fract_z> <VRPTx:occupancy>0.40</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="KAu(CN)2" id="2"> <VRPTx:B_iso>25.9</VRPTx:B_iso> <VRPTx:atom_type_symbol>Au</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.607</VRPTx:fract_x> <VRPTx:fract_y>0.217</VRPTx:fract_y> <VRPTx:fract_z>0.816</VRPTx:fract_z> <VRPTx:occupancy>0.03</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="KAu(CN)2" id="3"> <VRPTx:B_iso>15.7</VRPTx:B_iso> <VRPTx:atom_type_symbol>Au</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.263</VRPTx:fract_x> <VRPTx:fract_y>0.782</VRPTx:fract_y> <VRPTx:fract_z>0.906</VRPTx:fract_z> <VRPTx:occupancy>0.02</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="1"> <VRPTx:B_iso>33.7</VRPTx:B_iso> <VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.048</VRPTx:fract_x> <VRPTx:fract_y>0.286</VRPTx:fract_y> <VRPTx:fract_z>0.636</VRPTx:fract_z> <VRPTx:occupancy>0.63</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="2"> <VRPTx:B_iso>36.7</VRPTx:B_iso> <VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.913</VRPTx:fract_x> <VRPTx:fract_y>0.768</VRPTx:fract_y> <VRPTx:fract_z>0.889</VRPTx:fract_z> <VRPTx:occupancy>0.34</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="3"> <VRPTx:B_iso>24.2</VRPTx:B_iso> <VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.974</VRPTx:fract_x> <VRPTx:fract_y>0.455</VRPTx:fract_y> <VRPTx:fract_z>0.974</VRPTx:fract_z> <VRPTx:occupancy>0.23</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="4"> <VRPTx:B_iso>14.7</VRPTx:B_iso> <VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.903</VRPTx:fract_x> <VRPTx:fract_y>0.836</VRPTx:fract_y> <VRPTx:fract_z>0.859</VRPTx:fract_z> <VRPTx:occupancy>0.28</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="5"> <VRPTx:B_iso>6.4</VRPTx:B_iso> <VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.489</VRPTx:fract_x> <VRPTx:fract_y>0.200</VRPTx:fract_y> <VRPTx:fract_z>0.885</VRPTx:fract_z> <VRPTx:occupancy>0.07</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="6"> <VRPTx:B_iso>32.9</VRPTx:B_iso> <VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.162</VRPTx:fract_x> <VRPTx:fract_y>0.799</VRPTx:fract_y> <VRPTx:fract_z>0.889</VRPTx:fract_z> <VRPTx:occupancy>0.07</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K3IrCl6" id="1"> <VRPTx:B_iso>40.8</VRPTx:B_iso> <VRPTx:atom_type_symbol>Ir</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.209</VRPTx:fract_x> <VRPTx:fract_y>0.739</VRPTx:fract_y> <VRPTx:fract_z>0.758</VRPTx:fract_z> <VRPTx:occupancy>0.26</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> <VRPTx:phasing_MIR_der_site der_id="K3IrCl6" id="2"> <VRPTx:B_iso>24.9</VRPTx:B_iso> <VRPTx:atom_type_symbol>Ir</VRPTx:atom_type_symbol> <VRPTx:fract_x>0.279</VRPTx:fract_x> <VRPTx:fract_y>0.613</VRPTx:fract_y> <VRPTx:fract_z>0.752</VRPTx:fract_z> <VRPTx:occupancy>0.05</VRPTx:occupancy> </VRPTx:phasing_MIR_der_site> </VRPTx:phasing_MIR_der_siteCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 phasing_MIR_der_siteCategory This property indicates that datablock has a category holder phasing_MIR_der_siteCategory. phasing_MIR_der_siteCategory This property indicates that phasing_MIR_der_siteCategory. has a category phasing_MIR_der_site. phasing_MIR_der_siteItem Abstract datatype property for phasing_MIR_der_site items. reference_to_phasing_MIR_der_site cross-reference to phasing_MIR_der_site. referenced_by_phasing_MIR_der_site cross-reference from phasing_MIR_der_site. phasing_MIR_der_site.B_iso Isotropic displacement parameter for this heavy-atom site in this derivative. phasing_MIR_der_site.B_iso_esd The standard uncertainty (estimated standard deviation) of attribute B_iso in category phasing_MIR_der_site. phasing_MIR_der_site.Cartn_x The x coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. phasing_MIR_der_site.Cartn_x_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_x in category phasing_MIR_der_site. phasing_MIR_der_site.Cartn_y The y coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. phasing_MIR_der_site.Cartn_y_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_y in category phasing_MIR_der_site. phasing_MIR_der_site.Cartn_z The z coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. phasing_MIR_der_site.Cartn_z_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_z in category phasing_MIR_der_site. phasing_MIR_der_site.atom_type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy-atom data; in some cases this is the scattering factor for the single heavy atom, in other cases these are the scattering factors for an atomic cluster. phasing_MIR_der_site.details A description of special aspects of the derivative site. binds to His 117 minor site obtained from difference Fourier same as site 2 in the K2HgI4 derivative phasing_MIR_der_site.fract_x The x coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_a in category cell. phasing_MIR_der_site.fract_x_esd The standard uncertainty (estimated standard deviation) of attribute fract_x in category phasing_MIR_der_site. phasing_MIR_der_site.fract_y The y coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_b in category cell. phasing_MIR_der_site.fract_y_esd The standard uncertainty (estimated standard deviation) of attribute fract_y in category phasing_MIR_der_site. phasing_MIR_der_site.fract_z The z coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_c in category cell. phasing_MIR_der_site.fract_z_esd The standard uncertainty (estimated standard deviation) of attribute fract_z in category phasing_MIR_der_site. phasing_MIR_der_site.occupancy The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. phasing_MIR_der_site.occupancy_anom The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. phasing_MIR_der_site.occupancy_anom_su The standard uncertainty (estimated standard deviation) of attribute occupancy_anom in category phasing_MIR_der_site. phasing_MIR_der_site.occupancy_iso The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. phasing_MIR_der_site.occupancy_iso_su The standard uncertainty (estimated standard deviation) of attribute occupancy_iso in category phasing_MIR_der_site. phasing_MIR_der_site.der_id This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. phasing_MIR_der_site.id The value of attribute id in category phasing_MIR_der_site must uniquely identify each site in each derivative in the PHASING_MIR_DER_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier. 0 phasing_MIR_shell Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution. Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. <VRPTx:phasing_MIR_shellCategory> <VRPTx:phasing_MIR_shell d_res_high="8.3" d_res_low="15.0"> <VRPTx:FOM>0.69</VRPTx:FOM> <VRPTx:reflns>80</VRPTx:reflns> </VRPTx:phasing_MIR_shell> <VRPTx:phasing_MIR_shell d_res_high="6.4" d_res_low="8.3"> <VRPTx:FOM>0.73</VRPTx:FOM> <VRPTx:reflns>184</VRPTx:reflns> </VRPTx:phasing_MIR_shell> <VRPTx:phasing_MIR_shell d_res_high="5.2" d_res_low="6.4"> <VRPTx:FOM>0.72</VRPTx:FOM> <VRPTx:reflns>288</VRPTx:reflns> </VRPTx:phasing_MIR_shell> <VRPTx:phasing_MIR_shell d_res_high="4.4" d_res_low="5.2"> <VRPTx:FOM>0.65</VRPTx:FOM> <VRPTx:reflns>406</VRPTx:reflns> </VRPTx:phasing_MIR_shell> <VRPTx:phasing_MIR_shell d_res_high="3.8" d_res_low="4.4"> <VRPTx:FOM>0.54</VRPTx:FOM> <VRPTx:reflns>554</VRPTx:reflns> </VRPTx:phasing_MIR_shell> <VRPTx:phasing_MIR_shell d_res_high="3.4" d_res_low="3.8"> <VRPTx:FOM>0.53</VRPTx:FOM> <VRPTx:reflns>730</VRPTx:reflns> </VRPTx:phasing_MIR_shell> <VRPTx:phasing_MIR_shell d_res_high="3.0" d_res_low="3.4"> <VRPTx:FOM>0.50</VRPTx:FOM> <VRPTx:reflns>939</VRPTx:reflns> </VRPTx:phasing_MIR_shell> </VRPTx:phasing_MIR_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 phasing_MIR_shellCategory This property indicates that datablock has a category holder phasing_MIR_shellCategory. phasing_MIR_shellCategory This property indicates that phasing_MIR_shellCategory. has a category phasing_MIR_shell. phasing_MIR_shellItem Abstract datatype property for phasing_MIR_shell items. reference_to_phasing_MIR_shell cross-reference to phasing_MIR_shell. referenced_by_phasing_MIR_shell cross-reference from phasing_MIR_shell. phasing_MIR_shell.FOM The mean value of the figure of merit m for reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct the integral is taken over the range alpha = 0 to 2 pi. phasing_MIR_shell.FOM_acentric The mean value of the figure of merit m for acentric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. phasing_MIR_shell.FOM_centric The mean value of the figure of merit m for centric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. phasing_MIR_shell.R_cullis Residual factor R~cullis~ for centric reflections in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. phasing_MIR_shell.R_kraut Residual factor R~kraut~ for general reflections in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. phasing_MIR_shell.loc The mean lack-of-closure error loc for reflections in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections phasing_MIR_shell.mean_phase The mean of the phase values for all reflections in this shell. phasing_MIR_shell.pdbx_R_cullis_acentric Record R_Cullis from from acentric reflection for each shell. phasing_MIR_shell.pdbx_R_cullis_centric Record R_Cullis from from centric reflection for each shell. phasing_MIR_shell.pdbx_R_kraut_acentric Record R_kraut from from acentric reflection for each shell. phasing_MIR_shell.pdbx_R_kraut_centric Record R_Kraut from from centric reflection for each shell. phasing_MIR_shell.pdbx_loc_acentric Record lack of closure from acentric reflection for each shell. phasing_MIR_shell.pdbx_loc_centric Record lack of closure from centric reflection for each shell. phasing_MIR_shell.pdbx_power_acentric Record phasing power from acentric reflection for each shell. phasing_MIR_shell.pdbx_power_centric Record phasing power from centric reflection for each shell. phasing_MIR_shell.power The mean phasing power P for reflections in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections phasing_MIR_shell.reflns The number of reflections in this shell. phasing_MIR_shell.reflns_acentric The number of acentric reflections in this shell. phasing_MIR_shell.reflns_anomalous The number of anomalous reflections in this shell. phasing_MIR_shell.reflns_centric The number of centric reflections in this shell. phasing_MIR_shell.d_res_high The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. Note that the resolution limits of shells in the items attribute d_res_high in category phasing_MIR_shell and attribute d_res_low in category phasing_MIR_shell are independent of the resolution limits of shells in the items attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell. phasing_MIR_shell.d_res_low The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. Note that the resolution limits of shells in the items attribute d_res_high in category phasing_MIR_shell and attribute d_res_low in category phasing_MIR_shell are independent of the resolution limits of shells in the items attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell. 0 phasing_averaging Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved. Example 1 - hypothetical example. <VRPTx:phasing_averagingCategory> <VRPTx:phasing_averaging entry_id="EXAMHYPO"> <VRPTx:details> The position of the threefold axis was redetermined every five cycles.</VRPTx:details> <VRPTx:method> Iterative threefold averaging alternating with phase extensions by 0.5 reciprocal lattice units per cycle.</VRPTx:method> </VRPTx:phasing_averaging> </VRPTx:phasing_averagingCategory> 0 1 0 1 1 phasing_averagingCategory This property indicates that datablock has a category holder phasing_averagingCategory. phasing_averagingCategory This property indicates that phasing_averagingCategory. has a category phasing_averaging. phasing_averagingItem Abstract datatype property for phasing_averaging items. reference_to_phasing_averaging cross-reference to phasing_averaging. referenced_by_phasing_averaging cross-reference from phasing_averaging. phasing_averaging.details A description of special aspects of the averaging process. phasing_averaging.method A description of the phase-averaging phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the phase-averaging program. phasing_averaging.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 phasing_isomorphous Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases. Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV. <VRPTx:phasing_isomorphousCategory> <VRPTx:phasing_isomorphous entry_id="1ABC"> <VRPTx:details> The inhibitor and all solvent atoms were removed from the parent structure before beginning refinement. All static disorder present in the parent structure was also removed.</VRPTx:details> <VRPTx:parent>PDB entry 5HVP</VRPTx:parent> </VRPTx:phasing_isomorphous> </VRPTx:phasing_isomorphousCategory> 0 1 0 1 0 1 1 phasing_isomorphousCategory This property indicates that datablock has a category holder phasing_isomorphousCategory. phasing_isomorphousCategory This property indicates that phasing_isomorphousCategory. has a category phasing_isomorphous. phasing_isomorphousItem Abstract datatype property for phasing_isomorphous items. reference_to_phasing_isomorphous cross-reference to phasing_isomorphous. referenced_by_phasing_isomorphous cross-reference from phasing_isomorphous. phasing_isomorphous.details A description of special aspects of the isomorphous phasing. Residues 13-18 were eliminated from the starting model as it was anticipated that binding of the inhibitor would cause a structural rearrangement in this part of the structure. phasing_isomorphous.method A description of the isomorphous-phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the isomorphous phasing program. Iterative threefold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle. phasing_isomorphous.parent Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g. a mutant that crystallizes in the same space group as the wild-type protein.) phasing_isomorphous.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 phasing_set Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block. Example 1 - based on laboratory records for an Hg/Pt derivative of protein NS1. <VRPTx:phasing_setCategory> <VRPTx:phasing_set id="NS1-96"> <VRPTx:cell_angle_alpha>90.0</VRPTx:cell_angle_alpha> <VRPTx:cell_angle_beta>90.0</VRPTx:cell_angle_beta> <VRPTx:cell_angle_gamma>90.0</VRPTx:cell_angle_gamma> <VRPTx:cell_length_a>38.63</VRPTx:cell_length_a> <VRPTx:cell_length_b>38.63</VRPTx:cell_length_b> <VRPTx:cell_length_c>82.88</VRPTx:cell_length_c> <VRPTx:detector_specific>RXII</VRPTx:detector_specific> <VRPTx:detector_type>image plate</VRPTx:detector_type> <VRPTx:radiation_wavelength>1.5145</VRPTx:radiation_wavelength> </VRPTx:phasing_set> </VRPTx:phasing_setCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 1 phasing_setCategory This property indicates that datablock has a category holder phasing_setCategory. phasing_setCategory This property indicates that phasing_setCategory. has a category phasing_set. phasing_setItem Abstract datatype property for phasing_set items. reference_to_phasing_set cross-reference to phasing_set. referenced_by_phasing_set cross-reference from phasing_set. phasing_set.cell_angle_alpha Unit-cell angle alpha for this data set in degrees. phasing_set.cell_angle_beta Unit-cell angle beta for this data set in degrees. phasing_set.cell_angle_gamma Unit-cell angle gamma for this data set in degrees. phasing_set.cell_length_a Unit-cell length a for this data set in angstroms. phasing_set.cell_length_b Unit-cell length b for this data set in angstroms. phasing_set.cell_length_c Unit-cell length c for this data set in angstroms. phasing_set.detector_specific The particular radiation detector. In general, this will be a manufacturer, description, model number or some combination of these. Siemens model x Kodak XG MAR Research model y phasing_set.detector_type The general class of the radiation detector. multiwire imaging plate CCD film phasing_set.pdbx_d_res_high The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. phasing_set.pdbx_d_res_low The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. phasing_set.pdbx_temp_details The value of attribute pdbx_temp_details in category phasing_set describes any special details about the data collection temperature for this phasing data set. phasing_set.radiation_source_specific The particular source of radiation. In general, this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources. Rigaku RU200 Philips fine focus Mo NSLS beamline X8C phasing_set.radiation_wavelength The mean wavelength of the radiation used to measure this data set. phasing_set.temp The temperature in kelvins at which the data set was measured. phasing_set.id The value of attribute id in category phasing_set must uniquely identify a record in the PHASING_SET list. Note that this item need not be a number; it can be any unique identifier. KAu(CN)2 K2HgI4 0 phasing_set_refln Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; attribute set_id in category phasing_set_refln indicates the data set to which a given record corresponds. Example 1 - based on laboratory records for the 15,15,32 reflection of an Hg/Pt derivative of protein NS1. <VRPTx:phasing_set_reflnCategory> <VRPTx:phasing_set_refln index_h="15" index_k="15" index_l="32" set_id="NS1-96"> <VRPTx:F_meas_au>181.79</VRPTx:F_meas_au> <VRPTx:F_meas_sigma_au>3.72</VRPTx:F_meas_sigma_au> </VRPTx:phasing_set_refln> </VRPTx:phasing_set_reflnCategory> 0 1 0 1 0 1 0 1 1 1 1 1 phasing_set_reflnCategory This property indicates that datablock has a category holder phasing_set_reflnCategory. phasing_set_reflnCategory This property indicates that phasing_set_reflnCategory. has a category phasing_set_refln. phasing_set_reflnItem Abstract datatype property for phasing_set_refln items. reference_to_phasing_set_refln cross-reference to phasing_set_refln. referenced_by_phasing_set_refln cross-reference from phasing_set_refln. phasing_set_refln.F_meas The measured value of the structure factor for this reflection in this data set in electrons. phasing_set_refln.F_meas_au The measured value of the structure factor for this reflection in this data set in arbitrary units. phasing_set_refln.F_meas_sigma The standard uncertainty (estimated standard deviation) of attribute F_meas in category phasing_set_refln in electrons. phasing_set_refln.F_meas_sigma_au The standard uncertainty (estimated standard deviation) of attribute F_meas_au in category phasing_set_refln in arbitrary units. phasing_set_refln.index_h Miller index h of this reflection in this data set. phasing_set_refln.index_k Miller index k of this reflection in this data set. phasing_set_refln.index_l Miller index l of this reflection in this data set. phasing_set_refln.set_id This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. 0 refine Data items in the REFINE category record details about the structure-refinement parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:refineCategory> <VRPTx:refine entry_id="5HVP" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:ls_R_factor_obs>0.176</VRPTx:ls_R_factor_obs> <VRPTx:ls_number_parameters>7032</VRPTx:ls_number_parameters> <VRPTx:ls_number_reflns_obs>12901</VRPTx:ls_number_reflns_obs> <VRPTx:ls_number_restraints>6609</VRPTx:ls_number_restraints> <VRPTx:ls_weighting_details> Sigdel model of Konnert-Hendrickson: Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = -150.0 at beginning of refinement Afsig = 15.5, Bfsig = -50.0 at end of refinement</VRPTx:ls_weighting_details> <VRPTx:ls_weighting_scheme>calc</VRPTx:ls_weighting_scheme> </VRPTx:refine> </VRPTx:refineCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:refineCategory> <VRPTx:refine entry_id="TOZ" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:details>sfls:_F_calc_weight_full_matrix</VRPTx:details> <VRPTx:diff_density_max>.131</VRPTx:diff_density_max> <VRPTx:diff_density_min>-.108</VRPTx:diff_density_min> <VRPTx:ls_R_factor_all>.038</VRPTx:ls_R_factor_all> <VRPTx:ls_R_factor_obs>.034</VRPTx:ls_R_factor_obs> <VRPTx:ls_abs_structure_Flack>0</VRPTx:ls_abs_structure_Flack> <VRPTx:ls_abs_structure_details> The absolute configuration was assigned to agree with the known chirality at C3 arising from its precursor l-leucine.</VRPTx:ls_abs_structure_details> <VRPTx:ls_extinction_coef>3514</VRPTx:ls_extinction_coef> <VRPTx:ls_extinction_expression> Larson, A. C. (1970). &quot;Crystallographic Computing&quot;, edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.</VRPTx:ls_extinction_expression> <VRPTx:ls_extinction_method>Zachariasen</VRPTx:ls_extinction_method> <VRPTx:ls_goodness_of_fit_all>1.462</VRPTx:ls_goodness_of_fit_all> <VRPTx:ls_goodness_of_fit_obs>1.515</VRPTx:ls_goodness_of_fit_obs> <VRPTx:ls_hydrogen_treatment>refxyz except H332B noref</VRPTx:ls_hydrogen_treatment> <VRPTx:ls_matrix_type>full</VRPTx:ls_matrix_type> <VRPTx:ls_number_constraints>0</VRPTx:ls_number_constraints> <VRPTx:ls_number_parameters>272</VRPTx:ls_number_parameters> <VRPTx:ls_number_reflns_obs>1408</VRPTx:ls_number_reflns_obs> <VRPTx:ls_number_restraints>0</VRPTx:ls_number_restraints> <VRPTx:ls_shift_over_esd_max>.535</VRPTx:ls_shift_over_esd_max> <VRPTx:ls_shift_over_esd_mean>.044</VRPTx:ls_shift_over_esd_mean> <VRPTx:ls_structure_factor_coef>F</VRPTx:ls_structure_factor_coef> <VRPTx:ls_wR_factor_all>.044</VRPTx:ls_wR_factor_all> <VRPTx:ls_wR_factor_obs>.042</VRPTx:ls_wR_factor_obs> <VRPTx:ls_weighting_details>w=1/(\s^2^(F)+0.0004F^2^)</VRPTx:ls_weighting_details> <VRPTx:ls_weighting_scheme>calc</VRPTx:ls_weighting_scheme> </VRPTx:refine> </VRPTx:refineCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 refineCategory This property indicates that datablock has a category holder refineCategory. refineCategory This property indicates that refineCategory. has a category refine. refineItem Abstract datatype property for refine items. reference_to_refine cross-reference to refine. referenced_by_refine cross-reference from refine. refine.B_iso_max The maximum isotropic displacement parameter (B value) found in the coordinate set. refine.B_iso_mean The mean isotropic displacement parameter (B value) for the coordinate set. refine.B_iso_min The minimum isotropic displacement parameter (B value) found in the coordinate set. refine.aniso_B11 The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. refine.aniso_B12 The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. refine.aniso_B13 The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. refine.aniso_B22 The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. refine.aniso_B23 The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. refine.aniso_B33 The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. refine.correlation_coeff_Fo_to_Fc The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections included in the refinement refine.correlation_coeff_Fo_to_Fc_free The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections not included in the refinement (free reflections) refine.details Description of special aspects of the refinement process. refine.diff_density_max The maximum value of the electron density in the final difference Fourier map. refine.diff_density_max_esd The standard uncertainty (estimated standard deviation) of attribute diff_density_max in category refine. refine.diff_density_min The minimum value of the electron density in the final difference Fourier map. refine.diff_density_min_esd The standard uncertainty (estimated standard deviation) of attribute diff_density_min in category refine. refine.diff_density_rms The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. refine.diff_density_rms_esd The standard uncertainty (estimated standard deviation) of attribute diff_density_rms in category refine. refine.ls_R_Fsqd_factor_obs Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, calculated on the squares of the observed and calculated structure-factor amplitudes. sum|F~obs~^2^ - F~calc~^2^| R(Fsqd) = --------------------------- sum|F~obs~^2^| F~obs~^2^ = squares of the observed structure-factor amplitudes F~calc~^2^ = squares of the calculated structure-factor amplitudes sum is taken over the specified reflections refine.ls_R_I_factor_obs Residual factor R(I) for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum|I~obs~ - I~calc~| R(I) = --------------------- sum|I~obs~| I~obs~ = the net observed intensities I~calc~ = the net calculated intensities sum is taken over the specified reflections refine.ls_R_factor_R_free Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine.ls_R_factor_R_free_error The estimated error in attribute ls_R_factor_R_free. in category refine The method used to estimate the error is described in the item attribute ls_R_factor_R_free_error_details in category refine. refine.ls_R_factor_R_free_error_details Special aspects of the method used to estimated the error in attribute ls_R_factor_R_free in category refine. refine.ls_R_factor_R_work Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine.ls_R_factor_all Residual factor R for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine.ls_R_factor_gt Residual factor for the reflections (with number given by attribute number_gt) in category reflns judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. The reflections also satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine. This is the conventional R factor. See also attribute ls_wR_factor_ in category refine definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections refine.ls_R_factor_obs Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine.ls_abs_structure_Flack The measure of absolute structure (enantiomorph or polarity) as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data name is present, is 'inapplicable', represented by '.' . For noncentrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [0.0:1.0] is correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. refine.ls_abs_structure_Flack_esd The standard uncertainty (estimated standard deviation) of attribute ls_abs_structure_Flack in category refine. refine.ls_abs_structure_Rogers The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< \h =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [-1.0, 1.0] is correctly interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. refine.ls_abs_structure_Rogers_esd The standard uncertainty (estimated standard deviation) of attribute ls_abs_structure_Rogers in category refine. refine.ls_abs_structure_details The nature of the absolute structure and how it was determined. For example, this may describe the Friedel pairs used. refine.ls_d_res_high The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution. refine.ls_d_res_low The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution. refine.ls_extinction_coef The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of attribute ls_extinction_expression in category refine and attribute ls_extinction_method. in category refine For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-47, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. Zachariasen coefficient r* = 0.347 E04 3472 refine.ls_extinction_coef_esd The standard uncertainty (estimated standard deviation) of attribute ls_extinction_coef in category refine. refine.ls_extinction_expression A description of or reference to the extinction-correction equation used to apply the data item attribute ls_extinction_coef in category refine. This information must be sufficient to reproduce the extinction-correction factors applied to the structure factors. Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard. refine.ls_extinction_method A description of the extinction-correction method applied. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method, it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian' and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied, the multiple coefficients cannot be contained in *_extinction_coef and must be listed in attribute details. in category refine Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. B-C type 2 Gaussian isotropic refine.ls_goodness_of_fit_all The least-squares goodness-of-fit parameter S for all data after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of attribute ls_restrained_S_all. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections refine.ls_goodness_of_fit_all_esd The standard uncertainty (estimated standard deviation) of attribute ls_goodness_of_fit_all in category refine. refine.ls_goodness_of_fit_gt The least-squares goodness-of-fit parameter S for significantly intense reflections (see attribute threshold_expression) in category reflns after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also attribute ls_restrained_S_ in category refine definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections refine.ls_goodness_of_fit_obs The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see attribute observed_criterion) in category reflns after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of attribute ls_restrained_S_obs. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections refine.ls_goodness_of_fit_obs_esd The standard uncertainty (estimated standard deviation) of attribute ls_goodness_of_fit_obs in category refine. refine.ls_goodness_of_fit_ref The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections refall refxyz refU noref constr mixed undef Treatment of hydrogen atoms in the least-squares refinement. full fullcycle atomblock userblock diagonal sparse Type of matrix used to accumulate the least-squares derivatives. refine.ls_number_constraints The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site.refinement_flags. A general description of constraints may appear in attribute details in category refine. refine.ls_number_parameters The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. refine.ls_number_reflns_R_free The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. refine.ls_number_reflns_R_work The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. refine.ls_number_reflns_all The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. refine.ls_number_reflns_obs The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns. refine.ls_number_restraints The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in attribute details in category refine. refine.ls_percent_reflns_R_free The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. refine.ls_percent_reflns_obs The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. refine.ls_redundancy_reflns_all The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits. refine.ls_redundancy_reflns_obs The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns to the number of crystallographically unique reflections that satisfy the same limits. refine.ls_restrained_S_all The least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of attribute ls_goodness_of_fit_all. in category refine ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see attribute ls_number_reflns_obs) in category refine N~restr~ = the number of restraints (see attribute ls_number_restraints) in category refine N~param~ = the number of refined parameters (see attribute ls_number_parameters) in category refine sum is taken over the specified reflections sumr is taken over the restraints refine.ls_restrained_S_obs The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see attribute observed_criterion) in category reflns after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of attribute ls_goodness_of_fit_obs. in category refine ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see attribute ls_number_reflns_obs) in category refine N~restr~ = the number of restraints (see attribute ls_number_restraints) in category refine N~param~ = the number of refined parameters (see attribute ls_number_parameters) in category refine sum is taken over the specified reflections sumr is taken over the restraints refine.ls_shift_over_esd_max The largest ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). refine.ls_shift_over_esd_mean The average ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). refine.ls_shift_over_su_max The largest ratio of the final least-squares parameter shift to the final standard uncertainty. refine.ls_shift_over_su_max_lt An upper limit for the largest ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the largest value of the shift divided by the final standard uncertainty is too small to measure. refine.ls_shift_over_su_mean The average ratio of the final least-squares parameter shift to the final standard uncertainty. refine.ls_shift_over_su_mean_lt An upper limit for the average ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the average value of the shift divided by the final standard uncertainty is too small to measure. F Fsqd Inet Structure-factor coefficient |F|, F^2^ or I used in the least- squares refinement process. refine.ls_wR_factor_R_free Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine.ls_wR_factor_R_work Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine.ls_wR_factor_all Weighted residual factor wR for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine.ls_wR_factor_obs Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine.ls_weighting_details A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of attribute ls_weighting_scheme in category refine is specified as 'calc'. Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. sigma unit calc The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see attribute ls_weighting_details in category refine for a preferred approach). refine.occupancy_max The maximum value for occupancy found in the coordinate set. refine.occupancy_min The minimum value for occupancy found in the coordinate set. refine.overall_FOM_free_R_set Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I~1~(X)/I~0~(X) I~0~, I~1~ = zero- and first-order modified Bessel functions of the first kind X = sigma~A~ |E~o~| |E~c~|/SIGMA E~o~, E~c~ = normalized observed and calculated structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = form factor of atoms delta~x~ = expected error SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. refine.overall_FOM_work_R_set Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function. FOM = I~1~(X)/I~0~(X) I~0~, I~1~ = zero- and first-order modified Bessel functions of the first kind X = sigma~A~ |E~o~| |E~c~|/SIGMA E~o~, E~c~ = normalized observed and calculated structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = form factor of atoms delta~x~ = expected error SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. refine.overall_SU_B The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum-likelihood residual. The overall standard uncertainty (sigma~B~)^2^ gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 8 ---------------------------------------------- sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^} N~a~ = number of atoms E~o~ = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigma~A~)^2^/Sigma^2^ Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = experimental uncertainties of normalized structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = atom form factor delta~x~ = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma~A~ estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU B estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html refine.overall_SU_ML The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2^ gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N~a~ (sigma~X~)^2^ = --------------------------------------------------------- 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^} N~a~ = number of atoms E~o~ = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigma~A~)^2^/Sigma^2^ Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = experimental uncertainties of normalized structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = atom form factor delta~x~ = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html refine.overall_SU_R_Cruickshank_DPI The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^ (N~o~-N~p~) N~a~ = number of atoms included in refinement N~o~ = number of observations N~p~ = number of parameters refined R~value~ = conventional crystallographic R value D~min~ = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html refine.overall_SU_R_free The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value. The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^ (N~o~-N~p~) N~a~ = number of atoms included in refinement N~o~ = number of observations N~p~ = number of parameters refined R~free~ = conventional free crystallographic R value calculated using reflections not included in refinement D~min~ = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html refine.pdbx_R_Free_selection_details Details of the manner in which the cross validation reflections were selected. Random selection refine.pdbx_R_complete The crystallographic reliability index Rcomplete for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns Ref: Luebben, J., Gruene, T., (2015). Proc.Nat.Acad.Sci. 112(29) 8999-9003 LIKELY RESIDUAL UNVERIFIED A flag for TLS refinements identifying the type of atomic displacement parameters stored in attribute B_iso_or_equiv in category atom_site. refine.pdbx_average_fsc_free Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections not included in refinement. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~free-i~) avgFSC~free~ = --------------------- sum(N~i~) N~i~ = the number of free reflections in the resolution shell i FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free-i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~free-i~ is carried over all free reflections in the resolution shell. Summation of avgFSC~free~ is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). refine.pdbx_average_fsc_overall Overall average Fourier Shell Correlation (avgFSC) between model and observed structure factors for all reflections. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~i~) avgFSC = ---------------- sum(N~i~) N~i~ = the number of all reflections in the resolution shell i FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~i~ is carried over all reflections in the resolution shell. Summation of avgFSC is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). refine.pdbx_average_fsc_work Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections included in refinement. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~work-i~) avgFSC~work~ = --------------------- sum(N~i~) N~i~ = the number of working reflections in the resolution shell i FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work-i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~work-i~ is carried over all working reflections in the resolution shell. Summation of avgFSC~work~ is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). refine.pdbx_data_cutoff_high_absF Value of F at "high end" of data cutoff. 17600 refine.pdbx_data_cutoff_high_rms_absF Value of RMS |F| used as high data cutoff. 205.1 refine.pdbx_data_cutoff_low_absF Value of F at "low end" of data cutoff. 0.30 refine.pdbx_density_correlation The density correlation coefficient is calculated from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of all atoms <Rcalc> is the mean of "calculated" densities of all atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 refine.pdbx_diffrn_id An identifier for the diffraction data set used in this refinement. Multiple diffraction data sets specified as a comma separated list. refine.pdbx_isotropic_thermal_model Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor. Isotropic Overall refine.pdbx_ls_cross_valid_method Whether the cross validataion method was used through out or only at the end. FREE R-VALUE refine.pdbx_ls_sigma_F Data cutoff (SIGMA(F)) refine.pdbx_ls_sigma_Fsqd Data cutoff (SIGMA(F^2)) refine.pdbx_ls_sigma_I Data cutoff (SIGMA(I)) refine.pdbx_method_to_determine_struct Method(s) used to determine the structure. AB INITIO PHASING Direct Methods DM Iterative Single wavelength Anomalous Scattering ISAS Iterative Single Isomorphous Replacement ISIR Iterative Single Isomorphous Replacement with Anomalous Scattering ISIRAS Multi wavelength Anomalous Diffraction MAD Multiple Isomorphous Replacement MIR Multiple Isomorphous Replacement with Anomalous Scattering MIRAS Molecular Replacement MR Single Isomorphous Replacement SIR Single Isomorphous Replacement with Anomalous Scattering SIRAS refine.pdbx_overall_ESU_R Overall estimated standard uncertainties of positional parameters based on R value. refine.pdbx_overall_ESU_R_Free Overall estimated standard uncertainties of positional parameters based on R free value. refine.pdbx_overall_SU_R_Blow_DPI The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Blow, D (2002) Acta Cryst. D58, 792-797 refine.pdbx_overall_SU_R_free_Blow_DPI The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Blow, D (2002) Acta Cryst. D58, 792-797 refine.pdbx_overall_SU_R_free_Cruickshank_DPI The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. refine.pdbx_overall_phase_error The overall phase error for all reflections after refinement using the current refinement target. 0.30 refine.pdbx_pd_Fsqrd_R_factor Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns sum|F~obs~**2 - F~calc~**2| R = --------------------- sum|F~obs~**2| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine.pdbx_pd_Marquardt_correlation_coeff The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. This correlation factor is found in the fitting using the Levenberg-Marquardt algorithm to search for the minimum value of chisquare. Almost all computer codes for Rietveld refinement employ the Gauss-Newton algorithm to find parameters which minimize the weighted sum of squares of the residuals. A description of the equations is given on http://www.water.hut.fi/~tkarvone/fr_org_s.htm refine.pdbx_pd_ls_matrix_band_width The least squares refinement "band matrix" approximation to the full matrix. refine.pdbx_pd_meas_number_of_points The total number of points in the measured diffractogram. refine.pdbx_pd_number_of_points The total number of data points in the processed diffractogram. refine.pdbx_pd_number_of_powder_patterns The total number of powder patterns used. refine.pdbx_pd_proc_ls_prof_R_factor Rietveld/Profile fit R factors. Note that the R factor computed for Rietveld refinements using the extracted reflection intensity values (often called the Rietveld or Bragg R factor, R~B~) is not properly a profile R factor. pdbx_pd_proc_ls_prof_R_factor, often called R~p~, is an unweighted fitness metric for the agreement between the observed and computed diffraction patterns R~p~ = sum~i~ | I~obs~(i) - I~calc~(i) | / sum~i~ ( I~obs~(i) ) Note that in the above equations, w(i) is the weight for the ith data point I~obs~(i) is the observed intensity for the ith data point, sometimes referred to as y~i~(obs) or y~oi~. I~calc~(i) is the computed intensity for the ith data point with background and other corrections applied to match the scale of the observed dataset, sometimes referred to as y~i~(calc) or y~ci~. n is the total number of data points (see attribute pdbx_pd_number_of_points) in category refine less the number of data points excluded from the refinement. p is the total number of refined parameters. refine.pdbx_pd_proc_ls_prof_wR_factor Rietveld/Profile fit R factors. Note that the R factor computed for Rietveld refinements using the extracted reflection intensity values (often called the Rietveld or Bragg R factor, R~B~) is not properly a profile R factor. pdbx_pd_proc_ls_prof_wR_factor often called R~wp~, is a weighted fitness metric for the agreement between the observed and computed diffraction patterns R~wp~ = SQRT { sum~i~ ( w(i) [ I~obs~(i) - I~calc~(i) ]^2^ ) / sum~i~ ( w(i) [I~obs~(i)]^2^ ) } Note that in the above equations, w(i) is the weight for the ith data point I~obs~(i) is the observed intensity for the ith data point, sometimes referred to as y~i~(obs) or y~oi~. I~calc~(i) is the computed intensity for the ith data point with background and other corrections applied to match the scale of the observed dataset, sometimes referred to as y~i~(calc) or y~ci~. n is the total number of data points (see attribute pdbx_pd_number_of_points) in category refine less the number of data points excluded from the refinement. p is the total number of refined parameters. refine.pdbx_real_space_R Real space R factor of electron density for all atoms. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 refine.pdbx_solvent_ion_probe_radii For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used. refine.pdbx_solvent_shrinkage_radii For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region. refine.pdbx_solvent_vdw_probe_radii For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used. refine.pdbx_starting_model Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment. BDL001 refine.pdbx_stereochem_target_val_spec_case Special case of stereochemistry target values used in SHELXL refinement. refine.pdbx_stereochemistry_target_values Stereochemistry target values used in refinement. refine.solvent_model_details Special aspects of the solvent model used during refinement. refine.solvent_model_param_bsol The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms. This is one of the two parameters (the other is attribute solvent_model_param_ksol) in category refine in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. refine.solvent_model_param_ksol The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute. This is one of the two parameters (the other is attribute solvent_model_param_bsol) in category refine in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. refine.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. refine.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine can be used to distinguish the results of joint refinements. 0 refine_B_iso Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:refine_B_isoCategory> <VRPTx:refine_B_iso class="protein" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:treatment>isotropic</VRPTx:treatment> </VRPTx:refine_B_iso> <VRPTx:refine_B_iso class="solvent" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:treatment>isotropic</VRPTx:treatment> </VRPTx:refine_B_iso> <VRPTx:refine_B_iso class="inhibitor" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:treatment>isotropic</VRPTx:treatment> </VRPTx:refine_B_iso> </VRPTx:refine_B_isoCategory> 0 1 0 1 0 1 1 1 refine_B_isoCategory This property indicates that datablock has a category holder refine_B_isoCategory. refine_B_isoCategory This property indicates that refine_B_isoCategory. has a category refine_B_iso. refine_B_isoItem Abstract datatype property for refine_B_iso items. reference_to_refine_B_iso cross-reference to refine_B_iso. referenced_by_refine_B_iso cross-reference from refine_B_iso. refine_B_iso.details A description of special aspects of the isotropic B-factor (displacement-parameter) refinement for the class of atoms described in attribute class in category refine_B_iso. The temperature factors of atoms in the side chain of Arg 92 were held fixed due to unstable behavior in refinement. fixed isotropic anisotropic The treatment of isotropic B-factor (displacement-parameter) refinement for a class of atoms defined in attribute class in category refine_B_iso. refine_B_iso.value The value of the isotropic B factor (displacement parameter) assigned to a class of atoms defined in attribute class. in category refine_B_iso Meaningful only for atoms with fixed isotropic B factors. refine_B_iso.class A class of atoms treated similarly for isotropic B-factor (displacement-parameter) refinement. all protein solvent sugar-phosphate backbone refine_B_iso.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_B_iso can be used to distinguish the results of joint refinements. 0 refine_analyze Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:refine_analyzeCategory> <VRPTx:refine_analyze entry_id="5HVP" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:Luzzati_coordinate_error_obs>0.056</VRPTx:Luzzati_coordinate_error_obs> <VRPTx:Luzzati_d_res_low_obs>2.51</VRPTx:Luzzati_d_res_low_obs> </VRPTx:refine_analyze> </VRPTx:refine_analyzeCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 refine_analyzeCategory This property indicates that datablock has a category holder refine_analyzeCategory. refine_analyzeCategory This property indicates that refine_analyzeCategory. has a category refine_analyze. refine_analyzeItem Abstract datatype property for refine_analyze items. reference_to_refine_analyze cross-reference to refine_analyze. referenced_by_refine_analyze cross-reference from refine_analyze. refine_analyze.Luzzati_coordinate_error_free The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_coordinate_error_obs The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_d_res_low_free The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_d_res_low_obs The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_sigma_a_free The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigma~a~ can be specified in attribute Luzzati_sigma_a_free_details. in category refine_analyze Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_sigma_a_free_details Details of the estimation of sigma~a~ for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_sigma_a_obs The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigma~a~ can be specified in attribute Luzzati_sigma_a_obs_details. in category refine_analyze Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.Luzzati_sigma_a_obs_details Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. refine_analyze.RG_d_res_high The value of the high-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in attribute RG_work in category refine_analyze and attribute RG_free. in category refine_analyze Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. refine_analyze.RG_d_res_low The value of the low-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in attribute RG_work in category refine_analyze and attribute RG_free. in category refine_analyze Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. refine_analyze.RG_free The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by attribute RG_d_res_high in category refine_analyze and attribute RG_d_res_low in category refine_analyze for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. refine_analyze.RG_free_work_ratio The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in the data and the model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement, the ratio of RGfree to RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters according to sqrt[(f + m) / (f - m) ] where f = the number of included structure amplitudes and target distances, and m = the number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in the refinement, the RG ratio requires a term for the contribution to the minimized residual at convergence, D~restr~, due to those restraints: D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i] where r is the number of geometrical, displacement-parameter and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ] There is no data name for the expected value of RGfree/RGwork yet. Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557. refine_analyze.RG_work The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by attribute RG_d_res_high in category refine_analyze and attribute RG_d_res_low in category refine_analyze and for those reflections included in the working set when a free R set of reflections is omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. refine_analyze.number_disordered_residues The number of discretely disordered residues in the refined model. refine_analyze.occupancy_sum_hydrogen The sum of the occupancies of the hydrogen atoms in the refined model. refine_analyze.occupancy_sum_non_hydrogen The sum of the occupancies of the non-hydrogen atoms in the refined model. refine_analyze.pdbx_Luzzati_d_res_high_obs Record the high resolution for calculating Luzzati statistics. refine_analyze.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. refine_analyze.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_analyze can be used to distinguish the results of joint refinements. 0 refine_funct_minimized Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement. Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. <VRPTx:refine_funct_minimizedCategory> <VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Amplitude)^2"> <VRPTx:number_terms>3009</VRPTx:number_terms> <VRPTx:residual>1621.3</VRPTx:residual> </VRPTx:refine_funct_minimized> <VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Plane+Rigid)^2"> <VRPTx:number_terms>85</VRPTx:number_terms> <VRPTx:residual>56.68</VRPTx:residual> </VRPTx:refine_funct_minimized> <VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Distance)^2"> <VRPTx:number_terms>1219</VRPTx:number_terms> <VRPTx:residual>163.59</VRPTx:residual> </VRPTx:refine_funct_minimized> <VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(U-tempfactors)^2"> <VRPTx:number_terms>1192</VRPTx:number_terms> <VRPTx:residual>69.338</VRPTx:residual> </VRPTx:refine_funct_minimized> </VRPTx:refine_funct_minimizedCategory> 0 1 0 1 0 1 1 1 refine_funct_minimizedCategory This property indicates that datablock has a category holder refine_funct_minimizedCategory. refine_funct_minimizedCategory This property indicates that refine_funct_minimizedCategory. has a category refine_funct_minimized. refine_funct_minimizedItem Abstract datatype property for refine_funct_minimized items. reference_to_refine_funct_minimized cross-reference to refine_funct_minimized. referenced_by_refine_funct_minimized cross-reference from refine_funct_minimized. refine_funct_minimized.number_terms The number of observations in this term. For example, if the term is a residual of the X-ray intensities, this item would contain the number of reflections used in the refinement. refine_funct_minimized.residual The residual for this term of the function that was minimized during the refinement. refine_funct_minimized.weight The weight applied to this term of the function that was minimized during the refinement. refine_funct_minimized.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_funct_minimized can be used to distinguish the results of joint refinements. refine_funct_minimized.type The type of the function being minimized. 0 refine_hist Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics. Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. <VRPTx:refine_histCategory> <VRPTx:refine_hist cycle_id="C134" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_R_free>.274</VRPTx:R_factor_R_free> <VRPTx:R_factor_R_work>.160</VRPTx:R_factor_R_work> <VRPTx:R_factor_all>.265</VRPTx:R_factor_all> <VRPTx:R_factor_obs>.195</VRPTx:R_factor_obs> <VRPTx:d_res_high>1.85</VRPTx:d_res_high> <VRPTx:d_res_low>20.0</VRPTx:d_res_low> <VRPTx:details> Add majority of solvent molecules. B factors refined by group. Continued to remove misplaced water molecules.</VRPTx:details> <VRPTx:number_atoms_solvent>217</VRPTx:number_atoms_solvent> <VRPTx:number_atoms_total>808</VRPTx:number_atoms_total> <VRPTx:number_reflns_R_free>476</VRPTx:number_reflns_R_free> <VRPTx:number_reflns_R_work>4410</VRPTx:number_reflns_R_work> <VRPTx:number_reflns_all>6174</VRPTx:number_reflns_all> <VRPTx:number_reflns_obs>4886</VRPTx:number_reflns_obs> </VRPTx:refine_hist> </VRPTx:refine_histCategory> 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 refine_histCategory This property indicates that datablock has a category holder refine_histCategory. refine_histCategory This property indicates that refine_histCategory. has a category refine_hist. refine_histItem Abstract datatype property for refine_hist items. reference_to_refine_hist cross-reference to refine_hist. referenced_by_refine_hist cross-reference from refine_hist. refine_hist.R_factor_R_free Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_hist.R_factor_R_work Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_hist.R_factor_all Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low. in category refine_hist sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_hist.R_factor_obs Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation criterion established by attribute observed_criterion. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_hist.d_res_high The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution. refine_hist.d_res_low The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution. refine_hist.details A description of special aspects of this cycle of the refinement process. Residues 13-17 fit and added to model; substantial rebuilding of loop containing residues 43-48; addition of first atoms to solvent model; ten cycles of Prolsq refinement. refine_hist.number_atoms_solvent The number of solvent atoms that were included in the model at this cycle of the refinement. refine_hist.number_atoms_total The total number of atoms that were included in the model at this cycle of the refinement. refine_hist.number_reflns_R_free The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. refine_hist.number_reflns_R_work The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. refine_hist.number_reflns_all The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist. refine_hist.number_reflns_obs The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation criterion established by attribute observed_criterion in category reflns. refine_hist.pdbx_B_iso_mean_ligand Mean isotropic B-value for ligand molecules included in refinement. refine_hist.pdbx_B_iso_mean_solvent Mean isotropic B-value for solvent molecules included in refinement. refine_hist.pdbx_number_atoms_carb Number of carbohydrate atoms included in refinement refine_hist.pdbx_number_atoms_ligand Number of ligand atoms included in refinement refine_hist.pdbx_number_atoms_lipid Number of lipid atoms included in refinement refine_hist.pdbx_number_atoms_nucleic_acid Number of nucleic atoms included in refinement refine_hist.pdbx_number_atoms_protein Number of protein atoms included in refinement refine_hist.pdbx_number_residues_total Total number of polymer residues included in refinement. refine_hist.pdbx_pseudo_atom_details Details of pseduo atoms used to model unexplained density refine_hist.cycle_id The value of attribute cycle_id in category refine_hist must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. refine_hist.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_hist can be used to distinguish the results of joint refinements. 0 refine_ls_class Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately. Example 1 - data for a modulated structure from van Smaalen [J. Phys. Condens. Matter (1991), 3, 1247-1263]. <VRPTx:refine_ls_classCategory> <VRPTx:refine_ls_class code="Main"> <VRPTx:R_factor_gt>0.057</VRPTx:R_factor_gt> </VRPTx:refine_ls_class> <VRPTx:refine_ls_class code="Com"> <VRPTx:R_factor_gt>0.074</VRPTx:R_factor_gt> </VRPTx:refine_ls_class> <VRPTx:refine_ls_class code="NbRefls"> <VRPTx:R_factor_gt>0.064</VRPTx:R_factor_gt> </VRPTx:refine_ls_class> <VRPTx:refine_ls_class code="LaRefls"> <VRPTx:R_factor_gt>0.046</VRPTx:R_factor_gt> </VRPTx:refine_ls_class> <VRPTx:refine_ls_class code="Sat1"> <VRPTx:R_factor_gt>0.112</VRPTx:R_factor_gt> </VRPTx:refine_ls_class> <VRPTx:refine_ls_class code="Sat2"> <VRPTx:R_factor_gt>0.177</VRPTx:R_factor_gt> </VRPTx:refine_ls_class> </VRPTx:refine_ls_classCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 refine_ls_classCategory This property indicates that datablock has a category holder refine_ls_classCategory. refine_ls_classCategory This property indicates that refine_ls_classCategory. has a category refine_ls_class. refine_ls_classItem Abstract datatype property for refine_ls_class items. reference_to_refine_ls_class cross-reference to refine_ls_class. referenced_by_refine_ls_class cross-reference from refine_ls_class. refine_ls_class.R_Fsqd_factor For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors, for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. refine_ls_class.R_I_factor For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~ sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. refine_ls_class.R_factor_all For each reflection class, the residual factor for all reflections satisfying the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category refine_ls_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. refine_ls_class.R_factor_gt For each reflection class, the residual factor for significantly intense reflections (see attribute threshold_expression) in category reflns included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category refine_ls_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. refine_ls_class.d_res_high For each reflection class, the lowest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. refine_ls_class.d_res_low For each reflection class, the highest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. refine_ls_class.wR_factor_all For each reflection class, the weighted residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. See also the attribute R_factor_ in category refine_ls_class definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y(calc) = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight and the sum is taken over the reflections of this class. refine_ls_class.code The code identifying a certain reflection class. This code must match a attribute code in category reflns_class. 1 m1 s2 0 refine_ls_restr Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:refine_ls_restrCategory> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="bond_d"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.018</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.020</VRPTx:dev_ideal_target> <VRPTx:number>1654</VRPTx:number> <VRPTx:rejects>22</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="angle_d"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.038</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.030</VRPTx:dev_ideal_target> <VRPTx:number>2246</VRPTx:number> <VRPTx:rejects>139</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar_d"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.043</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.040</VRPTx:dev_ideal_target> <VRPTx:number>498</VRPTx:number> <VRPTx:rejects>21</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.015</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.020</VRPTx:dev_ideal_target> <VRPTx:number>270</VRPTx:number> <VRPTx:rejects>1</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="chiral"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.177</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.150</VRPTx:dev_ideal_target> <VRPTx:number>278</VRPTx:number> <VRPTx:rejects>2</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="singtor_nbd"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.216</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.500</VRPTx:dev_ideal_target> <VRPTx:number>582</VRPTx:number> <VRPTx:rejects>0</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="multtor_nbd"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.207</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.500</VRPTx:dev_ideal_target> <VRPTx:number>419</VRPTx:number> <VRPTx:rejects>0</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="xyhbond_nbd"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>0.245</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.500</VRPTx:dev_ideal_target> <VRPTx:number>149</VRPTx:number> <VRPTx:rejects>0</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar_tor"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>2.6</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>3.0</VRPTx:dev_ideal_target> <VRPTx:number>203</VRPTx:number> <VRPTx:rejects>9</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="staggered_tor"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>17.4</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>15.0</VRPTx:dev_ideal_target> <VRPTx:number>298</VRPTx:number> <VRPTx:rejects>31</VRPTx:rejects> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="orthonormal_tor"> <VRPTx:criterion>&gt; 2\s</VRPTx:criterion> <VRPTx:dev_ideal>18.1</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>20.0</VRPTx:dev_ideal_target> <VRPTx:number>12</VRPTx:number> <VRPTx:rejects>1</VRPTx:rejects> </VRPTx:refine_ls_restr> </VRPTx:refine_ls_restrCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 refine_ls_restrCategory This property indicates that datablock has a category holder refine_ls_restrCategory. refine_ls_restrCategory This property indicates that refine_ls_restrCategory. has a category refine_ls_restr. refine_ls_restrItem Abstract datatype property for refine_ls_restr items. reference_to_refine_ls_restr cross-reference to refine_ls_restr. referenced_by_refine_ls_restr cross-reference from refine_ls_restr. refine_ls_restr.criterion A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement. > 3\s refine_ls_restr.dev_ideal For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (r.m.s.) from ideal values in the current model. refine_ls_restr.dev_ideal_target For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. refine_ls_restr.number The number of parameters of this type subjected to restraint in least-squares refinement. refine_ls_restr.pdbx_restraint_function The functional form of the restraint function used in the least-squares refinement. SINUSOIDAL HARMONIC SEMIHARMONIC refine_ls_restr.rejects The number of parameters of this type that deviate from ideal values by more than the amount defined in attribute criterion in category refine_ls_restr in the model obtained by restrained least-squares refinement. refine_ls_restr.weight The weighting value applied to this type of restraint in the least-squares refinement. refine_ls_restr.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_ls_restr can be used to distinguish the results of joint refinements. refine_ls_restr.type The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs change, these data values are given as examples, not as an enumeration list. Computer programs that convert a data block to a refinement table will expect the exact form of the data values given here to be used. bond distance p_bond_d bond angle expressed as a distance p_angle_d planar 1,4 distance p_planar_d X-H bond distance p_xhbond_d X-H bond angle expressed as a distance p_xhangle_d hydrogen distance p_hydrog_d special distance p_special_d planes p_planar chiral centres p_chiral single-torsion non-bonded contact p_singtor_nbd multiple-torsion non-bonded contact p_multtor_nbd possible (X...Y) hydrogen bond p_xyhbond_nbd possible (X-H...Y) hydrogen bond p_xhyhbond_nbd special torsion angle p_special_tor planar torsion angle p_planar_tor staggered torsion angle p_staggered_tor orthonormal torsion angle p_orthonormal_tor main-chain bond isotropic displacement parameter p_mcbond_it main-chain angle isotropic displacement parameter p_mcangle_it side-chain bond isotropic displacement parameter p_scbond_it side-chain angle isotropic displacement parameter p_scangle_it X-H bond isotropic displacement parameter p_xhbond_it X-H angle isotropic displacement parameter p_xhangle_it special isotropic displacement parameter p_special_it The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 angstroms. RESTRAIN_Distances < 2.12 The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 angstroms. RESTRAIN_Distances 2.12 < D < 2.625 The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 angstroms. RESTRAIN_Distances > 2.625 The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. RESTRAIN_Peptide Planes The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. RESTRAIN_Ring and other planes RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4 RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6 RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0 RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2 RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4 RESTRAIN_rms diffs for Uiso atoms at dist >2.4 0 refine_ls_restr_ncs Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <VRPTx:refine_ls_restr_ncsCategory> <VRPTx:refine_ls_restr_ncs pdbx_ordinal="1"> <VRPTx:dom_id>d2</VRPTx:dom_id> <VRPTx:ncs_model_details> NCS restraint for pseudo-twofold symmetry between domains d1 and d2. Position weight coefficient given in Kcal/(mol \&#37;A^2^) and isotropic B weight coefficient given in \&#37;A^2^.</VRPTx:ncs_model_details> <VRPTx:pdbx_asym_id>A</VRPTx:pdbx_asym_id> <VRPTx:pdbx_ens_id>1</VRPTx:pdbx_ens_id> <VRPTx:pdbx_refine_id>X-RAY DIFFRACTION</VRPTx:pdbx_refine_id> <VRPTx:pdbx_type>medium positional</VRPTx:pdbx_type> <VRPTx:rms_dev_B_iso>0.16</VRPTx:rms_dev_B_iso> <VRPTx:rms_dev_position>0.09</VRPTx:rms_dev_position> <VRPTx:weight_B_iso>2.0</VRPTx:weight_B_iso> <VRPTx:weight_position>300.0</VRPTx:weight_position> </VRPTx:refine_ls_restr_ncs> </VRPTx:refine_ls_restr_ncsCategory> 1 1 0 1 0 1 1 1 1 1 0 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 refine_ls_restr_ncsCategory This property indicates that datablock has a category holder refine_ls_restr_ncsCategory. refine_ls_restr_ncsCategory This property indicates that refine_ls_restr_ncsCategory. has a category refine_ls_restr_ncs. refine_ls_restr_ncsItem Abstract datatype property for refine_ls_restr_ncs items. reference_to_refine_ls_restr_ncs cross-reference to refine_ls_restr_ncs. referenced_by_refine_ls_restr_ncs cross-reference from refine_ls_restr_ncs. refine_ls_restr_ncs.dom_id This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. refine_ls_restr_ncs.ncs_model_details Special aspects of the manner in which noncrystallographic restraints were applied to atomic parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs and equivalent atomic parameters in the domains against which it was restrained. refine_ls_restr_ncs.pdbx_asym_id A reference to attribute id in category struct_asym. refine_ls_restr_ncs.pdbx_auth_asym_id A reference to the PDB Chain ID refine_ls_restr_ncs.pdbx_ens_id This is a unique identifier for a collection NCS related domains. This references item '_struct_ncs_dom.pdbx_ens_id'. refine_ls_restr_ncs.pdbx_number Records the number restraints in the contributing to the RMS statistic. refine_ls_restr_ncs.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_ls_restr_ncs can be used to distinguish the results of joint refinements. refine_ls_restr_ncs.pdbx_rms Records the standard deviation in the restraint between NCS related domains. refine_ls_restr_ncs.pdbx_type The type of NCS restraint. (for example: tight positional) refine_ls_restr_ncs.pdbx_weight Records the weight used for NCS restraint. refine_ls_restr_ncs.rms_dev_B_iso The root-mean-square deviation in equivalent isotropic displacement parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the domains against which it was restrained. refine_ls_restr_ncs.rms_dev_position The root-mean-square deviation in equivalent atom positions in the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the domains against which it was restrained. refine_ls_restr_ncs.weight_B_iso The value of the weighting coefficient used in noncrystallographic symmetry restraint of isotropic displacement parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent isotropic displacement parameters in the domains against which it was restrained. refine_ls_restr_ncs.weight_position The value of the weighting coefficient used in noncrystallographic symmetry restraint of atom positions in the domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent atom positions in the domains against which it was restrained. refine_ls_restr_ncs.pdbx_ordinal An ordinal index for the list of NCS restraints. 0 refine_ls_restr_type Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement. Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. <VRPTx:refine_ls_restrCategory> <VRPTx:refine_ls_restr type="RESTRAIN_Distances &lt; 2.12"> <VRPTx:dev_ideal>0.005</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.022</VRPTx:dev_ideal_target> <VRPTx:number>509</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_Distances 2.12 &lt; D &lt; 2.625"> <VRPTx:dev_ideal>0.016</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.037</VRPTx:dev_ideal_target> <VRPTx:number>671</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_Distances &gt; 2.625"> <VRPTx:dev_ideal>0.034</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.043</VRPTx:dev_ideal_target> <VRPTx:number>39</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_Peptide Planes"> <VRPTx:dev_ideal>0.002</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.010</VRPTx:dev_ideal_target> <VRPTx:number>59</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_Ring and other planes"> <VRPTx:dev_ideal>0.014</VRPTx:dev_ideal> <VRPTx:dev_ideal_target>0.010</VRPTx:dev_ideal_target> <VRPTx:number>26</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4"> <VRPTx:dev_ideal>0.106</VRPTx:dev_ideal> <VRPTx:dev_ideal_target xsi:nil="true" /> <VRPTx:number>212</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6"> <VRPTx:dev_ideal>0.101</VRPTx:dev_ideal> <VRPTx:dev_ideal_target xsi:nil="true" /> <VRPTx:number>288</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0"> <VRPTx:dev_ideal>0.077</VRPTx:dev_ideal> <VRPTx:dev_ideal_target xsi:nil="true" /> <VRPTx:number>6</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2"> <VRPTx:dev_ideal>0.114</VRPTx:dev_ideal> <VRPTx:dev_ideal_target xsi:nil="true" /> <VRPTx:number>10</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4"> <VRPTx:dev_ideal>0.119</VRPTx:dev_ideal> <VRPTx:dev_ideal_target xsi:nil="true" /> <VRPTx:number>215</VRPTx:number> </VRPTx:refine_ls_restr> <VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist &gt;2.4"> <VRPTx:dev_ideal>0.106</VRPTx:dev_ideal> <VRPTx:dev_ideal_target xsi:nil="true" /> <VRPTx:number>461</VRPTx:number> </VRPTx:refine_ls_restr> </VRPTx:refine_ls_restrCategory> <VRPTx:refine_ls_restr_typeCategory> <VRPTx:refine_ls_restr_type type="RESTRAIN_Distances &lt; 2.12"> <VRPTx:distance_cutoff_high>2.12</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low xsi:nil="true" /> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_Distances 2.12 &lt; D &lt; 2.625"> <VRPTx:distance_cutoff_high>2.625</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low>2.12</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_Distances &gt; 2.625"> <VRPTx:distance_cutoff_high xsi:nil="true" /> <VRPTx:distance_cutoff_low>2.625</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_Peptide Planes"> <VRPTx:distance_cutoff_high xsi:nil="true" /> <VRPTx:distance_cutoff_low xsi:nil="true" /> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_Ring and other planes"> <VRPTx:distance_cutoff_high xsi:nil="true" /> <VRPTx:distance_cutoff_low xsi:nil="true" /> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4"> <VRPTx:distance_cutoff_high>1.4</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low>1.2</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6"> <VRPTx:distance_cutoff_high>1.6</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low>1.4</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0"> <VRPTx:distance_cutoff_high>2.0</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low>1.8</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2"> <VRPTx:distance_cutoff_high>2.2</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low>2.0</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4"> <VRPTx:distance_cutoff_high>2.4</VRPTx:distance_cutoff_high> <VRPTx:distance_cutoff_low>2.2</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> <VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist &gt;2.4"> <VRPTx:distance_cutoff_high xsi:nil="true" /> <VRPTx:distance_cutoff_low>2.4</VRPTx:distance_cutoff_low> </VRPTx:refine_ls_restr_type> </VRPTx:refine_ls_restr_typeCategory> 0 1 0 1 1 refine_ls_restr_typeCategory This property indicates that datablock has a category holder refine_ls_restr_typeCategory. refine_ls_restr_typeCategory This property indicates that refine_ls_restr_typeCategory. has a category refine_ls_restr_type. refine_ls_restr_typeItem Abstract datatype property for refine_ls_restr_type items. reference_to_refine_ls_restr_type cross-reference to refine_ls_restr_type. referenced_by_refine_ls_restr_type cross-reference from refine_ls_restr_type. refine_ls_restr_type.distance_cutoff_high The upper limit in angstroms of the distance range applied to the current restraint type. refine_ls_restr_type.distance_cutoff_low The lower limit in angstroms of the distance range applied to the current restraint type. refine_ls_restr_type.type This data item is a pointer to attribute type in category refine_ls_restr in the REFINE_LS_RESTR category. 0 refine_ls_shell Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:refine_ls_shellCategory> <VRPTx:refine_ls_shell d_res_high="4.51" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.196</VRPTx:R_factor_obs> <VRPTx:d_res_low>8.00</VRPTx:d_res_low> <VRPTx:number_reflns_obs>1226</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> <VRPTx:refine_ls_shell d_res_high="3.48" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.146</VRPTx:R_factor_obs> <VRPTx:d_res_low>4.51</VRPTx:d_res_low> <VRPTx:number_reflns_obs>1679</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> <VRPTx:refine_ls_shell d_res_high="2.94" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.160</VRPTx:R_factor_obs> <VRPTx:d_res_low>3.48</VRPTx:d_res_low> <VRPTx:number_reflns_obs>2014</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> <VRPTx:refine_ls_shell d_res_high="2.59" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.182</VRPTx:R_factor_obs> <VRPTx:d_res_low>2.94</VRPTx:d_res_low> <VRPTx:number_reflns_obs>2147</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> <VRPTx:refine_ls_shell d_res_high="2.34" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.193</VRPTx:R_factor_obs> <VRPTx:d_res_low>2.59</VRPTx:d_res_low> <VRPTx:number_reflns_obs>2127</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> <VRPTx:refine_ls_shell d_res_high="2.15" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.203</VRPTx:R_factor_obs> <VRPTx:d_res_low>2.34</VRPTx:d_res_low> <VRPTx:number_reflns_obs>2061</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> <VRPTx:refine_ls_shell d_res_high="2.00" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:R_factor_obs>0.188</VRPTx:R_factor_obs> <VRPTx:d_res_low>2.15</VRPTx:d_res_low> <VRPTx:number_reflns_obs>1647</VRPTx:number_reflns_obs> </VRPTx:refine_ls_shell> </VRPTx:refine_ls_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 refine_ls_shellCategory This property indicates that datablock has a category holder refine_ls_shellCategory. refine_ls_shellCategory This property indicates that refine_ls_shellCategory. has a category refine_ls_shell. refine_ls_shellItem Abstract datatype property for refine_ls_shell items. reference_to_refine_ls_shell cross-reference to refine_ls_shell. referenced_by_refine_ls_shell cross-reference from refine_ls_shell. refine_ls_shell.R_factor_R_free Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_ls_shell.R_factor_R_free_error The estimated error in attribute R_factor_R_free. in category refine_ls_shell The method used to estimate the error is described in the item attribute ls_R_factor_R_free_error_details in category refine. refine_ls_shell.R_factor_R_work Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_ls_shell.R_factor_all Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low. in category refine_ls_shell sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_ls_shell.R_factor_obs Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections refine_ls_shell.d_res_low The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. refine_ls_shell.number_reflns_R_free The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. refine_ls_shell.number_reflns_R_work The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. refine_ls_shell.number_reflns_all The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell. refine_ls_shell.number_reflns_obs The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion in category reflns. refine_ls_shell.pdbx_R_complete The crystallographic reliability index Rcomplete for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns Ref: Luebben, J., Gruene, T., (2015). Proc.Nat.Acad.Sci. 112(29) 8999-9003 refine_ls_shell.pdbx_fsc_free Fourier Shell Correlation (FSC) between model and observed structure factors for reflections not included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all free reflections in the resolution shell. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). refine_ls_shell.pdbx_fsc_work Fourier Shell Correlation (FSC) between model and observed structure factors for reflections included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all working reflections in the resolution shell. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). refine_ls_shell.pdbx_phase_error The average phase error for all reflections in the resolution shell. 0.30 refine_ls_shell.pdbx_total_number_of_bins_used Total number of bins used. refine_ls_shell.percent_reflns_R_free The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the reflection limits. refine_ls_shell.percent_reflns_obs The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion in category reflns, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. refine_ls_shell.redundancy_reflns_all The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits. refine_ls_shell.redundancy_reflns_obs The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by attribute observed_criterion in category reflns to the number of crystallographically unique reflections that satisfy the same limits. refine_ls_shell.wR_factor_R_free Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine_ls_shell.wR_factor_R_work Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine_ls_shell.wR_factor_all Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low. in category refine_ls_shell ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine_ls_shell.wR_factor_obs Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections refine_ls_shell.d_res_high The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. refine_ls_shell.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_ls_shell can be used to distinguish the results of joint refinements. 0 refine_occupancy Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:refine_occupancyCategory> <VRPTx:refine_occupancy class="protein" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:details xsi:nil="true" /> <VRPTx:treatment>fix</VRPTx:treatment> <VRPTx:value>1.00</VRPTx:value> </VRPTx:refine_occupancy> <VRPTx:refine_occupancy class="solvent" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:details xsi:nil="true" /> <VRPTx:treatment>fix</VRPTx:treatment> <VRPTx:value>1.00</VRPTx:value> </VRPTx:refine_occupancy> <VRPTx:refine_occupancy class="inhibitor orientation 1" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:details xsi:nil="true" /> <VRPTx:treatment>fix</VRPTx:treatment> <VRPTx:value>0.65</VRPTx:value> </VRPTx:refine_occupancy> <VRPTx:refine_occupancy class="inhibitor orientation 2" pdbx_refine_id="X-RAY DIFFRACTION"> <VRPTx:details> The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation.</VRPTx:details> <VRPTx:treatment>fix</VRPTx:treatment> <VRPTx:value>0.35</VRPTx:value> </VRPTx:refine_occupancy> </VRPTx:refine_occupancyCategory> 0 1 0 1 0 1 1 1 refine_occupancyCategory This property indicates that datablock has a category holder refine_occupancyCategory. refine_occupancyCategory This property indicates that refine_occupancyCategory. has a category refine_occupancy. refine_occupancyItem Abstract datatype property for refine_occupancy items. reference_to_refine_occupancy cross-reference to refine_occupancy. referenced_by_refine_occupancy cross-reference from refine_occupancy. refine_occupancy.details A description of special aspects of the occupancy refinement for a class of atoms described in attribute class in category refine_occupancy. The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. fix ref The treatment of occupancies for a class of atoms described in attribute class in category refine_occupancy. refine_occupancy.value The value of occupancy assigned to a class of atoms defined in attribute class in category refine_occupancy. Meaningful only for atoms with fixed occupancy. 1.0 0.41 refine_occupancy.class The class of atoms treated similarly for occupancy refinement. all protein solvent sugar-phosphate backbone refine_occupancy.pdbx_refine_id This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_occupancy can be used to distinguish the results of joint refinements. 0 refln Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [Acta Cryst. (1993), C49, 1352-1354]. <VRPTx:reflnCategory> <VRPTx:refln index_h="2" index_k="0" index_l="0"> <VRPTx:F_squared_calc>85.57</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>58.90</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>1.45</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="3" index_k="0" index_l="0"> <VRPTx:F_squared_calc>15718.18</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>15631.06</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>30.40</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="4" index_k="0" index_l="0"> <VRPTx:F_squared_calc>55613.11</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>49840.09</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>61.86</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="5" index_k="0" index_l="0"> <VRPTx:F_squared_calc>246.85</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>241.86</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>10.02</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="6" index_k="0" index_l="0"> <VRPTx:F_squared_calc>82.16</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>69.97</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>1.93</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="7" index_k="0" index_l="0"> <VRPTx:F_squared_calc>1133.62</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>947.79</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>11.78</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="8" index_k="0" index_l="0"> <VRPTx:F_squared_calc>2558.04</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>2453.33</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>20.44</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="9" index_k="0" index_l="0"> <VRPTx:F_squared_calc>283.88</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>393.66</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>7.79</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> <VRPTx:refln index_h="10" index_k="0" index_l="0"> <VRPTx:F_squared_calc>283.70</VRPTx:F_squared_calc> <VRPTx:F_squared_meas>171.98</VRPTx:F_squared_meas> <VRPTx:F_squared_sigma>4.26</VRPTx:F_squared_sigma> <VRPTx:status>o</VRPTx:status> </VRPTx:refln> </VRPTx:reflnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 reflnCategory This property indicates that datablock has a category holder reflnCategory. reflnCategory This property indicates that reflnCategory. has a category refln. reflnItem Abstract datatype property for refln items. reference_to_refln cross-reference to refln. referenced_by_refln cross-reference from refln. refln.A_calc The calculated value of structure-factor component A in electrons. A = |F|cos(phase) refln.A_calc_au The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase) refln.A_meas The measured value of structure-factor component A in electrons. A = |F|cos(phase) refln.A_meas_au The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase) refln.B_calc The calculated value of structure-factor component B in electrons. B = |F|sin(phase) refln.B_calc_au The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase) refln.B_meas The measured value of structure-factor component B in electrons. B = |F|sin(phase) refln.B_meas_au The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase) refln.F_calc The calculated value of the structure factor in electrons. refln.F_calc_au The calculated value of the structure factor in arbitrary units. refln.F_meas The measured value of the structure factor in electrons. refln.F_meas_au The measured value of the structure factor in arbitrary units. refln.F_meas_sigma The standard uncertainty (estimated standard deviation) of attribute F_meas in category refln in electrons. refln.F_meas_sigma_au The standard uncertainty (estimated standard deviation) of attribute F_meas_au in category refln in arbitrary units. refln.F_squared_calc The calculated value of the squared structure factor in electrons squared. refln.F_squared_meas The measured value of the squared structure factor in electrons squared. refln.F_squared_sigma The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared. refln.class_code The code identifying the class to which this reflection has been assigned. This code must match a value of attribute code. in category reflns_class Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. refln.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. refln.d_spacing The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression attribute d_spacing in category refln = 2/(_refln.sint/lambda). refln.fom The figure of merit m for this reflection. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct int is taken over the range alpha = 0 to 2 pi. o < - x h l Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. refln.intensity_calc The calculated value of the intensity in the same units as attribute intensity_meas in category refln. refln.intensity_meas The measured value of the intensity. refln.intensity_sigma The standard uncertainty (derived from measurement) of the intensity in the same units as attribute intensity_meas in category refln. refln.mean_path_length_tbar Mean path length in millimetres through the crystal for this reflection. refln.pdbx_DELFWT The weighted structure factor amplitude for the mFo-DFc map. refln.pdbx_DELPHWT The weighted phase for the mFo-DFc map. refln.pdbx_FWT The weighted structure factor amplitude for the 2mFo-DFc map. refln.pdbx_F_calc_part_solvent The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model. refln.pdbx_F_calc_with_solvent The calculated value of the structure factor in arbitrary units including the contribution of the solvent model. refln.pdbx_F_minus The structure factor F(-h,-k,-l) of the Friedel pair. refln.pdbx_F_minus_sigma The standard uncertainty (derived from measurement) of the structure factor F(-h,-k,-l) of the Friedel pair. refln.pdbx_F_plus The structure factor F(h,k,l) of the Friedel pair. refln.pdbx_F_plus_sigma The standard uncertainty (derived from measurement) of the structure factor F(h,k,l) of the Friedel pair. refln.pdbx_HL_A_iso The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. refln.pdbx_HL_B_iso The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. refln.pdbx_HL_C_iso The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. refln.pdbx_HL_D_iso The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. refln.pdbx_I_minus The intensity of the I(-h,-k,-l) partner of the Friedel pair. refln.pdbx_I_minus_sigma The standard uncertainty (derived from measurement) of the intensity I(-h,-k,-l) partner of the Friedel pair. refln.pdbx_I_plus The intensity of the I(h,k,l) partner of the Friedel pair. refln.pdbx_I_plus_sigma The standard uncertainty (derived from measurement) of the intensity I(h,k,l) partner of the Friedel pair. refln.pdbx_PHWT The weighted phase for the 2mFo-DFc map. refln.pdbx_anom_difference The amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l). refln.pdbx_anom_difference_sigma The standard deviation of the amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l). refln.pdbx_diffrn_id An optional identifier for the diffraction data set containing this reflection. refln.pdbx_fiber_F_meas_au The measured diffraction amplitude for this fiber reflection in arbitrary units. refln.pdbx_fiber_coordinate The coordinate position in reciprocal space along the fiber layer line for this reflection. refln.pdbx_fiber_layer The fiber layer line for this reflection. refln.pdbx_phase_calc_part_solvent The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model. refln.pdbx_phase_calc_with_solvent The calculated structure-factor phase in degrees including the contribution of the solvent model. refln.pdbx_r_free_flag The R-free flag originally assigned to the reflection. The convention used for labeling the work and test sets differs depending on choice of data processing software and refinement program. refln.pdbx_signal The signal value for this reflection as defined by _reflns.pdbx_signal_type and _reflns.pdbx_signal_details as calculated by attribute pdbx_signal_software_id in category reflns. m o u The status of a reflection related to attribute pdbx_signal. in category refln A measured reflection counts as observed if: _refln.pdbx_signal >= _reflns.pdbx_observed_signal_threshold and unobserved if: _refln.pdbx_signal < _reflns.pdbx_observed_signal_threshold An unmeasured but observable reflection is one that has not been measured, but the data processing has determined that it would have been expected to be observed had it been measured. An unmeasured and unobservable reflection is one that the data processing has determined would not have been expected to be observed. In datasets in which attribute pdbx_signal in category refln has been populated, a null (?) value for this item indicates an unmeasured reflection for which it is not known whether it is observable or not. refln.phase_calc The calculated structure-factor phase in degrees. refln.phase_meas The measured structure-factor phase in degrees. incl excl extn Status of a reflection in the structure-refinement process. refln.scale_group_code This data item is a pointer to attribute group_code in category reflns_scale in the REFLNS_SCALE category. refln.sint_over_lambda The (sin theta)/lambda value in reciprocal angstroms for this reflection. o < - x h l f Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. refln.symmetry_epsilon The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. refln.symmetry_multiplicity The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship. refln.wavelength The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. refln.wavelength_id This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. refln.index_h Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. refln.index_k Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. refln.index_l Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. 0 refln_sys_abs Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group. Example 1 - hypothetical example. <VRPTx:refln_sys_absCategory> <VRPTx:refln_sys_abs index_h="0" index_k="3" index_l="0"> <VRPTx:I>28.32</VRPTx:I> <VRPTx:I_over_sigmaI>1.23</VRPTx:I_over_sigmaI> <VRPTx:sigmaI>22.95</VRPTx:sigmaI> </VRPTx:refln_sys_abs> <VRPTx:refln_sys_abs index_h="0" index_k="5" index_l="0"> <VRPTx:I>14.11</VRPTx:I> <VRPTx:I_over_sigmaI>0.86</VRPTx:I_over_sigmaI> <VRPTx:sigmaI>16.38</VRPTx:sigmaI> </VRPTx:refln_sys_abs> <VRPTx:refln_sys_abs index_h="0" index_k="7" index_l="0"> <VRPTx:I>114.81</VRPTx:I> <VRPTx:I_over_sigmaI>5.67</VRPTx:I_over_sigmaI> <VRPTx:sigmaI>20.22</VRPTx:sigmaI> </VRPTx:refln_sys_abs> <VRPTx:refln_sys_abs index_h="0" index_k="9" index_l="0"> <VRPTx:I>32.99</VRPTx:I> <VRPTx:I_over_sigmaI>1.35</VRPTx:I_over_sigmaI> <VRPTx:sigmaI>24.51</VRPTx:sigmaI> </VRPTx:refln_sys_abs> </VRPTx:refln_sys_absCategory> 0 1 0 1 0 1 1 1 1 refln_sys_absCategory This property indicates that datablock has a category holder refln_sys_absCategory. refln_sys_absCategory This property indicates that refln_sys_absCategory. has a category refln_sys_abs. refln_sys_absItem Abstract datatype property for refln_sys_abs items. reference_to_refln_sys_abs cross-reference to refln_sys_abs. referenced_by_refln_sys_abs cross-reference from refln_sys_abs. refln_sys_abs.I The measured value of the intensity in arbitrary units. refln_sys_abs.I_over_sigmaI The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent. refln_sys_abs.sigmaI The standard uncertainty (estimated standard deviation) of attribute I in category refln_sys_abs in arbitrary units. refln_sys_abs.index_h Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. refln_sys_abs.index_k Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. refln_sys_abs.index_l Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. 0 reflns Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:reflnsCategory> <VRPTx:reflns pdbx_ordinal="1"> <VRPTx:d_resolution_high>2.00</VRPTx:d_resolution_high> <VRPTx:d_resolution_low>8.00</VRPTx:d_resolution_low> <VRPTx:data_reduction_details> Merging and scaling based on only those reflections with I &gt; \s(I).</VRPTx:data_reduction_details> <VRPTx:data_reduction_method> Xengen program scalei. Anomalous pairs were merged. Scaling proceeded in several passes, beginning with 1-parameter fit and ending with 3-parameter fit.</VRPTx:data_reduction_method> <VRPTx:details>none</VRPTx:details> <VRPTx:entry_id>5HVP</VRPTx:entry_id> <VRPTx:limit_h_max>22</VRPTx:limit_h_max> <VRPTx:limit_h_min>0</VRPTx:limit_h_min> <VRPTx:limit_k_max>46</VRPTx:limit_k_max> <VRPTx:limit_k_min>0</VRPTx:limit_k_min> <VRPTx:limit_l_max>57</VRPTx:limit_l_max> <VRPTx:limit_l_min>0</VRPTx:limit_l_min> <VRPTx:number_obs>7228</VRPTx:number_obs> <VRPTx:observed_criterion>&gt; 1 \s(I)</VRPTx:observed_criterion> <VRPTx:pdbx_diffrn_id>1</VRPTx:pdbx_diffrn_id> </VRPTx:reflns> </VRPTx:reflnsCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <VRPTx:reflnsCategory> <VRPTx:reflns pdbx_ordinal="1"> <VRPTx:d_resolution_high>0.8733</VRPTx:d_resolution_high> <VRPTx:d_resolution_low>11.9202</VRPTx:d_resolution_low> <VRPTx:entry_id>1TOZ</VRPTx:entry_id> <VRPTx:limit_h_max>6</VRPTx:limit_h_max> <VRPTx:limit_h_min>0</VRPTx:limit_h_min> <VRPTx:limit_k_max>17</VRPTx:limit_k_max> <VRPTx:limit_k_min>0</VRPTx:limit_k_min> <VRPTx:limit_l_max>22</VRPTx:limit_l_max> <VRPTx:limit_l_min>0</VRPTx:limit_l_min> <VRPTx:number_all>1592</VRPTx:number_all> <VRPTx:number_obs>1408</VRPTx:number_obs> <VRPTx:observed_criterion>F_&gt;_6.0_\s(F)</VRPTx:observed_criterion> <VRPTx:pdbx_diffrn_id>1</VRPTx:pdbx_diffrn_id> </VRPTx:reflns> </VRPTx:reflnsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 reflnsCategory This property indicates that datablock has a category holder reflnsCategory. reflnsCategory This property indicates that reflnsCategory. has a category reflns. reflnsItem Abstract datatype property for reflns items. reference_to_reflns cross-reference to reflns. referenced_by_reflns cross-reference from reflns. reflns.B_iso_Wilson_estimate The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot. reflns.Friedel_coverage The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item attribute number_all. in category reflns This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, the value of attribute Friedel_coverage in category reflns is necessarily equal to 0.0, as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, attribute Friedel_coverage in category reflns is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, attribute Friedel_coverage in category reflns will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in space group Pmm2, measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for attribute Friedel_coverage in category reflns. reflns.R_free_details A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor. The data set was sorted with l varying most rapidly and h varying least rapidly. Every 10th reflection in this sorted list was excluded from refinement and included in the calculation of a 'free' R factor. reflns.Rmerge_F_all Residual factor Rmerge for all reflections that satisfy the resolution limits established by attribute d_resolution_high in category reflns and attribute d_resolution_low. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection reflns.Rmerge_F_obs Residual factor Rmerge for reflections that satisfy the resolution limits established by attribute d_resolution_high in category reflns and attribute d_resolution_low in category reflns and the observation limit established by attribute observed_criterion. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection reflns.d_resolution_high The smallest value in angstroms for the interplanar spacings for the reflection data. This is called the highest resolution. reflns.d_resolution_low The largest value in angstroms for the interplanar spacings for the reflection data. This is called the lowest resolution. reflns.data_reduction_details A description of special aspects of the data-reduction procedures. Merging and scaling based on only those reflections with I > sig(I). reflns.data_reduction_method The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs. Profile fitting by method of Kabsch (1987). Scaling used spherical harmonic coefficients. reflns.details A description of reflection data not covered by other data names. This should include details of the Friedel pairs. reflns.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. reflns.limit_h_max Maximum value of the Miller index h for the reflection data. This need not have the same value as attribute limit_h_max in category diffrn_reflns. reflns.limit_h_min Minimum value of the Miller index h for the reflection data. This need not have the same value as attribute limit_h_min in category diffrn_reflns. reflns.limit_k_max Maximum value of the Miller index k for the reflection data. This need not have the same value as attribute limit_k_max in category diffrn_reflns. reflns.limit_k_min Minimum value of the Miller index k for the reflection data. This need not have the same value as attribute limit_k_min in category diffrn_reflns. reflns.limit_l_max Maximum value of the Miller index l for the reflection data. This need not have the same value as attribute limit_l_max in category diffrn_reflns. reflns.limit_l_min Minimum value of the Miller index l for the reflection data. This need not have the same value as attribute limit_l_min in category diffrn_reflns. reflns.number_all The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item attribute details in category reflns describes the reflection data. reflns.number_gt The number of reflections in the REFLN list (not the DIFFRN_REFLN list) that are significantly intense, satisfying the criterion specified by attribute threshold_expression in category reflns. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item attribute details in category reflns. reflns.number_obs The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see attribute observed_criterion). in category reflns This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. reflns.observed_criterion The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. >2sigma(I) reflns.observed_criterion_F_max The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F. reflns.observed_criterion_F_min The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F. reflns.observed_criterion_I_max The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I. reflns.observed_criterion_I_min The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I. reflns.observed_criterion_sigma_F The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F). reflns.observed_criterion_sigma_I The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I). reflns.pdbx_CC_half The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets. Ref: Karplus & Diederichs (2012), Science 336, 1030-33 reflns.pdbx_CC_half_anomalous The overall correlation coefficient between two randomly chosen half-sets of anomalous intensity differences, I(+)-I(-) for anomalous data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. reflns.pdbx_CC_star Estimates the value of CC_true, the true correlation coefficient between the average intensities from randomly selected half-datasets. CC_star = sqrt(2*CC_half/(1+CC_half)), where both CC_star and CC_half (CC1/2) Ref: Karplus & Diederichs (2012), Science 336, 1030-33 reflns.pdbx_R_split R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the overall data. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341 reflns.pdbx_Rmerge_I_all The R value for merging all intensities in this data set. reflns.pdbx_Rmerge_I_obs The R value for merging intensities satisfying the observed criteria in this data set. reflns.pdbx_Rpim_I_all The precision-indicating merging R factor value Rpim, for merging all intensities in this data set. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. reflns.pdbx_Rrim_I_all The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in this data set. sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rrim = ---------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. reflns.pdbx_Rsym_value The R sym value as a decimal number. 0.02 reflns.pdbx_absDiff_over_sigma_anomalous The overall mean ratio of absolute anomalous intensity differences to their standard deviation within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns and using data for which intensities for both instances of a Friedel pair are available for an acentric reflection. |Dano| ------------- sigma(Dano) with Dano = I(+) - I(-) sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 ) reflns.pdbx_aniso_B_tensor_eigenvalue_1 Eigen-B-factor along the first eigenvector of the diffraction anisotropy tensor reflns.pdbx_aniso_B_tensor_eigenvalue_2 Eigen-B-factor along the second eigenvector of the diffraction anisotropy tensor reflns.pdbx_aniso_B_tensor_eigenvalue_3 Eigen-B-factor along the third eigenvector of the diffraction anisotropy tensor reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho1 X component of the first eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho2 Y component of the first eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho3 Z component of the first eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho1 X component of the second eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho2 Y component of the second eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho3 Z component of the second eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho1 X component of the third eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho2 Y component of the third eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho3 Z component of the third eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_1 Anisotropic diffraction limit along principal axis 1 (of ellipsoid fitted to the diffraction cut-off surface). reflns.pdbx_aniso_diffraction_limit_2 Anisotropic diffraction limit along principal axis 2 (of ellipsoid fitted to the diffraction cut-off surface) reflns.pdbx_aniso_diffraction_limit_3 Anisotropic diffraction limit along principal axis 3 (of ellipsoid fitted to the diffraction cut-off surface) reflns.pdbx_aniso_diffraction_limit_axis_1_ortho1 Principal axis 1 (X component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_1_ortho2 Principal axis 1 (Y component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_1_ortho3 Principal axis 1 (Z component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_2_ortho1 Principal axis 2 (X component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_2_ortho2 Principal axis 2 (Y component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_2_ortho3 Principal axis 2 (Z component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_3_ortho1 Principal axis 3 (X component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_3_ortho2 Principal axis 3 (Y component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_aniso_diffraction_limit_axis_3_ortho3 Principal axis 3 (Z component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. reflns.pdbx_chi_squared Overall Chi-squared statistic. reflns.pdbx_d_opt The optical resolution of the data set, d(opt), is the expected minimum distance between two resolved peaks in an electron-density map. d(opt) = {2[sigma(Patt)2^ + sigma(sph)2^]}1/2^ sigma(Patt) = standard deviation of the Gaussian function fitted to the Patterson origin peak sigma(sph) = standard deviation of the Gaussian function fitted to the origin peak of the spherical interference function, representing the Fourier transform of a sphere with radius 1/dmin dmin = nominal resolution (_reflns.d_resolution_high) Ref: Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). Acta Cryst. D55, 191-205. (see also http://www.ysbl.york.ac.uk/~alexei/sfcheck.html) Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. reflns.pdbx_d_res_high_opt The highest optical resolution for this reflection data set as determined by computational method attribute pdbx_d_res_opt_method in category reflns. 1.2 reflns.pdbx_d_res_low_opt The lowest optical resolution for this reflection data set as determined by computational method attribute pdbx_d_res_opt_method in category reflns. 20.5 reflns.pdbx_d_res_opt_method The computational method used to determine the optical resolution limits attribute pdbx_d_res_high_opt in category reflns and attribute pdbx_d_res_low_opt in category reflns. SFCHECK reflns.pdbx_diffrn_id An identifier for the diffraction data set for this set of summary statistics. Multiple diffraction data sets entered as a comma separated list. reflns.pdbx_netI_over_av_sigmaI The ratio of the average intensity to the average uncertainty, <I>/<sigma(I)>. reflns.pdbx_netI_over_sigmaI The mean of the ratio of the intensities to their standard uncertainties, <I/sigma(I)>. reflns.pdbx_number_measured_all Total number of measured reflections. 23000 140000 reflns.pdbx_observed_signal_threshold The threshold value for attribute pdbx_signal in category refln as used to define the status of an individual reflection according to the description in attribute pdbx_signal_status in category refln. pdb Description of orthogonalization convention used. The notation can make use of unit cell axes "a", "b" and "c" and the reciprocal unit cell axes "astar", "bstar" and "cstar". Upper case letters "X", "Y" and "Z" denote the orthogonal axes, while lower case "x" stands for "cross product". reflns.pdbx_percent_possible_anomalous Completeness (as a percentage) of symmetry-unique anomalous difference data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns relative to all possible symmetry-unique anomalous difference data within that sphere. reflns.pdbx_percent_possible_ellipsoidal Completeness (as a percentage) of symmetry-unique data within the intersection of (1) a sphere (defined by the diffraction limits, attribute d_resolution_high in category reflns and attribute d_resolution_low) in category reflns and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique reflections within that intersection. reflns.pdbx_percent_possible_ellipsoidal_anomalous Completeness (as a percentage) of symmetry-unique anomalous difference data within the intersection of (1) a sphere (defined by the diffraction limits, _reflns.d_resolution_high and _reflns.d_resolution_low) and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique anomalous difference data within that intersection. reflns.pdbx_percent_possible_spherical Completeness (as a percentage) of symmetry-unique data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns relative to all possible symmetry-unique reflections within that sphere. In the absence of an anisotropy description this is identical to attribute percent_possible_obs in category reflns. reflns.pdbx_percent_possible_spherical_anomalous Completeness (as a percentage) of symmetry-unique anomalous difference data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns relative to all possible symmetry-unique anomalous difference data within that sphere. In the absence of an anisotropy description this is identical to attribute pdbx_percent_possible_anomalous in category reflns. reflns.pdbx_redundancy Overall redundancy for this data set. reflns.pdbx_redundancy_anomalous The overall redundancy of anomalous difference data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. reflns.pdbx_res_netI_over_av_sigmaI_2 Resolution (angstrom) for reflections with <I>/<sigma(I)> = 2. reflns.pdbx_res_netI_over_sigmaI_2 Resolution (angstroms) for reflections with <I/sigma(I)> = 2. reflns.pdbx_scaling_rejects Number of reflections rejected in scaling operations. reflns.pdbx_signal_details Further details about the calculation of the values assigned to attribute pdbx_signal in category refln reflns.pdbx_signal_software_id The software used to calculate the values of attribute pdbx_signal in category refln local <I/sigmaI> local wCC_half Type of signal used for _reflns.pdbx_observed_signal_threshold and _refln.pdbx_signal In the enumeration details: Imean is the inverse-variance weighted mean intensity of all measurements for a given symmetry-unique reflection Ihalf is the inverse-variance weighted mean intensity of a random half-selection of all measurements for a given symmetry-unique reflection reflns.percent_possible_obs The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by attribute observed_criterion in category reflns. reflns.phase_calculation_details The value of attribute phase_calculation_details in category reflns describes a special details about calculation of phases in attribute phase_calc in category refln. From model NCS averaging Solvent flipping Solvent flattening Multiple crystal averaging Multiple phase modification Other phase modification reflns.threshold_expression The threshold, usually based on multiples of u(I), u(F^2^) or u(F), that serves to identify significantly intense reflections, the number of which is given by attribute number_gt. in category reflns These reflections are used in the calculation of attribute ls_R_factor_gt in category refine. I>2u(I) reflns.pdbx_ordinal An ordinal identifier for this set of reflection statistics. 0 reflns_class Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class. Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <VRPTx:reflns_classCategory> <VRPTx:reflns_class code="Main"> <VRPTx:number_gt>584</VRPTx:number_gt> </VRPTx:reflns_class> <VRPTx:reflns_class code="Sat1"> <VRPTx:number_gt>226</VRPTx:number_gt> </VRPTx:reflns_class> <VRPTx:reflns_class code="Sat2"> <VRPTx:number_gt>50</VRPTx:number_gt> </VRPTx:reflns_class> </VRPTx:reflns_classCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 reflns_classCategory This property indicates that datablock has a category holder reflns_classCategory. reflns_classCategory This property indicates that reflns_classCategory. has a category reflns_class. reflns_classItem Abstract datatype property for reflns_class items. reference_to_reflns_class cross-reference to reflns_class. referenced_by_reflns_class cross-reference from reflns_class. reflns_class.R_Fsqd_factor For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. reflns_class.R_I_factor For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. reflns_class.R_factor_all For each reflection class, the residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category reflns_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. reflns_class.R_factor_gt For each reflection class, the residual factor for significantly intense reflections (see attribute threshold_expression) in category reflns included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category reflns_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. reflns_class.d_res_high For each reflection class, the smallest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. reflns_class.d_res_low For each reflection class, the largest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. reflns_class.description Description of each reflection class. m=1 first order satellites H0L0 common projection reflections reflns_class.number_gt For each reflection class, the number of significantly intense reflections (see attribute threshold_expression) in category reflns in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel- equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item attribute details in category reflns. reflns_class.number_total For each reflection class, the total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item attribute details in category reflns. reflns_class.wR_factor_all For each reflection class, the weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. See also attribute R_factor_ in category reflns_class definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y(calc) = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight and the sum is taken over the reflections of this class. reflns_class.code The code identifying a certain reflection class. 1 m1 s2 0 reflns_scale Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through attribute scale_group_code in category refln. Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. <VRPTx:reflns_scaleCategory> <VRPTx:reflns_scale group_code="SG1"> <VRPTx:meas_F>4.0</VRPTx:meas_F> </VRPTx:reflns_scale> </VRPTx:reflns_scaleCategory> 0 1 0 1 0 1 1 reflns_scaleCategory This property indicates that datablock has a category holder reflns_scaleCategory. reflns_scaleCategory This property indicates that reflns_scaleCategory. has a category reflns_scale. reflns_scaleItem Abstract datatype property for reflns_scale items. reference_to_reflns_scale cross-reference to reflns_scale. referenced_by_reflns_scale cross-reference from reflns_scale. reflns_scale.meas_F A scale associated with attribute group_code in category reflns_scale. reflns_scale.meas_F_squared A scale associated with attribute group_code in category reflns_scale. reflns_scale.meas_intensity A scale associated with attribute group_code in category reflns_scale. reflns_scale.group_code The code identifying a scale attribute meas_F, in category reflns_scale _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity. These are linked to the REFLN list by the attribute scale_group_code in category refln. These codes need not correspond to those in the DIFFRN_SCALE list. 1 2 c1 c2 0 reflns_shell Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:reflns_shellCategory> <VRPTx:reflns_shell pdbx_ordinal="1"> <VRPTx:Rmerge_F_obs>1.98</VRPTx:Rmerge_F_obs> <VRPTx:d_res_high>31.38</VRPTx:d_res_high> <VRPTx:d_res_low>3.82</VRPTx:d_res_low> <VRPTx:meanI_over_sigI_obs>69.8</VRPTx:meanI_over_sigI_obs> <VRPTx:number_measured_obs>9024</VRPTx:number_measured_obs> <VRPTx:number_unique_obs>2540</VRPTx:number_unique_obs> <VRPTx:percent_possible_obs>96.8</VRPTx:percent_possible_obs> </VRPTx:reflns_shell> <VRPTx:reflns_shell pdbx_ordinal="2"> <VRPTx:Rmerge_F_obs>3.85</VRPTx:Rmerge_F_obs> <VRPTx:d_res_high>3.82</VRPTx:d_res_high> <VRPTx:d_res_low>3.03</VRPTx:d_res_low> <VRPTx:meanI_over_sigI_obs>26.1</VRPTx:meanI_over_sigI_obs> <VRPTx:number_measured_obs>7413</VRPTx:number_measured_obs> <VRPTx:number_unique_obs>2364</VRPTx:number_unique_obs> <VRPTx:percent_possible_obs>95.1</VRPTx:percent_possible_obs> </VRPTx:reflns_shell> <VRPTx:reflns_shell pdbx_ordinal="3"> <VRPTx:Rmerge_F_obs>6.37</VRPTx:Rmerge_F_obs> <VRPTx:d_res_high>3.03</VRPTx:d_res_high> <VRPTx:d_res_low>2.65</VRPTx:d_res_low> <VRPTx:meanI_over_sigI_obs>10.5</VRPTx:meanI_over_sigI_obs> <VRPTx:number_measured_obs>5640</VRPTx:number_measured_obs> <VRPTx:number_unique_obs>2123</VRPTx:number_unique_obs> <VRPTx:percent_possible_obs>86.2</VRPTx:percent_possible_obs> </VRPTx:reflns_shell> <VRPTx:reflns_shell pdbx_ordinal="4"> <VRPTx:Rmerge_F_obs>8.01</VRPTx:Rmerge_F_obs> <VRPTx:d_res_high>2.65</VRPTx:d_res_high> <VRPTx:d_res_low>2.41</VRPTx:d_res_low> <VRPTx:meanI_over_sigI_obs>6.4</VRPTx:meanI_over_sigI_obs> <VRPTx:number_measured_obs>4322</VRPTx:number_measured_obs> <VRPTx:number_unique_obs>1882</VRPTx:number_unique_obs> <VRPTx:percent_possible_obs>76.8</VRPTx:percent_possible_obs> </VRPTx:reflns_shell> <VRPTx:reflns_shell pdbx_ordinal="5"> <VRPTx:Rmerge_F_obs>9.86</VRPTx:Rmerge_F_obs> <VRPTx:d_res_high>2.41</VRPTx:d_res_high> <VRPTx:d_res_low>2.23</VRPTx:d_res_low> <VRPTx:meanI_over_sigI_obs>4.3</VRPTx:meanI_over_sigI_obs> <VRPTx:number_measured_obs>3247</VRPTx:number_measured_obs> <VRPTx:number_unique_obs>1714</VRPTx:number_unique_obs> <VRPTx:percent_possible_obs>70.4</VRPTx:percent_possible_obs> </VRPTx:reflns_shell> <VRPTx:reflns_shell pdbx_ordinal="6"> <VRPTx:Rmerge_F_obs>13.99</VRPTx:Rmerge_F_obs> <VRPTx:d_res_high>2.23</VRPTx:d_res_high> <VRPTx:d_res_low>2.10</VRPTx:d_res_low> <VRPTx:meanI_over_sigI_obs>3.1</VRPTx:meanI_over_sigI_obs> <VRPTx:number_measured_obs>1140</VRPTx:number_measured_obs> <VRPTx:number_unique_obs>812</VRPTx:number_unique_obs> <VRPTx:percent_possible_obs>33.3</VRPTx:percent_possible_obs> </VRPTx:reflns_shell> </VRPTx:reflns_shellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 reflns_shellCategory This property indicates that datablock has a category holder reflns_shellCategory. reflns_shellCategory This property indicates that reflns_shellCategory. has a category reflns_shell. reflns_shellItem Abstract datatype property for reflns_shell items. reference_to_reflns_shell cross-reference to reflns_shell. referenced_by_reflns_shell cross-reference from reflns_shell. reflns_shell.Rmerge_F_all Residual factor Rmerge for all reflections that satisfy the resolution limits established by attribute d_res_high in category reflns_shell and attribute d_res_low. in category reflns_shell sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection reflns_shell.Rmerge_F_gt The value of Rmerge(F) for significantly intense reflections (see attribute threshold_expression) in category reflns in a given shell. sum~i~ ( sum~j~ | F~j~ - <F> | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ <F> ) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. reflns_shell.Rmerge_F_obs Residual factor Rmerge for reflections that satisfy the resolution limits established by attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell and the observation criterion established by attribute observed_criterion. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection reflns_shell.Rmerge_I_all The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection reflns_shell.Rmerge_I_gt The value of Rmerge(I) for significantly intense reflections (see attribute threshold_expression) in category reflns in a given shell. sum~i~ ( sum~j~ | I~j~ - <I> | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ <I> ) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. reflns_shell.Rmerge_I_obs The value of Rmerge(I) for reflections classified as 'observed' (see attribute observed_criterion) in category reflns in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection reflns_shell.d_res_high The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. reflns_shell.d_res_low The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. reflns_shell.meanI_over_sigI_all The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. reflns_shell.meanI_over_sigI_gt The ratio of the mean of the intensities of the significantly intense reflections (see attribute threshold_expression) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. reflns_shell.meanI_over_sigI_obs The ratio of the mean of the intensities of the reflections classified as 'observed' (see attribute observed_criterion) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell. reflns_shell.meanI_over_uI_all The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. reflns_shell.meanI_over_uI_gt The ratio of the mean of the intensities of the significantly intense reflections (see attribute threshold_expression) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. reflns_shell.number_measured_all The total number of reflections measured for this shell. reflns_shell.number_measured_gt The number of significantly intense reflections (see attribute threshold_expression) in category reflns measured for this shell. reflns_shell.number_measured_obs The number of reflections classified as 'observed' (see attribute observed_criterion) in category reflns for this shell. reflns_shell.number_possible The number of unique reflections it is possible to measure in this shell. reflns_shell.number_unique_all The total number of measured reflections which are symmetry- unique after merging for this shell. reflns_shell.number_unique_gt The total number of significantly intense reflections (see attribute threshold_expression) in category reflns resulting from merging measured symmetry-equivalent reflections for this resolution shell. reflns_shell.number_unique_obs The total number of measured reflections classified as 'observed' (see attribute observed_criterion) in category reflns which are symmetry-unique after merging for this shell. reflns_shell.pdbx_CC_half The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets within the resolution shell. Ref: Karplus & Diederichs (2012), Science 336, 1030-33 reflns_shell.pdbx_CC_half_anomalous The correlation coefficient within the spherical shell (defined by its diffraction limits attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell between two randomly chosen half-sets of anomalous intensity differences, I(+)-I(-) for anomalous data, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. reflns_shell.pdbx_CC_star Estimates the value of CC_true, the true correlation coefficient between the average intensities from randomly selected half-datasets within the resolution shell. CC_star = sqrt(2*CC_half/(1+CC_half)) Ref: Karplus & Diederichs (2012), Science 336, 1030-33 reflns_shell.pdbx_R_split R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the data within the resolution shell. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341 reflns_shell.pdbx_Rpim_I_all The precision-indicating merging R factor value Rpim, for merging all intensities in a given shell. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. reflns_shell.pdbx_Rrim_I_all The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in a given shell. sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rrim = -------------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. reflns_shell.pdbx_Rsym_value R sym value in percent. reflns_shell.pdbx_absDiff_over_sigma_anomalous The mean ratio of absolute anomalous intensity differences to their standard deviation within the spherical shell (defined by its diffraction limits attribute d_resolution_high in category reflns_shell and attribute d_resolution_low). in category reflns_shell |Dano| ------------- sigma(Dano) with Dano = I(+) - I(-) sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 ) reflns_shell.pdbx_chi_squared Chi-squared statistic for this resolution shell. reflns_shell.pdbx_diffrn_id An identifier for the diffraction data set corresponding to this resolution shell. Multiple diffraction data sets specified as a comma separated list. reflns_shell.pdbx_netI_over_sigmaI_all The mean of the ratio of the intensities to their standard uncertainties of all reflections in the resolution shell. attribute pdbx_netI_over_sigmaI_all in category reflns_shell = <I/sigma(I)> reflns_shell.pdbx_netI_over_sigmaI_obs The mean of the ratio of the intensities to their standard uncertainties of observed reflections (see attribute observed_criterion) in category reflns in the resolution shell. attribute pdbx_netI_over_sigmaI_obs in category reflns_shell = <I/sigma(I)> reflns_shell.pdbx_percent_possible_anomalous Completeness (as a percentage) of symmetry-unique anomalous difference data within the spherical shell defined by its diffraction limits (_reflns_shell.d_resolution_high and attribute d_resolution_low) in category reflns_shell relative to all possible symmetry-unique anomalous difference data within that shell. reflns_shell.pdbx_percent_possible_ellipsoidal Completeness (as a percentage) of symmetry-unique data within the intersection of (1) a spherical shell (defined by its diffraction limits, attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique reflections within that intersection. reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous Completeness (as a percentage) of symmetry-unique anomalous difference data within the intersection of (1) a spherical shell (defined by its diffraction limits, attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique anomalous difference data within that intersection. reflns_shell.pdbx_percent_possible_spherical Completeness (as a percentage) of symmetry-unique data within the spherical shell defined by its diffraction limits (_reflns_shell.d_resolution_high and attribute d_resolution_low) in category reflns_shell relative to all possible symmetry-unique reflections within that shell. In the absence of an anisotropy description this is identical to attribute percent_possible_all in category reflns_shell. reflns_shell.pdbx_percent_possible_spherical_anomalous Completeness (as a percentage) of symmetry-unique anomalous difference data within the spherical shell defined by its diffraction limits (_reflns_shell.d_resolution_high and attribute d_resolution_low) in category reflns_shell relative to all possible symmetry-unique anomalous difference data within that shell. In the absence of an anisotropy description this is identical to attribute pdbx_percent_possible_anomalous in category reflns. reflns_shell.pdbx_redundancy Redundancy for the current shell. reflns_shell.pdbx_redundancy_anomalous The redundancy of anomalous difference data within the spherical shell (defined by its diffraction limits attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. reflns_shell.pdbx_rejects The number of rejected reflections in the resolution shell. Reflections may be rejected from scaling by setting the observation criterion, attribute observed_criterion in category reflns. reflns_shell.percent_possible_all The percentage of geometrically possible reflections represented by all reflections measured for this shell. reflns_shell.percent_possible_gt The percentage of geometrically possible reflections represented by significantly intense reflections (see attribute threshold_expression) in category reflns measured for this shell. reflns_shell.percent_possible_obs The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see attribute observed_criterion) in category reflns for this shell. reflns_shell.pdbx_ordinal An ordinal identifier for this resolution shell. 0 space_group Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary. Example 1 - the monoclinic space group No. 15 with unique axis b. <VRPTx:space_groupCategory> <VRPTx:space_group id="1"> <VRPTx:IT_number>15</VRPTx:IT_number> <VRPTx:crystal_system>monoclinic</VRPTx:crystal_system> <VRPTx:name_H-M_alt>C 2/c</VRPTx:name_H-M_alt> <VRPTx:name_Hall>-C 2yc</VRPTx:name_Hall> </VRPTx:space_group> </VRPTx:space_groupCategory> 0 1 0 1 0 1 0 1 1 space_groupCategory This property indicates that datablock has a category holder space_groupCategory. space_groupCategory This property indicates that space_groupCategory. has a category space_group. space_groupItem Abstract datatype property for space_group items. reference_to_space_group cross-reference to space_group. referenced_by_space_group cross-reference from space_group. space_group.IT_number The number as assigned in International Tables for Crystallography Vol. A, specifying the proper affine class (i.e. the orientation-preserving affine class) of space groups (crystallographic space-group type) to which the space group belongs. This number defines the space-group type but not the coordinate system in which it is expressed. triclinic monoclinic orthorhombic tetragonal trigonal hexagonal cubic The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs. Note that rhombohedral space groups belong to the trigonal system. space_group.name_H-M_alt attribute name_H-M_alt in category space_group allows any Hermann-Mauguin symbol to be given. The way in which this item is used is determined by the user and in general is not intended to be interpreted by computer. It may, for example, be used to give one of the extended Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. Subscripts should appear without special symbols. Bars should be given as negative signs before the numbers to which they apply. The commonly used Hermann-Mauguin symbol determines the space- group type uniquely but a given space-group type may be described by more than one Hermann-Mauguin symbol. The space- group type is best described using attribute IT_number. in category space_group The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use attribute name_Hall in category space_group or list the symmetry operations. three examples for space group No. 63 loop_ _space_group.name_H-M_alt 'C m c m' 'C 2/c 2/m 21/m' 'A m a m' space_group.name_Hall Space-group symbol defined by Hall. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. attribute name_Hall in category space_group uniquely defines the space group and its reference to a particular coordinate system. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. [See also International Tables for Crystallography Vol. B (2001), Chapter 1.4, Appendix 1.4.2.] equivalent to Pca21 P 2c -2ac equivalent to Ia3d -I 4bd 2ab 3 space_group.id This is the unique identifier for the SPACE_GROUP category. 0 space_group_symop Contains information about the symmetry operations of the space group. Example 1 - The symmetry operations for the space group P21/c. <VRPTx:space_group_symopCategory> <VRPTx:space_group_symop id="1"> <VRPTx:operation_xyz>x,y,z</VRPTx:operation_xyz> </VRPTx:space_group_symop> <VRPTx:space_group_symop id="2"> <VRPTx:operation_xyz>-x,-y,-z</VRPTx:operation_xyz> </VRPTx:space_group_symop> <VRPTx:space_group_symop id="3"> <VRPTx:operation_xyz>-x,1/2+y,1/2-z</VRPTx:operation_xyz> </VRPTx:space_group_symop> <VRPTx:space_group_symop id="4"> <VRPTx:operation_xyz>x,1/2-y,1/2+z</VRPTx:operation_xyz> </VRPTx:space_group_symop> </VRPTx:space_group_symopCategory> 0 1 0 1 1 space_group_symopCategory This property indicates that datablock has a category holder space_group_symopCategory. space_group_symopCategory This property indicates that space_group_symopCategory. has a category space_group_symop. space_group_symopItem Abstract datatype property for space_group_symop items. reference_to_space_group_symop cross-reference to space_group_symop. referenced_by_space_group_symop cross-reference from space_group_symop. space_group_symop.operation_xyz A parsable string giving one of the symmetry operations of the space group in algebraic form. If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by the fractions, an equivalent position X' is generated from a given position X by the equation X' = WX + w (Note: X is used to represent bold_italics_x in International Tables for Crystallography Vol. A, Part 5) When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicity all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used. glide reflection through the plane (x,1/4,z), with glide vector 1/2 c x,1/2-y,1/2+z space_group_symop.sg_id This must match a particular value of attribute id in category space_group, allowing the symmetry operation to be identified with a particular space group. space_group_symop.id An arbitrary identifier that uniquely labels each symmetry operation in the list. 0 struct Data items in the STRUCT category record details about the description of the crystallographic structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:structCategory> <VRPTx:struct entry_id="5HVP"> <VRPTx:title> HIV-1 protease complex with acetyl-pepstatin</VRPTx:title> </VRPTx:struct> </VRPTx:structCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 structCategory This property indicates that datablock has a category holder structCategory. structCategory This property indicates that structCategory. has a category struct. structItem Abstract datatype property for struct items. reference_to_struct cross-reference to struct. referenced_by_struct cross-reference from struct. Y N The item indicates whether the entry is a CASP target, a CASD-NMR target, or similar target participating in methods development experiments. Y struct.pdbx_descriptor An automatically generated descriptor for an NDB structure or the unstructured content of the PDB COMPND record. 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3' struct.pdbx_formula_weight Estimated formula mass in daltons of the deposited structure assembly. struct.pdbx_formula_weight_method Method used to determine attribute pdbx_formula_weight in category struct. MASS SPEC CALCULATION struct.pdbx_model_details Text description of the methodology which produced this model structure. This model was produced from a 10 nanosecond Amber/MD simulation starting from PDB structure ID 1ABC. struct.pdbx_model_type_details A description of the type of structure model. MINIMIZED AVERAGE experimental integrative computational Indicates if the structure was determined using experimental, computational, or integrative methods struct.title A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. 5'-D(*(I)CP*CP*GP*G)-3 T4 lysozyme mutant - S32A hen egg white lysozyme at -30 degrees C quail egg white lysozyme at 2 atmospheres struct.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 struct_asym Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_asymCategory> <VRPTx:struct_asym id="A"> <VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details> <VRPTx:entity_id>1</VRPTx:entity_id> </VRPTx:struct_asym> <VRPTx:struct_asym id="B"> <VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details> <VRPTx:entity_id>1</VRPTx:entity_id> </VRPTx:struct_asym> <VRPTx:struct_asym id="C"> <VRPTx:details>one partially occupied position for the inhibitor</VRPTx:details> <VRPTx:entity_id>2</VRPTx:entity_id> </VRPTx:struct_asym> <VRPTx:struct_asym id="D"> <VRPTx:details>one partially occupied position for the inhibitor</VRPTx:details> <VRPTx:entity_id>2</VRPTx:entity_id> </VRPTx:struct_asym> </VRPTx:struct_asymCategory> 0 1 1 1 0 1 0 1 1 struct_asymCategory This property indicates that datablock has a category holder struct_asymCategory. struct_asymCategory This property indicates that struct_asymCategory. has a category struct_asym. struct_asymItem Abstract datatype property for struct_asym items. reference_to_struct_asym cross-reference to struct_asym. referenced_by_struct_asym cross-reference from struct_asym. struct_asym.details A description of special aspects of this portion of the contents of the asymmetric unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. struct_asym.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. Y N A flag indicating that this entity was originally labeled with a blank PDB chain id. struct_asym.pdbx_modified This data item indicates whether the structural elements are modified. y struct_asym.id The value of attribute id in category struct_asym must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. 1 A 2B3 0 struct_biol Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_biolCategory> <VRPTx:struct_biol id="1"> <VRPTx:details> significant deviations from twofold symmetry exist in this dimeric enzyme</VRPTx:details> </VRPTx:struct_biol> <VRPTx:struct_biol id="2"> <VRPTx:details> The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (2) is roughly twofold symmetric to biological unit (3). Disorder in the protein chain indicated with alternative ID 1 should be used with this biological unit.</VRPTx:details> </VRPTx:struct_biol> <VRPTx:struct_biol id="3"> <VRPTx:details> The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit.</VRPTx:details> </VRPTx:struct_biol> </VRPTx:struct_biolCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_biolCategory This property indicates that datablock has a category holder struct_biolCategory. struct_biolCategory This property indicates that struct_biolCategory. has a category struct_biol. struct_biolItem Abstract datatype property for struct_biol items. reference_to_struct_biol cross-reference to struct_biol. referenced_by_struct_biol cross-reference from struct_biol. struct_biol.details A description of special aspects of the biological unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. MONOMER DIMER TRIMER TETRAMER HEXAMER MORE A description of the structural aggregation in this assembly. struct_biol.pdbx_assembly_method The method or experiment used to determine this assembly. AUTHOR PROVIDED', 'LCMS', 'PISA', 'PQS struct_biol.pdbx_formula_weight Estimated formula mass in daltons of the biological assembly. struct_biol.pdbx_formula_weight_method Method used to determine attribute pdbx_formula_weight in category struct_biol. MASS SPEC CALCULATION struct_biol.pdbx_parent_biol_id An identifier for the parent biological assembly if this biological unit is part of a complex assembly. 1 2 3 struct_biol.id The value of attribute id in category struct_biol must uniquely identify a record in the STRUCT_BIOL list. Note that this item need not be a number; it can be any unique identifier. 0 struct_biol_view Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure. Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry, (1989), 28, 310-320]. <VRPTx:struct_biol_viewCategory> <VRPTx:struct_biol_view biol_id="c1" id="1"> <VRPTx:details> This view highlights the ATAT-Netropsin interaction in the DNA-drug complex.</VRPTx:details> <VRPTx:rot_matrix11>0.132</VRPTx:rot_matrix11> <VRPTx:rot_matrix12>0.922</VRPTx:rot_matrix12> <VRPTx:rot_matrix13>-0.363</VRPTx:rot_matrix13> <VRPTx:rot_matrix21>0.131</VRPTx:rot_matrix21> <VRPTx:rot_matrix22>-0.380</VRPTx:rot_matrix22> <VRPTx:rot_matrix23>-0.916</VRPTx:rot_matrix23> <VRPTx:rot_matrix31>-0.982</VRPTx:rot_matrix31> <VRPTx:rot_matrix32>0.073</VRPTx:rot_matrix32> <VRPTx:rot_matrix33>-0.172</VRPTx:rot_matrix33> </VRPTx:struct_biol_view> </VRPTx:struct_biol_viewCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 struct_biol_viewCategory This property indicates that datablock has a category holder struct_biol_viewCategory. struct_biol_viewCategory This property indicates that struct_biol_viewCategory. has a category struct_biol_view. struct_biol_viewItem Abstract datatype property for struct_biol_view items. reference_to_struct_biol_view cross-reference to struct_biol_view. referenced_by_struct_biol_view cross-reference from struct_biol_view. struct_biol_view.details A description of special aspects of this view of the biological structure. This data item can be used as a figure legend. The enzyme has been oriented with the molecular twofold axis aligned with the horizontal axis of the figure. struct_biol_view.rot_matrix11 The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix12 The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix13 The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix21 The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix22 The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix23 The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix31 The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix32 The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.rot_matrix33 The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_biol_view.biol_id This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. struct_biol_view.id The value of attribute id in category struct_biol_view must uniquely identify a record in the STRUCT_BIOL_VIEW list. Note that this item need not be a number; it can be any unique identifier. Figure 1 unliganded enzyme view down enzyme active site 0 struct_conf Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_confCategory> <VRPTx:struct_conf id="HELX1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ARG</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>87</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>HELX_RH_AL_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLN</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>92</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="HELX2"> <VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ARG</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>287</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>HELX_RH_AL_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLN</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>292</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="STRN1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>1</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>LEU</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>5</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="STRN2"> <VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>CYS</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>295</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>PHE</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>299</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="STRN3"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>CYS</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>95</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>PHE</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>299</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="STRN4"> <VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>201</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>LEU</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>205</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="TURN1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ILE</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>15</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>TURN_TY1P_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLN</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>18</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="TURN2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>GLY</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>49</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>TURN_TY2_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>52</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="TURN3"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ILE</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>55</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>TURN_TY1P_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>HIS</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>69</VRPTx:end_label_seq_id> </VRPTx:struct_conf> <VRPTx:struct_conf id="TURN4"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>THR</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>91</VRPTx:beg_label_seq_id> <VRPTx:conf_type_id>TURN_TY1_P</VRPTx:conf_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>94</VRPTx:end_label_seq_id> </VRPTx:struct_conf> </VRPTx:struct_confCategory> 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 struct_confCategory This property indicates that datablock has a category holder struct_confCategory. struct_confCategory This property indicates that struct_confCategory. has a category struct_conf. struct_confItem Abstract datatype property for struct_conf items. reference_to_struct_conf cross-reference to struct_conf. referenced_by_struct_conf cross-reference from struct_conf. struct_conf.beg_auth_asym_id A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_conf.beg_auth_comp_id A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_conf.beg_auth_seq_id A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_conf.beg_label_asym_id A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_conf.beg_label_comp_id A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_conf.beg_label_seq_id A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_conf.conf_type_id This data item is a pointer to attribute id in category struct_conf_type in the STRUCT_CONF_TYPE category. struct_conf.details A description of special aspects of the conformation assignment. struct_conf.end_auth_asym_id A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_conf.end_auth_comp_id A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_conf.end_auth_seq_id A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_conf.end_label_asym_id A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_conf.end_label_comp_id A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_conf.end_label_seq_id A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_conf.pdbx_PDB_helix_class This item is a place holder for the helix class used in the PDB HELIX record. struct_conf.pdbx_PDB_helix_id A placeholder for the helix identifier of the PDB HELIX record. struct_conf.pdbx_PDB_helix_length A placeholder for the lengths of the helix of the PDB HELIX record. struct_conf.pdbx_beg_PDB_ins_code A component of the identifier for the residue at which the conformation segment starts. struct_conf.pdbx_end_PDB_ins_code A component of the identifier for the residue at which the conformation segment ends. struct_conf.id The value of attribute id in category struct_conf must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier. 0 struct_conf_type Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_conf_typeCategory> <VRPTx:struct_conf_type id="HELX_RH_AL_P"> <VRPTx:criteria>author judgement</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conf_type> <VRPTx:struct_conf_type id="STRN_P"> <VRPTx:criteria>author judgement</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conf_type> <VRPTx:struct_conf_type id="TURN_TY1_P"> <VRPTx:criteria>author judgement</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conf_type> <VRPTx:struct_conf_type id="TURN_TY1P_P"> <VRPTx:criteria>author judgement</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conf_type> <VRPTx:struct_conf_type id="TURN_TY2_P"> <VRPTx:criteria>author judgement</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conf_type> <VRPTx:struct_conf_type id="TURN_TY2P_P"> <VRPTx:criteria>author judgement</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conf_type> </VRPTx:struct_conf_typeCategory> 0 1 0 1 1 struct_conf_typeCategory This property indicates that datablock has a category holder struct_conf_typeCategory. struct_conf_typeCategory This property indicates that struct_conf_typeCategory. has a category struct_conf_type. struct_conf_typeItem Abstract datatype property for struct_conf_type items. reference_to_struct_conf_type cross-reference to struct_conf_type. referenced_by_struct_conf_type cross-reference from struct_conf_type. struct_conf_type.criteria The criteria used to assign this conformation type. author judgement phi=54-74, psi=30-50 struct_conf_type.reference A literature reference that defines the criteria used to assign this conformation type and subtype. BEND HELX_P HELX_OT_P HELX_RH_P HELX_RH_OT_P HELX_RH_AL_P HELX_RH_GA_P HELX_RH_OM_P HELX_RH_PI_P HELX_RH_27_P HELX_RH_3T_P HELX_RH_PP_P HELX_LH_P HELX_LH_OT_P HELX_LH_AL_P HELX_LH_GA_P HELX_LH_OM_P HELX_LH_PI_P HELX_LH_27_P HELX_LH_3T_P HELX_LH_PP_P HELX_N HELX_OT_N HELX_RH_N HELX_RH_OT_N HELX_RH_A_N HELX_RH_B_N HELX_RH_Z_N HELX_LH_N HELX_LH_OT_N HELX_LH_A_N HELX_LH_B_N HELX_LH_Z_N TURN_P TURN_OT_P TURN_TY1_P TURN_TY1P_P TURN_TY2_P TURN_TY2P_P TURN_TY3_P TURN_TY3P_P STRN OTHER The descriptor that categorizes the type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsion angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. 0 struct_conn Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_connCategory> <VRPTx:struct_conn id="C1"> <VRPTx:conn_type_id>saltbr</VRPTx:conn_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>NZ1</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ARG</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>87</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr1_role>positive</VRPTx:ptnr1_role> <VRPTx:ptnr1_symmetry>1_555</VRPTx:ptnr1_symmetry> <VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id>OE1</VRPTx:ptnr2_label_atom_id> <VRPTx:ptnr2_label_comp_id>GLU</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>92</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr2_role>negative</VRPTx:ptnr2_role> <VRPTx:ptnr2_symmetry>1_555</VRPTx:ptnr2_symmetry> </VRPTx:struct_conn> <VRPTx:struct_conn id="C2"> <VRPTx:conn_type_id>hydrog</VRPTx:conn_type_id> <VRPTx:details xsi:nil="true" /> <VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id> <VRPTx:ptnr1_label_atom_id>N</VRPTx:ptnr1_label_atom_id> <VRPTx:ptnr1_label_comp_id>ARG</VRPTx:ptnr1_label_comp_id> <VRPTx:ptnr1_label_seq_id>287</VRPTx:ptnr1_label_seq_id> <VRPTx:ptnr1_role>donor</VRPTx:ptnr1_role> <VRPTx:ptnr1_symmetry>1_555</VRPTx:ptnr1_symmetry> <VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id> <VRPTx:ptnr2_label_atom_id>O</VRPTx:ptnr2_label_atom_id> <VRPTx:ptnr2_label_comp_id>GLY</VRPTx:ptnr2_label_comp_id> <VRPTx:ptnr2_label_seq_id>292</VRPTx:ptnr2_label_seq_id> <VRPTx:ptnr2_role>acceptor</VRPTx:ptnr2_role> <VRPTx:ptnr2_symmetry>1_555</VRPTx:ptnr2_symmetry> </VRPTx:struct_conn> </VRPTx:struct_connCategory> 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 1 0 1 0 1 1 struct_connCategory This property indicates that datablock has a category holder struct_connCategory. struct_connCategory This property indicates that struct_connCategory. has a category struct_conn. struct_connItem Abstract datatype property for struct_conn items. reference_to_struct_conn cross-reference to struct_conn. referenced_by_struct_conn cross-reference from struct_conn. covale disulf metalc hydrog This data item is a pointer to attribute id in category struct_conn_type in the STRUCT_CONN_TYPE category. struct_conn.details A description of special aspects of the connection. disulfide bridge C-S-S-C is highly distorted struct_conn.pdbx_PDB_id A placeholder for the PDB id in the case the category is used to hold the information of the MODRES record of a PDB file. 1ABC struct_conn.pdbx_dist_value Distance value for this contact. both one none This data item identifies if the linkage has displaced leaving atoms on both, one or none of the connected atoms forming the linkage. Leaving atoms are defined within their chemical definitions of each connected component. struct_conn.pdbx_ptnr1_PDB_ins_code A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 R S N The chiral configuration of the first atom making the linkage. struct_conn.pdbx_ptnr1_auth_alt_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A B struct_conn.pdbx_ptnr1_label_alt_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A B struct_conn.pdbx_ptnr1_leaving_atom_id The leaving atom that is removed from first atom making the linkage. struct_conn.pdbx_ptnr1_standard_comp_id A placeholder for the standard residue name found in the MODRES record of a PDB file. A T C G GLY ALA MET struct_conn.pdbx_ptnr2_PDB_ins_code A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 R S N The chiral configuration of the second atom making the linkage. struct_conn.pdbx_ptnr2_auth_alt_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A B struct_conn.pdbx_ptnr2_label_alt_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A B struct_conn.pdbx_ptnr2_leaving_atom_id The leaving atom that is removed from second atom making the linkage. struct_conn.pdbx_ptnr3_PDB_ins_code A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 struct_conn.pdbx_ptnr3_auth_alt_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A B struct_conn.pdbx_ptnr3_auth_asym_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A B C struct_conn.pdbx_ptnr3_auth_atom_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. O5* struct_conn.pdbx_ptnr3_auth_comp_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A T C G GLY ALA MET struct_conn.pdbx_ptnr3_auth_seq_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 12 struct_conn.pdbx_ptnr3_label_alt_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A B struct_conn.pdbx_ptnr3_label_asym_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A B C struct_conn.pdbx_ptnr3_label_atom_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. O5* struct_conn.pdbx_ptnr3_label_comp_id A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A T C G GLY ALA MET struct_conn.pdbx_ptnr3_label_seq_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 12 N-Glycosylation O-Glycosylation S-Glycosylation C-Mannosylation The chemical or structural role of the interaction N-Glycosylation O-Glycosylation sing doub trip quad The chemical bond order associated with the specified atoms in this contact. struct_conn.ptnr1_auth_asym_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_auth_atom_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_auth_comp_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_auth_seq_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_label_alt_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. struct_conn.ptnr1_label_asym_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_label_atom_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. struct_conn.ptnr1_label_comp_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_label_seq_id A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr1_role The chemical or structural role of the first partner in the structure connection. donor acceptor negative positive metal metal coordination struct_conn.ptnr1_symmetry Describes the symmetry operation that should be applied to the atom set specified by attribute ptnr1_label* in category struct_conn to generate the first partner in the structure connection. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 struct_conn.ptnr2_auth_asym_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_auth_atom_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_auth_comp_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_auth_seq_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_label_alt_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. struct_conn.ptnr2_label_asym_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_label_atom_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. struct_conn.ptnr2_label_comp_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_label_seq_id A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_conn.ptnr2_role The chemical or structural role of the second partner in the structure connection. donor acceptor negative positive metal metal coordination struct_conn.ptnr2_symmetry Describes the symmetry operation that should be applied to the atom set specified by attribute ptnr2_label* in category struct_conn to generate the second partner in the structure connection. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 struct_conn.id The value of attribute id in category struct_conn must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier. 0 struct_conn_type Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_conn_typeCategory> <VRPTx:struct_conn_type id="saltbr"> <VRPTx:criteria>negative to positive distance &gt; 2.5 \&#37;A, &lt; 3.2 \&#37;A</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conn_type> <VRPTx:struct_conn_type id="hydrog"> <VRPTx:criteria>NO distance &gt; 2.5\&#37;A, &lt; 3.5\&#37;A, NOC angle &lt; 120 degrees</VRPTx:criteria> <VRPTx:reference xsi:nil="true" /> </VRPTx:struct_conn_type> </VRPTx:struct_conn_typeCategory> 0 1 0 1 1 struct_conn_typeCategory This property indicates that datablock has a category holder struct_conn_typeCategory. struct_conn_typeCategory This property indicates that struct_conn_typeCategory. has a category struct_conn_type. struct_conn_typeItem Abstract datatype property for struct_conn_type items. reference_to_struct_conn_type cross-reference to struct_conn_type. referenced_by_struct_conn_type cross-reference from struct_conn_type. struct_conn_type.criteria The criteria used to define the interaction. O to N distance > 2.5 \%A, < 3.2 \%A authors judgement struct_conn_type.reference A reference that specifies the criteria used to define the interaction. covale disulf hydrog metalc mismat saltbr modres covale_base covale_sugar covale_phosphate The chemical or structural type of the interaction. 0 struct_mon_details Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on. 0 1 0 1 0 1 1 struct_mon_detailsCategory This property indicates that datablock has a category holder struct_mon_detailsCategory. struct_mon_detailsCategory This property indicates that struct_mon_detailsCategory. has a category struct_mon_details. struct_mon_detailsItem Abstract datatype property for struct_mon_details items. reference_to_struct_mon_details cross-reference to struct_mon_details. referenced_by_struct_mon_details cross-reference from struct_mon_details. struct_mon_details.RSCC This data item describes the specifics of the calculations that generated the values given in attribute RSCC_all, in category struct_mon_prot _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. struct_mon_details.RSR This data item describes the specifics of the calculations that generated the values given in attribute RSR_all, in category struct_mon_prot _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. struct_mon_details.prot_cis An ideal cis peptide bond would have an omega torsion angle of zero. This data item gives the value in degrees by which the observed torsion angle can differ from 0.0 and still be considered cis. 30.0 struct_mon_details.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 struct_mon_nucl Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. Example 1 - based on NDB structure BDL028. <VRPTx:struct_mon_nuclCategory> <VRPTx:struct_mon_nucl pdbx_id="1"> <VRPTx:alpha xsi:nil="true" /> <VRPTx:beta xsi:nil="true" /> <VRPTx:delta>131.9</VRPTx:delta> <VRPTx:epsilon>222.1</VRPTx:epsilon> <VRPTx:gamma>29.9</VRPTx:gamma> <VRPTx:label_alt_id>A</VRPTx:label_alt_id> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>C</VRPTx:label_comp_id> <VRPTx:label_seq_id>1</VRPTx:label_seq_id> <VRPTx:zeta>174.2</VRPTx:zeta> </VRPTx:struct_mon_nucl> <VRPTx:struct_mon_nucl pdbx_id="2"> <VRPTx:alpha>334.0</VRPTx:alpha> <VRPTx:beta>130.6</VRPTx:beta> <VRPTx:delta>125.6</VRPTx:delta> <VRPTx:epsilon>167.6</VRPTx:epsilon> <VRPTx:gamma>33.1</VRPTx:gamma> <VRPTx:label_alt_id>A</VRPTx:label_alt_id> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>G</VRPTx:label_comp_id> <VRPTx:label_seq_id>2</VRPTx:label_seq_id> <VRPTx:zeta>270.9</VRPTx:zeta> </VRPTx:struct_mon_nucl> <VRPTx:struct_mon_nucl pdbx_id="3"> <VRPTx:alpha>258.2</VRPTx:alpha> <VRPTx:beta>178.7</VRPTx:beta> <VRPTx:delta>114.6</VRPTx:delta> <VRPTx:epsilon>216.6</VRPTx:epsilon> <VRPTx:gamma>101.0</VRPTx:gamma> <VRPTx:label_alt_id>A</VRPTx:label_alt_id> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>T</VRPTx:label_comp_id> <VRPTx:label_seq_id>3</VRPTx:label_seq_id> <VRPTx:zeta>259.3</VRPTx:zeta> </VRPTx:struct_mon_nucl> </VRPTx:struct_mon_nuclCategory> 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_mon_nuclCategory This property indicates that datablock has a category holder struct_mon_nuclCategory. struct_mon_nuclCategory This property indicates that struct_mon_nuclCategory. has a category struct_mon_nucl. struct_mon_nuclItem Abstract datatype property for struct_mon_nucl items. reference_to_struct_mon_nucl cross-reference to struct_mon_nucl. referenced_by_struct_mon_nucl cross-reference from struct_mon_nucl. struct_mon_nucl.P P is the phase angle of pseudorotation for five-membered rings. For ribose and deoxyribose sugars in nucleic acids (tau4 +tau1)-(tau3+tau0) P = ATAN (-------------------------) 2tau2 (sin 36+sin 72) If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam, 1972). Ref: Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212. struct_mon_nucl.PDB_model_num The model number for the given monomer struct_mon_nucl.RSCC_all The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_nucl.RSCC_base The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_nucl.RSCC_phos The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_nucl.RSCC_sugar The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_nucl.RSR_all The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_nucl.RSR_base The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_nucl.RSR_phos The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_nucl.RSR_sugar The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_nucl.alpha The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5'). struct_mon_nucl.auth_asym_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_mon_nucl.auth_comp_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_mon_nucl.auth_seq_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_mon_nucl.beta The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4'). struct_mon_nucl.chi1 The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2). struct_mon_nucl.chi2 The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4). struct_mon_nucl.delta The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3'). struct_mon_nucl.details A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. Part of the phosphodiester backbone not in density. struct_mon_nucl.epsilon The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P). struct_mon_nucl.gamma The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3'). struct_mon_nucl.label_alt_id A component of the identifier for participants in the site. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. struct_mon_nucl.label_asym_id A component of the identifier for participants in the site. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_mon_nucl.label_comp_id A component of the identifier for participants in the site. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_mon_nucl.label_seq_id A component of the identifier for participants in the site. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_mon_nucl.mean_B_all The mean value of the isotropic displacement parameter for all atoms in the monomer. struct_mon_nucl.mean_B_base The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer. struct_mon_nucl.mean_B_phos The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer. struct_mon_nucl.mean_B_sugar The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer. struct_mon_nucl.nu0 The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2'). struct_mon_nucl.nu1 The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3'). struct_mon_nucl.nu2 The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4'). struct_mon_nucl.nu3 The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4'). struct_mon_nucl.nu4 The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1'). Y N Whether RNA sugar pucker classified as outlier conformation of the monomer (Y) or not (N). The values are computed by MolProbity. NonRotameric Rotameric Triaged/NotBinned RNA backbone (suite) classification of the monomer. The values are computed by MolProbity. NonRotameric Rotameric Triaged/NotBinned struct_mon_nucl.pdbx_RNA_suiteness_score RNA suiteness score is the conformer matching score of RNA backbone (suite) in comparison to the consensus conformation. Higher score (closer to 1.0) indicates good agreement with the consensus conformation. The values are computed by MolProbity. Ref: Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM, RNA Ontology Consortium. "RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." RNA (2008), 14(3), 465-481 struct_mon_nucl.tau0 The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2'). struct_mon_nucl.tau1 The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3'). struct_mon_nucl.tau2 The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4'). struct_mon_nucl.tau3 The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4'). struct_mon_nucl.tau4 The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1'). struct_mon_nucl.taum The maximum amplitude of puckering. This is derived from the pseudorotation value P and the torsion angles in the ribose ring. Tau2= Taum cosP Tau3= Taum cos(P+144) Tau4= Taum cos(P+288) Tau0= Taum cos(P+ 72) Tau1= Taum cos(P+216) struct_mon_nucl.zeta The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5'). struct_mon_nucl.pdbx_id Ordinal index 0 struct_mon_prot Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. Example 1 - based on laboratory records for protein NS1. This example provides details for residue ARG 35. <VRPTx:struct_mon_protCategory> <VRPTx:struct_mon_prot pdbx_id="1"> <VRPTx:RSCC_all>0.90</VRPTx:RSCC_all> <VRPTx:RSR_all>0.18</VRPTx:RSR_all> <VRPTx:chi1>-67.9</VRPTx:chi1> <VRPTx:chi2>-174.7</VRPTx:chi2> <VRPTx:chi3>-67.7</VRPTx:chi3> <VRPTx:chi4>-86.3</VRPTx:chi4> <VRPTx:chi5>4.2</VRPTx:chi5> <VRPTx:label_alt_id>A</VRPTx:label_alt_id> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>ARG</VRPTx:label_comp_id> <VRPTx:label_seq_id>35</VRPTx:label_seq_id> <VRPTx:mean_B_all>30.0</VRPTx:mean_B_all> <VRPTx:mean_B_main>25.0</VRPTx:mean_B_main> <VRPTx:mean_B_side>35.1</VRPTx:mean_B_side> <VRPTx:omega>180.1</VRPTx:omega> <VRPTx:phi>-60.3</VRPTx:phi> <VRPTx:psi>-46.0</VRPTx:psi> </VRPTx:struct_mon_prot> </VRPTx:struct_mon_protCategory> 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_mon_protCategory This property indicates that datablock has a category holder struct_mon_protCategory. struct_mon_protCategory This property indicates that struct_mon_protCategory. has a category struct_mon_prot. struct_mon_protItem Abstract datatype property for struct_mon_prot items. reference_to_struct_mon_prot cross-reference to struct_mon_prot. referenced_by_struct_mon_prot cross-reference from struct_mon_prot. struct_mon_prot.PDB_model_num The model number for the given monomer struct_mon_prot.RSCC_all The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_prot.RSCC_main The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_prot.RSCC_side The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. struct_mon_prot.RSR_all The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_prot.RSR_main The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_prot.RSR_side The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. struct_mon_prot.auth_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_mon_prot.auth_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_mon_prot.auth_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_mon_prot.chi1 The value in degrees of the side-chain torsion angle chi1, for those residues containing such an angle. struct_mon_prot.chi2 The value in degrees of the side-chain torsion angle chi2, for those residues containing such an angle. struct_mon_prot.chi3 The value in degrees of the side-chain torsion angle chi3, for those residues containing such an angle. struct_mon_prot.chi4 The value in degrees of the side-chain torsion angle chi4, for those residues containing such an angle. struct_mon_prot.chi5 The value in degrees of the side-chain torsion angle chi5, for those residues containing such an angle. struct_mon_prot.details A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. very poor density The side chain of this density may occupy alternative conformations, but alternative conformations were not fit in this model. This residue has a close contact with the bound inhibitor, which may account for the nonstandard conformation of the side chain. struct_mon_prot.label_alt_id A component of the identifier for the monomer. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. struct_mon_prot.label_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_mon_prot.label_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_mon_prot.label_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_mon_prot.mean_B_all The mean value of the isotropic displacement parameter for all atoms in the monomer. struct_mon_prot.mean_B_main The mean value of the isotropic displacement parameter for atoms in the main chain of the monomer. struct_mon_prot.mean_B_side The mean value of the isotropic displacement parameter for atoms in the side chain of the monomer. struct_mon_prot.omega The value in degrees of the main-chain torsion angle omega. Favored Allowed OUTLIER Ramachandran plot classification for back bone conformation of the monomer. The values are computed by MolProbity. Favored Allowed OUTLIER Y N Whether side chains of asparagine, glutamine and histidine can be be rotated to make optimal hydrogen bonds, improving its contacts with its neighbors, without affecting their fit to the experimental electron density (Y) or not (N). The values are computed by MolProbity. struct_mon_prot.pdbx_rotamer Rotamer classification for side chain conformation of the monomer. The values are computed by MolProbity. mt t OUTLIER m p m-20 m-85 tp t80 mt-10 Cg-endo Cg-exo struct_mon_prot.phi The value in degrees of the main-chain torsion angle phi. struct_mon_prot.psi The value in degrees of the main-chain torsion angle psi. struct_mon_prot.pdbx_id Ordinal index 0 struct_mon_prot_cis Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in attribute prot_cis in category struct_mon_details. Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield, Profy & Wilson [Science (1994), 264, 82-85]. <VRPTx:struct_mon_prot_cisCategory> <VRPTx:struct_mon_prot_cis pdbx_id="1"> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:label_asym_id>L</VRPTx:label_asym_id> <VRPTx:label_comp_id>PRO</VRPTx:label_comp_id> <VRPTx:label_seq_id>8</VRPTx:label_seq_id> <VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num> </VRPTx:struct_mon_prot_cis> <VRPTx:struct_mon_prot_cis pdbx_id="2"> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:label_asym_id>L</VRPTx:label_asym_id> <VRPTx:label_comp_id>PRO</VRPTx:label_comp_id> <VRPTx:label_seq_id>77</VRPTx:label_seq_id> <VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num> </VRPTx:struct_mon_prot_cis> <VRPTx:struct_mon_prot_cis pdbx_id="3"> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:label_asym_id>L</VRPTx:label_asym_id> <VRPTx:label_comp_id>PRO</VRPTx:label_comp_id> <VRPTx:label_seq_id>95</VRPTx:label_seq_id> <VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num> </VRPTx:struct_mon_prot_cis> <VRPTx:struct_mon_prot_cis pdbx_id="4"> <VRPTx:label_alt_id xsi:nil="true" /> <VRPTx:label_asym_id>L</VRPTx:label_asym_id> <VRPTx:label_comp_id>PRO</VRPTx:label_comp_id> <VRPTx:label_seq_id>141</VRPTx:label_seq_id> <VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num> </VRPTx:struct_mon_prot_cis> </VRPTx:struct_mon_prot_cisCategory> 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_mon_prot_cisCategory This property indicates that datablock has a category holder struct_mon_prot_cisCategory. struct_mon_prot_cisCategory This property indicates that struct_mon_prot_cisCategory. has a category struct_mon_prot_cis. struct_mon_prot_cisItem Abstract datatype property for struct_mon_prot_cis items. reference_to_struct_mon_prot_cis cross-reference to struct_mon_prot_cis. referenced_by_struct_mon_prot_cis cross-reference from struct_mon_prot_cis. struct_mon_prot_cis.auth_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_mon_prot_cis.auth_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_mon_prot_cis.auth_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_mon_prot_cis.label_alt_id A component of the identifier for the monomer. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. struct_mon_prot_cis.label_asym_id A component of the identifier for the monomer. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_mon_prot_cis.label_comp_id A component of the identifier for the monomer. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_mon_prot_cis.label_seq_id A component of the identifier for the monomer. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_mon_prot_cis.pdbx_PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site struct_mon_prot_cis.pdbx_PDB_ins_code_2 Pointer to attribute pdbx_PDB_ins_code in category atom_site struct_mon_prot_cis.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site struct_mon_prot_cis.pdbx_auth_asym_id_2 Pointer to attribute auth_asym_id in category atom_site. struct_mon_prot_cis.pdbx_auth_comp_id_2 Pointer to attribute auth_comp_id in category atom_site. struct_mon_prot_cis.pdbx_auth_seq_id_2 Pointer to attribute auth_seq_id in category atom_site struct_mon_prot_cis.pdbx_label_asym_id_2 Pointer to attribute label_asym_id in category atom_site. struct_mon_prot_cis.pdbx_label_comp_id_2 Pointer to attribute label_comp_id in category atom_site. struct_mon_prot_cis.pdbx_label_seq_id_2 Pointer to attribute label_seq_id in category atom_site struct_mon_prot_cis.pdbx_omega_angle Omega torsion angle struct_mon_prot_cis.pdbx_id Ordinal index 0 struct_ncs_dom Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <VRPTx:struct_ncs_domCategory> <VRPTx:struct_ncs_dom id="d1" pdbx_ens_id="1"> <VRPTx:details>Chains A, B, and C</VRPTx:details> </VRPTx:struct_ncs_dom> <VRPTx:struct_ncs_dom id="d2" pdbx_ens_id="1"> <VRPTx:details>Chains D, E, and F</VRPTx:details> </VRPTx:struct_ncs_dom> </VRPTx:struct_ncs_domCategory> 0 1 1 1 struct_ncs_domCategory This property indicates that datablock has a category holder struct_ncs_domCategory. struct_ncs_domCategory This property indicates that struct_ncs_domCategory. has a category struct_ncs_dom. struct_ncs_domItem Abstract datatype property for struct_ncs_dom items. reference_to_struct_ncs_dom cross-reference to struct_ncs_dom. referenced_by_struct_ncs_dom cross-reference from struct_ncs_dom. struct_ncs_dom.details A description of special aspects of the structural elements that comprise a domain in an ensemble of domains related by noncrystallographic symmetry. The loop between residues 18 and 23 in this domain interacts with a symmetry-related molecule, and thus deviates significantly from the noncrystallographic threefold. struct_ncs_dom.id The value of attribute id in category struct_ncs_dom must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. struct_ncs_dom.pdbx_ens_id This is a unique identifier for a collection NCS related domains. This references item '_struct_ncs_ens.id'. 0 struct_ncs_dom_lim Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <VRPTx:struct_ncs_dom_limCategory> <VRPTx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="1" pdbx_ens_id="1"> <VRPTx:beg_label_alt_id xsi:nil="true" /> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>1</VRPTx:beg_label_seq_id> <VRPTx:end_label_alt_id xsi:nil="true" /> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>29</VRPTx:end_label_seq_id> </VRPTx:struct_ncs_dom_lim> <VRPTx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="2" pdbx_ens_id="1"> <VRPTx:beg_label_alt_id xsi:nil="true" /> <VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>31</VRPTx:beg_label_seq_id> <VRPTx:end_label_alt_id xsi:nil="true" /> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>59</VRPTx:end_label_seq_id> </VRPTx:struct_ncs_dom_lim> <VRPTx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="3" pdbx_ens_id="1"> <VRPTx:beg_label_alt_id xsi:nil="true" /> <VRPTx:beg_label_asym_id>C</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>61</VRPTx:beg_label_seq_id> <VRPTx:end_label_alt_id xsi:nil="true" /> <VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>89</VRPTx:end_label_seq_id> </VRPTx:struct_ncs_dom_lim> <VRPTx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="1" pdbx_ens_id="1"> <VRPTx:beg_label_alt_id xsi:nil="true" /> <VRPTx:beg_label_asym_id>D</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>91</VRPTx:beg_label_seq_id> <VRPTx:end_label_alt_id xsi:nil="true" /> <VRPTx:end_label_asym_id>D</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>119</VRPTx:end_label_seq_id> </VRPTx:struct_ncs_dom_lim> <VRPTx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="2" pdbx_ens_id="1"> <VRPTx:beg_label_alt_id xsi:nil="true" /> <VRPTx:beg_label_asym_id>E</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>121</VRPTx:beg_label_seq_id> <VRPTx:end_label_alt_id xsi:nil="true" /> <VRPTx:end_label_asym_id>E</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>149</VRPTx:end_label_seq_id> </VRPTx:struct_ncs_dom_lim> <VRPTx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="3" pdbx_ens_id="1"> <VRPTx:beg_label_alt_id xsi:nil="true" /> <VRPTx:beg_label_asym_id>F</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>151</VRPTx:beg_label_seq_id> <VRPTx:end_label_alt_id xsi:nil="true" /> <VRPTx:end_label_asym_id>F</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>179</VRPTx:end_label_seq_id> </VRPTx:struct_ncs_dom_lim> </VRPTx:struct_ncs_dom_limCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 struct_ncs_dom_limCategory This property indicates that datablock has a category holder struct_ncs_dom_limCategory. struct_ncs_dom_limCategory This property indicates that struct_ncs_dom_limCategory. has a category struct_ncs_dom_lim. struct_ncs_dom_limItem Abstract datatype property for struct_ncs_dom_lim items. reference_to_struct_ncs_dom_lim cross-reference to struct_ncs_dom_lim. referenced_by_struct_ncs_dom_lim cross-reference from struct_ncs_dom_lim. struct_ncs_dom_lim.beg_auth_asym_id A component of the identifier for the monomer at which this segment of the domain begins. struct_ncs_dom_lim.beg_auth_comp_id A component of the identifier for the monomer at which this segment of the domain begins. struct_ncs_dom_lim.beg_auth_seq_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_ncs_dom_lim.beg_label_alt_id A component of the identifier for the monomer at which this segment of the domain begins. struct_ncs_dom_lim.beg_label_asym_id A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. struct_ncs_dom_lim.beg_label_comp_id A component of the identifier for the monomer at which this segment of the domain begins. struct_ncs_dom_lim.beg_label_seq_id A component of the identifier for the monomer at which this segment of the domain begins. struct_ncs_dom_lim.end_auth_asym_id A component of the identifier for the monomer at which this segment of the domain ends. struct_ncs_dom_lim.end_auth_comp_id A component of the identifier for the monomer at which this segment of the domain ends. struct_ncs_dom_lim.end_auth_seq_id A component of the identifier for the monomer at which this segment of the domain ends. struct_ncs_dom_lim.end_label_alt_id A component of the identifier for the monomer at which this segment of the domain ends. struct_ncs_dom_lim.end_label_asym_id A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. struct_ncs_dom_lim.end_label_comp_id A component of the identifier for the monomer at which this segment of the domain ends. struct_ncs_dom_lim.end_label_seq_id A component of the identifier for the monomer at which this segment of the domain ends. struct_ncs_dom_lim.pdbx_refine_code Record the refinement code number (from CCP4.) struct_ncs_dom_lim.selection_details A text description of the selection of residues that correspond to this domain. struct_ncs_dom_lim.dom_id This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. struct_ncs_dom_lim.pdbx_component_id Record number of the NCS domain limit assignment. struct_ncs_dom_lim.pdbx_ens_id This is a unique identifier for a collection NCS related domains. This references item '_struct_ncs_dom.pdbx_ens_id'. 0 struct_ncs_ens Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <VRPTx:struct_ncs_ensCategory> <VRPTx:struct_ncs_ens id="en1"> <VRPTx:details> The ensemble represents the pseudo-twofold symmetry between domains d1 and d2.</VRPTx:details> </VRPTx:struct_ncs_ens> </VRPTx:struct_ncs_ensCategory> 0 1 0 1 1 struct_ncs_ensCategory This property indicates that datablock has a category holder struct_ncs_ensCategory. struct_ncs_ensCategory This property indicates that struct_ncs_ensCategory. has a category struct_ncs_ens. struct_ncs_ensItem Abstract datatype property for struct_ncs_ens items. reference_to_struct_ncs_ens cross-reference to struct_ncs_ens. referenced_by_struct_ncs_ens cross-reference from struct_ncs_ens. struct_ncs_ens.details A description of special aspects of the ensemble. The ensemble has a slight translation between domains 1 and 4, but overall it can accurately be described as point group 222 struct_ncs_ens.point_group The point group of the ensemble of structural elements related by one or more noncrystallographic symmetry operations. The relationships need not be precise; this data item is intended to give a rough description of the noncrystallographic symmetry relationships. 3 422 non-proper struct_ncs_ens.id The value of attribute id in category struct_ncs_ens must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier. 0 struct_ncs_ens_gen Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <VRPTx:struct_ncs_ens_genCategory> <VRPTx:struct_ncs_ens_gen dom_id_1="d1" dom_id_2="d2" ens_id="en1" oper_id="1"></VRPTx:struct_ncs_ens_gen> </VRPTx:struct_ncs_ens_genCategory> 1 1 1 1 struct_ncs_ens_genCategory This property indicates that datablock has a category holder struct_ncs_ens_genCategory. struct_ncs_ens_genCategory This property indicates that struct_ncs_ens_genCategory. has a category struct_ncs_ens_gen. struct_ncs_ens_genItem Abstract datatype property for struct_ncs_ens_gen items. reference_to_struct_ncs_ens_gen cross-reference to struct_ncs_ens_gen. referenced_by_struct_ncs_ens_gen cross-reference from struct_ncs_ens_gen. struct_ncs_ens_gen.dom_id_1 The identifier for the domain that will remain unchanged by the transformation operator. This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. struct_ncs_ens_gen.dom_id_2 The identifier for the domain that will be transformed by application of the transformation operator. This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. struct_ncs_ens_gen.ens_id This data item is a pointer to attribute id in category struct_ncs_ens in the STRUCT_NCS_ENS category. struct_ncs_ens_gen.oper_id This data item is a pointer to attribute id in category struct_ncs_oper in the STRUCT_NCS_OPER category. 0 struct_ncs_oper Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations. Example 1 - based on laboratory records for the protein NS1. <VRPTx:struct_ncs_operCategory> <VRPTx:struct_ncs_oper id="1"> <VRPTx:code>given</VRPTx:code> <VRPTx:details> Matrix and translation vector for pseudo-twofold operation.</VRPTx:details> <VRPTx:matrix11>0.247</VRPTx:matrix11> <VRPTx:matrix12>0.935</VRPTx:matrix12> <VRPTx:matrix13>0.256</VRPTx:matrix13> <VRPTx:matrix21>0.929</VRPTx:matrix21> <VRPTx:matrix22>0.153</VRPTx:matrix22> <VRPTx:matrix23>0.337</VRPTx:matrix23> <VRPTx:matrix31>0.276</VRPTx:matrix31> <VRPTx:matrix32>0.321</VRPTx:matrix32> <VRPTx:matrix33>-0.906</VRPTx:matrix33> <VRPTx:vector1>-8.253</VRPTx:vector1> <VRPTx:vector2>-11.743</VRPTx:vector2> <VRPTx:vector3>-1.782</VRPTx:vector3> </VRPTx:struct_ncs_oper> </VRPTx:struct_ncs_operCategory> 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 struct_ncs_operCategory This property indicates that datablock has a category holder struct_ncs_operCategory. struct_ncs_operCategory This property indicates that struct_ncs_operCategory. has a category struct_ncs_oper. struct_ncs_operItem Abstract datatype property for struct_ncs_oper items. reference_to_struct_ncs_oper cross-reference to struct_ncs_oper. referenced_by_struct_ncs_oper cross-reference from struct_ncs_oper. given generate A code to indicate whether this operator describes a relationship between coordinates all of which are given in the data block (in which case the value of code is 'given'), or whether the operator is used to generate new coordinates from those that are given in the data block (in which case the value of code is 'generate'). struct_ncs_oper.details A description of special aspects of the noncrystallographic symmetry operator. The operation is given as a precise threefold rotation, despite the fact the best rms fit between domain 1 and domain 2 yields a rotation of 119.7 degrees and a translation of 0.13 angstroms. struct_ncs_oper.matrix11 The [1][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix12 The [1][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix13 The [1][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix21 The [2][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix22 The [2][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix23 The [2][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix31 The [3][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix32 The [3][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.matrix33 The [3][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. struct_ncs_oper.vector1 The [1] element of the three-element vector component of a noncrystallographic symmetry operation. struct_ncs_oper.vector2 The [2] element of the three-element vector component of a noncrystallographic symmetry operation. struct_ncs_oper.vector3 The [3] element of the three-element vector component of a noncrystallographic symmetry operation. struct_ncs_oper.id The value of attribute id in category struct_ncs_oper must uniquely identify a record in the STRUCT_NCS_OPER list. Note that for PDB attribute id in category struct_ncs_oper must be a number. 0 struct_ref Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item attribute seq_align in category struct_ref is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of attribute seq_dif in category struct_ref is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_refCategory> <VRPTx:struct_ref id="1"> <VRPTx:biol_id xsi:nil="true" /> <VRPTx:db_code>12345</VRPTx:db_code> <VRPTx:db_name>Genbank</VRPTx:db_name> <VRPTx:details xsi:nil="true" /> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:seq_align>entire</VRPTx:seq_align> <VRPTx:seq_dif>yes</VRPTx:seq_dif> </VRPTx:struct_ref> <VRPTx:struct_ref id="2"> <VRPTx:biol_id>2</VRPTx:biol_id> <VRPTx:db_code>1ABC</VRPTx:db_code> <VRPTx:db_name>PDB</VRPTx:db_name> <VRPTx:details> The structure of the closely related compound, isobutyryl-pepstatin (pepstatin A) in complex with rhizopuspepsin</VRPTx:details> <VRPTx:entity_id xsi:nil="true" /> <VRPTx:seq_align xsi:nil="true" /> <VRPTx:seq_dif xsi:nil="true" /> </VRPTx:struct_ref> </VRPTx:struct_refCategory> 0 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_refCategory This property indicates that datablock has a category holder struct_refCategory. struct_refCategory This property indicates that struct_refCategory. has a category struct_ref. struct_refItem Abstract datatype property for struct_ref items. reference_to_struct_ref cross-reference to struct_ref. referenced_by_struct_ref cross-reference from struct_ref. struct_ref.biol_id This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. struct_ref.db_code The code for this entity or biological unit or for a closely related entity or biological unit in the named database. 1ABC ABCDEF struct_ref.db_name The name of the database containing reference information about this entity or biological unit. PDB CSD Genbank struct_ref.details A description of special aspects of the relationship between the entity or biological unit described in the data block and that in the referenced database entry. struct_ref.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. struct_ref.pdbx_align_begin Beginning index in the chemical sequence from the reference database. 1 2 struct_ref.pdbx_align_end Ending index in the chemical sequence from the reference database. 105 245 struct_ref.pdbx_db_accession Accession code assigned by the reference database. P07617 struct_ref.pdbx_db_isoform Database code assigned by the reference database for a sequence isoform. An isoform sequence is an alternative protein sequence that can be generated from the same gene by a single or by a combination of biological events such as: alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting. P29994-6 struct_ref.pdbx_seq_one_letter_code Database chemical sequence expressed as string of one-letter amino acid codes. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other complete partial A flag to indicate the scope of the alignment between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. 'entire' indicates that alignment spans the entire length of both sequences (although point differences may occur and can be annotated using the data items in the STRUCT_REF_SEQ_DIF category). 'partial' indicates a partial alignment. The region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. This data item may also take the value '.', indicating that the reference is not to a sequence. no n yes y A flag to indicate the presence ('yes') or absence ('no') of point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item may also take the value '.', indicating that the reference is not to a sequence. struct_ref.id The value of attribute id in category struct_ref must uniquely identify a record in the STRUCT_REF list. Note that this item need not be a number; it can be any unique identifier. 0 struct_ref_seq Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry. Example 1 - based on the sequence alignment of CHER from M. xantus (36 to 288) and CHER from S. typhimurium (18 to 276). <VRPTx:struct_ref_seqCategory> <VRPTx:struct_ref_seq align_id="alg1"> <VRPTx:db_align_beg>18</VRPTx:db_align_beg> <VRPTx:db_align_end>276</VRPTx:db_align_end> <VRPTx:details> The alignment contains 3 gaps larger than 2 residues</VRPTx:details> <VRPTx:ref_id>seqdb1</VRPTx:ref_id> <VRPTx:seq_align_beg>36</VRPTx:seq_align_beg> <VRPTx:seq_align_end>288</VRPTx:seq_align_end> </VRPTx:struct_ref_seq> </VRPTx:struct_ref_seqCategory> 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 struct_ref_seqCategory This property indicates that datablock has a category holder struct_ref_seqCategory. struct_ref_seqCategory This property indicates that struct_ref_seqCategory. has a category struct_ref_seq. struct_ref_seqItem Abstract datatype property for struct_ref_seq items. reference_to_struct_ref_seq cross-reference to struct_ref_seq. referenced_by_struct_ref_seq cross-reference from struct_ref_seq. struct_ref_seq.db_align_beg The sequence position in the referenced database entry at which the alignment begins. struct_ref_seq.db_align_end The sequence position in the referenced database entry at which the alignment ends. struct_ref_seq.details A description of special aspects of the sequence alignment. struct_ref_seq.pdbx_PDB_id_code The PDB code of the structure. 1BBP struct_ref_seq.pdbx_auth_seq_align_beg Initial position in the PDB sequence segment. 1 2 struct_ref_seq.pdbx_auth_seq_align_end Ending position in the PDB sequence segment 1 2 struct_ref_seq.pdbx_db_accession Accession code of the reference database. P07617 struct_ref_seq.pdbx_db_align_beg_ins_code Initial insertion code of the sequence segment of the reference database. 1 2 struct_ref_seq.pdbx_db_align_end_ins_code Ending insertion code of the sequence segment of the reference database. 1 2 struct_ref_seq.pdbx_seq_align_beg_ins_code Initial insertion code of the PDB sequence segment. 1 2 struct_ref_seq.pdbx_seq_align_end_ins_code Ending insertion code of the sequence segment 1 2 struct_ref_seq.pdbx_strand_id The PDB strand/chain ID . A B struct_ref_seq.ref_id This data item is a pointer to attribute id in category struct_ref in the STRUCT_REF category. struct_ref_seq.seq_align_beg The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. struct_ref_seq.seq_align_end The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. struct_ref_seq.align_id The value of attribute align_id in category struct_ref_seq must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier. 0 struct_ref_seq_dif Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry. Example 1 - based on laboratory records for CAP-DNA complex. <VRPTx:struct_ref_seq_difCategory> <VRPTx:struct_ref_seq_dif pdbx_ordinal="1"> <VRPTx:align_id>algn2</VRPTx:align_id> <VRPTx:db_mon_id>GLU</VRPTx:db_mon_id> <VRPTx:details> A point mutation was introduced in the CAP at position 181 substituting PHE for GLU.</VRPTx:details> <VRPTx:mon_id>PHE</VRPTx:mon_id> <VRPTx:seq_num>181</VRPTx:seq_num> </VRPTx:struct_ref_seq_dif> </VRPTx:struct_ref_seq_difCategory> 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_ref_seq_difCategory This property indicates that datablock has a category holder struct_ref_seq_difCategory. struct_ref_seq_difCategory This property indicates that struct_ref_seq_difCategory. has a category struct_ref_seq_dif. struct_ref_seq_difItem Abstract datatype property for struct_ref_seq_dif items. reference_to_struct_ref_seq_dif cross-reference to struct_ref_seq_dif. referenced_by_struct_ref_seq_dif cross-reference from struct_ref_seq_dif. struct_ref_seq_dif.align_id This data item is a pointer to attribute align_id in category struct_ref_seq in the STRUCT_REF_SEQ category. struct_ref_seq_dif.db_mon_id The monomer type found at this position in the referenced database entry. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. struct_ref_seq_dif.details A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. struct_ref_seq_dif.mon_id The monomer type found at this position in the sequence of the entity or biological unit described in this data block. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. struct_ref_seq_dif.pdbx_auth_seq_num Insertion code in PDB sequence 1 2 struct_ref_seq_dif.pdbx_pdb_id_code The PDB ID code. 1BBP struct_ref_seq_dif.pdbx_pdb_ins_code Insertion code in PDB sequence 1 2 struct_ref_seq_dif.pdbx_pdb_strand_id PDB strand/chain id. A B struct_ref_seq_dif.pdbx_seq_db_accession_code Sequence database accession number. P07617 struct_ref_seq_dif.pdbx_seq_db_name Sequence database name. SWS struct_ref_seq_dif.pdbx_seq_db_seq_num Sequence database sequence number. 142 struct_ref_seq_dif.seq_num This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. struct_ref_seq_dif.pdbx_ordinal A synthetic integer primary key for this category. 0 struct_sheet Data items in the STRUCT_SHEET category record details about the beta-sheets. Example 1 - simple beta-barrel. N O N O N O N O N O N O 10--11--12--13--14--15--16--17--18--19--20 strand_a N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 30--31--32--33--34--35--36--37--38--39--40 strand_b N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 50--51--52--53--54--55--56--57--58--59--60 strand_c N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 70--71--72--73--74--75--76--77--78--79--80 strand_d N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 90--91--92--93--94--95--96--97--98--99-100 strand_e N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 110-111-112-113-114-115-116-117-118-119-120 strand_f N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 130-131-132-133-134-135-136-137-138-139-140 strand_g N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 150-151-152-153-154-155-156-157-158-159-160 strand_h N O N O N O N O N O / \ / \ / \ / \ / \ <VRPTx:struct_sheetCategory> <VRPTx:struct_sheet id="sheet_1"> <VRPTx:details xsi:nil="true" /> <VRPTx:number_strands>8</VRPTx:number_strands> <VRPTx:type>beta-barrel</VRPTx:type> </VRPTx:struct_sheet> </VRPTx:struct_sheetCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. N O N O N O N O -10--11--12--13--14--15--16--17--18-> strand_a N O N O N O N O N O | | | | | | | | | | O N O N O N O N O N <-119-118-117-116-115-114-113-112-111-110- strand_b O N O N O N O N O N \ / \ / \ / \ / \ O N O N O N O N O N O N <-41--40--39--38--37--36--35--34--33--32--31--30- strand_c O N O N O N O N O N O N | | | | | | | | | | | | N O N O N O N O N O N O strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2 N O N O N O N O N O | | | | | | | | | | | | O N O N O N O N O N O N <-80--79--78--77--76--75--74--73--72--71--70- strand_e O N O N O N O N O N <VRPTx:struct_sheetCategory> <VRPTx:struct_sheet id="sheet_2"> <VRPTx:details>strand_d is in two pieces</VRPTx:details> <VRPTx:number_strands>5</VRPTx:number_strands> <VRPTx:type>five stranded, mixed-sense</VRPTx:type> </VRPTx:struct_sheet> </VRPTx:struct_sheetCategory> 0 1 0 1 0 1 1 struct_sheetCategory This property indicates that datablock has a category holder struct_sheetCategory. struct_sheetCategory This property indicates that struct_sheetCategory. has a category struct_sheet. struct_sheetItem Abstract datatype property for struct_sheet items. reference_to_struct_sheet cross-reference to struct_sheet. referenced_by_struct_sheet cross-reference from struct_sheet. struct_sheet.details A description of special aspects of the beta-sheet. struct_sheet.number_strands The number of strands in the sheet. If a given range of residues bulges out from the strands, it is still counted as one strand. If a strand is composed of two different regions of polypeptide, it is still counted as one strand, as long as the proper hydrogen- bonding connections are made to adjacent strands. struct_sheet.type A simple descriptor for the type of the sheet. jelly-roll Rossmann fold beta barrel struct_sheet.id The value of attribute id in category struct_sheet must uniquely identify a record in the STRUCT_SHEET list. Note that this item need not be a number; it can be any unique identifier. 0 struct_sheet_hbond Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet. Example 1 - simple beta-barrel. <VRPTx:struct_sheet_hbondCategory> <VRPTx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>11</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>19</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>30</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>40</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>31</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>39</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>50</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>60</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>51</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>59</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>70</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>80</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>71</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>89</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>90</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>100</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>91</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>99</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>110</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>120</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>111</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>119</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>130</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>140</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>131</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>139</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>150</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>160</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>151</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>159</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>10</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>180</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> </VRPTx:struct_sheet_hbondCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <VRPTx:struct_sheet_hbondCategory> <VRPTx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>20</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>18</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>119</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>111</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>110</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>N</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>118</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>33</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>O</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>41</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>38</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>40</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>52</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>50</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>30</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>36</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>96</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>90</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>51</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>51</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>80</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>80</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> <VRPTx:struct_sheet_hbond range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2"> <VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id> <VRPTx:range_1_beg_label_seq_id>91</VRPTx:range_1_beg_label_seq_id> <VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id> <VRPTx:range_1_end_label_seq_id>97</VRPTx:range_1_end_label_seq_id> <VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id> <VRPTx:range_2_beg_label_seq_id>76</VRPTx:range_2_beg_label_seq_id> <VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id> <VRPTx:range_2_end_label_seq_id>70</VRPTx:range_2_end_label_seq_id> </VRPTx:struct_sheet_hbond> </VRPTx:struct_sheet_hbondCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 struct_sheet_hbondCategory This property indicates that datablock has a category holder struct_sheet_hbondCategory. struct_sheet_hbondCategory This property indicates that struct_sheet_hbondCategory. has a category struct_sheet_hbond. struct_sheet_hbondItem Abstract datatype property for struct_sheet_hbond items. reference_to_struct_sheet_hbond cross-reference to struct_sheet_hbond. referenced_by_struct_sheet_hbond cross-reference from struct_sheet_hbond. struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site. struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id Pointer to attribute auth_asym_id in category atom_site. struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id Pointer to attribute auth_comp_id in category atom_site struct_sheet_hbond.pdbx_range_1_beg_label_asym_id Pointer to attribute label_asym_id in category atom_site. struct_sheet_hbond.pdbx_range_1_beg_label_comp_id Pointer to attribute label_comp_id in category atom_site struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site. struct_sheet_hbond.pdbx_range_1_end_auth_asym_id Pointer to attribute auth_comp_id in category atom_site. struct_sheet_hbond.pdbx_range_1_end_auth_comp_id Pointer to attribute auth_comp_id in category atom_site. struct_sheet_hbond.pdbx_range_1_end_label_asym_id Pointer to attribute label_asym_id in category atom_site. struct_sheet_hbond.pdbx_range_1_end_label_comp_id Pointer to attribute label_comp_id in category atom_site. struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site. struct_sheet_hbond.pdbx_range_2_beg_label_asym_id Pointer to attribute label_asym_id in category atom_site. struct_sheet_hbond.pdbx_range_2_beg_label_comp_id Pointer to attribute label_comp_id in category atom_site. struct_sheet_hbond.pdbx_range_2_end_label_asym_id Pointer to attribute label_asym_id in category atom_site. struct_sheet_hbond.pdbx_range_2_end_label_comp_id Pointer to attribute label_comp_id in category atom_site. struct_sheet_hbond.pdbx_range_2_end_label_ins_code Place holder for PDB insertion code. struct_sheet_hbond.range_1_beg_auth_atom_id A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_beg_auth_seq_id A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_beg_label_atom_id A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_beg_label_seq_id A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_end_auth_atom_id A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_end_auth_seq_id A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_end_label_atom_id A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_1_end_label_seq_id A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_beg_auth_atom_id A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_beg_auth_seq_id A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_beg_label_atom_id A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_beg_label_seq_id A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_end_auth_atom_id A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_end_auth_seq_id A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_end_label_atom_id A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_2_end_label_seq_id A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_hbond.range_id_1 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. struct_sheet_hbond.range_id_2 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. struct_sheet_hbond.sheet_id This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. 0 struct_sheet_order Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described. Example 1 - simple beta-barrel. <VRPTx:struct_sheet_orderCategory> <VRPTx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> </VRPTx:struct_sheet_orderCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <VRPTx:struct_sheet_orderCategory> <VRPTx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_order> <VRPTx:struct_sheet_order range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_order> </VRPTx:struct_sheet_orderCategory> 0 1 0 1 1 1 1 struct_sheet_orderCategory This property indicates that datablock has a category holder struct_sheet_orderCategory. struct_sheet_orderCategory This property indicates that struct_sheet_orderCategory. has a category struct_sheet_order. struct_sheet_orderItem Abstract datatype property for struct_sheet_order items. reference_to_struct_sheet_order cross-reference to struct_sheet_order. referenced_by_struct_sheet_order cross-reference from struct_sheet_order. struct_sheet_order.offset Designates the relative position in the sheet, plus or minus, of the second residue range to the first. parallel anti-parallel A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. struct_sheet_order.range_id_1 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. struct_sheet_order.range_id_2 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. struct_sheet_order.sheet_id This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. 0 struct_sheet_range Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range. Example 1 - simple beta-barrel. <VRPTx:struct_sheet_rangeCategory> <VRPTx:struct_sheet_range id="strand_a" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>20</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>30</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_b" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>40</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>50</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_c" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>60</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>70</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_d" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>80</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>90</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_e" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>100</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>110</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_f" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>120</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>130</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_g" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>140</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>150</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_h" sheet_id="sheet_1"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>160</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>170</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> </VRPTx:struct_sheet_rangeCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <VRPTx:struct_sheet_rangeCategory> <VRPTx:struct_sheet_range id="strand_a" sheet_id="sheet_2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>10</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>18</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_b" sheet_id="sheet_2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>110</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>119</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_c" sheet_id="sheet_2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>30</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>41</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_d1" sheet_id="sheet_2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>50</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>52</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_d2" sheet_id="sheet_2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>90</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>97</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> <VRPTx:struct_sheet_range id="strand_e" sheet_id="sheet_2"> <VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id> <VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id> <VRPTx:beg_label_seq_id>70</VRPTx:beg_label_seq_id> <VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id> <VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id> <VRPTx:end_label_seq_id>80</VRPTx:end_label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_sheet_range> </VRPTx:struct_sheet_rangeCategory> 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 struct_sheet_rangeCategory This property indicates that datablock has a category holder struct_sheet_rangeCategory. struct_sheet_rangeCategory This property indicates that struct_sheet_rangeCategory. has a category struct_sheet_range. struct_sheet_rangeItem Abstract datatype property for struct_sheet_range items. reference_to_struct_sheet_range cross-reference to struct_sheet_range. referenced_by_struct_sheet_range cross-reference from struct_sheet_range. struct_sheet_range.beg_auth_asym_id A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_sheet_range.beg_auth_comp_id A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_sheet_range.beg_auth_seq_id A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_range.beg_label_asym_id A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. struct_sheet_range.beg_label_comp_id A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. struct_sheet_range.beg_label_seq_id A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_range.end_auth_asym_id A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_sheet_range.end_auth_comp_id A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_sheet_range.end_auth_seq_id A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_range.end_label_asym_id A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. struct_sheet_range.end_label_comp_id A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. struct_sheet_range.end_label_seq_id A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_sheet_range.pdbx_beg_PDB_ins_code A component of the identifier for the residue at which the beta sheet range begins. Insertion code. struct_sheet_range.pdbx_end_PDB_ins_code A component of the identifier for the residue at which the beta sheet range ends. Insertion code. struct_sheet_range.symmetry Describes the symmetry operation that should be applied to the residues delimited by the start and end designators in order to generate the appropriate strand in this sheet. struct_sheet_range.id The value of attribute id in category struct_sheet_range must uniquely identify a range in a given sheet in the STRUCT_SHEET_RANGE list. Note that this item need not be a number; it can be any unique identifier. struct_sheet_range.sheet_id This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. 0 struct_sheet_topology Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets. Example 1 - simple beta-barrel. <VRPTx:struct_sheet_topologyCategory> <VRPTx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> </VRPTx:struct_sheet_topologyCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <VRPTx:struct_sheet_topologyCategory> <VRPTx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_c" sheet_id="sheet_2"> <VRPTx:offset>+2</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2"> <VRPTx:offset>+1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_d2" sheet_id="sheet_2"> <VRPTx:offset>-1</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> <VRPTx:struct_sheet_topology range_id_1="strand_d2" range_id_2="strand_b" sheet_id="sheet_2"> <VRPTx:offset>-2</VRPTx:offset> <VRPTx:sense>anti-parallel</VRPTx:sense> </VRPTx:struct_sheet_topology> </VRPTx:struct_sheet_topologyCategory> 0 1 0 1 1 1 1 struct_sheet_topologyCategory This property indicates that datablock has a category holder struct_sheet_topologyCategory. struct_sheet_topologyCategory This property indicates that struct_sheet_topologyCategory. has a category struct_sheet_topology. struct_sheet_topologyItem Abstract datatype property for struct_sheet_topology items. reference_to_struct_sheet_topology cross-reference to struct_sheet_topology. referenced_by_struct_sheet_topology cross-reference from struct_sheet_topology. struct_sheet_topology.offset Designates the relative position in the sheet, plus or minus, of the second residue range to the first. parallel anti-parallel A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. struct_sheet_topology.range_id_1 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. struct_sheet_topology.range_id_2 This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. struct_sheet_topology.sheet_id This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. 0 struct_site Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites). Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_siteCategory> <VRPTx:struct_site id="P2 site C"> <VRPTx:details> residues with a contact &lt; 3.7 \&#37;A to an atom in the P2 moiety of the inhibitor in the conformation with _struct_asym.id = C</VRPTx:details> </VRPTx:struct_site> <VRPTx:struct_site id="P2 site D"> <VRPTx:details> residues with a contact &lt; 3.7 \&#37;A to an atom in the P1 moiety of the inhibitor in the conformation with _struct_asym.id = D</VRPTx:details> </VRPTx:struct_site> </VRPTx:struct_siteCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 struct_siteCategory This property indicates that datablock has a category holder struct_siteCategory. struct_siteCategory This property indicates that struct_siteCategory. has a category struct_site. struct_siteItem Abstract datatype property for struct_site items. reference_to_struct_site cross-reference to struct_site. referenced_by_struct_site cross-reference from struct_site. struct_site.details A description of special aspects of the site. struct_site.pdbx_auth_asym_id A component of the identifier for the ligand in the site. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_site.pdbx_auth_comp_id A component of the identifier for the ligand in the site. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_site.pdbx_auth_ins_code PDB insertion code for the ligand in the site. struct_site.pdbx_auth_seq_id A component of the identifier for the ligand in the site. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_site.pdbx_evidence_code Source of evidence supporting the assignment of this site. SOFTWARE AUTHOR UNKNOWN struct_site.pdbx_num_residues Number of residues in the site. struct_site.id The value of attribute id in category struct_site must uniquely identify a record in the STRUCT_SITE list. Note that this item need not be a number; it can be any unique identifier. 0 struct_site_gen Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:struct_site_genCategory> <VRPTx:struct_site_gen id="1" site_id="1"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>VAL</VRPTx:label_comp_id> <VRPTx:label_seq_id>32</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="2" site_id="1"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>ILE</VRPTx:label_comp_id> <VRPTx:label_seq_id>47</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="3" site_id="1"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>VAL</VRPTx:label_comp_id> <VRPTx:label_seq_id>82</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="4" site_id="1"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>A</VRPTx:label_asym_id> <VRPTx:label_comp_id>ILE</VRPTx:label_comp_id> <VRPTx:label_seq_id>84</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="5" site_id="2"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>B</VRPTx:label_asym_id> <VRPTx:label_comp_id>VAL</VRPTx:label_comp_id> <VRPTx:label_seq_id>232</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="6" site_id="2"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>B</VRPTx:label_asym_id> <VRPTx:label_comp_id>ILE</VRPTx:label_comp_id> <VRPTx:label_seq_id>247</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="7" site_id="2"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>B</VRPTx:label_asym_id> <VRPTx:label_comp_id>VAL</VRPTx:label_comp_id> <VRPTx:label_seq_id>282</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> <VRPTx:struct_site_gen id="8" site_id="2"> <VRPTx:details xsi:nil="true" /> <VRPTx:label_asym_id>B</VRPTx:label_asym_id> <VRPTx:label_comp_id>ILE</VRPTx:label_comp_id> <VRPTx:label_seq_id>284</VRPTx:label_seq_id> <VRPTx:symmetry>1_555</VRPTx:symmetry> </VRPTx:struct_site_gen> </VRPTx:struct_site_genCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 struct_site_genCategory This property indicates that datablock has a category holder struct_site_genCategory. struct_site_genCategory This property indicates that struct_site_genCategory. has a category struct_site_gen. struct_site_genItem Abstract datatype property for struct_site_gen items. reference_to_struct_site_gen cross-reference to struct_site_gen. referenced_by_struct_site_gen cross-reference from struct_site_gen. struct_site_gen.auth_asym_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. struct_site_gen.auth_atom_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. struct_site_gen.auth_comp_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. struct_site_gen.auth_seq_id A component of the identifier for participants in the site. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. struct_site_gen.details A description of special aspects of the symmetry generation of this portion of the structural site. The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. struct_site_gen.label_alt_id A component of the identifier for participants in the site. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. struct_site_gen.label_asym_id A component of the identifier for participants in the site. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. struct_site_gen.label_atom_id A component of the identifier for participants in the site. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. struct_site_gen.label_comp_id A component of the identifier for participants in the site. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. struct_site_gen.label_seq_id A component of the identifier for participants in the site. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. struct_site_gen.pdbx_auth_ins_code PDB insertion code. struct_site_gen.pdbx_num_res Number of residues in the site. struct_site_gen.symmetry Describes the symmetry operation that should be applied to the atom set specified by attribute label* in category struct_site_gen to generate a portion of the site. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 struct_site_gen.id The value of attribute id in category struct_site_gen must uniquely identify a record in the STRUCT_SITE_GEN list. Note that this item need not be a number; it can be any unique identifier. struct_site_gen.site_id This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE category. 0 struct_site_view Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site. Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry (1989), 28, 310-320]. <VRPTx:struct_site_viewCategory> <VRPTx:struct_site_view id="1"> <VRPTx:details> This view highlights the site of ATAT-Netropsin interaction.</VRPTx:details> <VRPTx:rot_matrix11>0.132</VRPTx:rot_matrix11> <VRPTx:rot_matrix12>0.922</VRPTx:rot_matrix12> <VRPTx:rot_matrix13>-0.363</VRPTx:rot_matrix13> <VRPTx:rot_matrix21>0.131</VRPTx:rot_matrix21> <VRPTx:rot_matrix22>-0.380</VRPTx:rot_matrix22> <VRPTx:rot_matrix23>-0.916</VRPTx:rot_matrix23> <VRPTx:rot_matrix31>-0.982</VRPTx:rot_matrix31> <VRPTx:rot_matrix32>0.073</VRPTx:rot_matrix32> <VRPTx:rot_matrix33>-0.172</VRPTx:rot_matrix33> </VRPTx:struct_site_view> </VRPTx:struct_site_viewCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 struct_site_viewCategory This property indicates that datablock has a category holder struct_site_viewCategory. struct_site_viewCategory This property indicates that struct_site_viewCategory. has a category struct_site_view. struct_site_viewItem Abstract datatype property for struct_site_view items. reference_to_struct_site_view cross-reference to struct_site_view. referenced_by_struct_site_view cross-reference from struct_site_view. struct_site_view.details A description of special aspects of this view of the site. This data item can be used as a figure legend. The active site has been oriented with the specificity pocket on the right and the active site machinery on the left. struct_site_view.rot_matrix11 The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix12 The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix13 The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix21 The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix22 The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix23 The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix31 The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix32 The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.rot_matrix33 The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| struct_site_view.site_id This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE category. struct_site_view.id The value of attribute id in category struct_site_view must uniquely identify a record in the STRUCT_SITE_VIEW list. Note that this item need not be a number; it can be any unique identifier. Figure 1 unliganded enzyme view down enzyme active site 0 symmetry Data items in the SYMMETRY category record details about the space-group symmetry. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:symmetryCategory> <VRPTx:symmetry entry_id="5HVP"> <VRPTx:Int_Tables_number>18</VRPTx:Int_Tables_number> <VRPTx:cell_setting>orthorhombic</VRPTx:cell_setting> <VRPTx:space_group_name_H-M>P 21 21 2</VRPTx:space_group_name_H-M> </VRPTx:symmetry> </VRPTx:symmetryCategory> 0 1 0 1 0 1 0 1 0 1 1 symmetryCategory This property indicates that datablock has a category holder symmetryCategory. symmetryCategory This property indicates that symmetryCategory. has a category symmetry. symmetryItem Abstract datatype property for symmetry items. reference_to_symmetry cross-reference to symmetry. referenced_by_symmetry cross-reference from symmetry. symmetry.Int_Tables_number Space-group number from International Tables for Crystallography Vol. A (2002). triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic The cell settings for this space-group symmetry. symmetry.pdbx_full_space_group_name_H-M Used for PDB space group: Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) symmetry.space_group_name_H-M Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the attribute pos_as_xyz in category symmetry_equiv or attribute space_group_name_Hall in category symmetry data items as well. Leave spaces between symbols referring to different axes. A 1 A 1 2 1 A 2 B 1 1 2 B 2 B 2 21 2 C 2 C 1 2 1 C 21 C 1 21 1 C 2(A 112) C 2 2 2 C 2 2 21 C 4 21 2 F 2 2 2 F 2 3 F 4 2 2 F 4 3 2 F 41 3 2 I 1 2 1 I 1 21 1 I 2 I 2 2 2 I 2 3 I 21 I 21 3 I 21 21 21 I 4 I 4 2 2 I 4 3 2 I 41 I 41/a I 41 2 2 I 41 3 2 P 1 P 1- P 2 P 1 2 1 P 1 1 2 P 2 2 2 P 2 3 P 2 2 21 P 2 21 21 P 21 P 1 21 1 P 1 21/c 1 P 1 1 21 P 21(C) P 21 2 21 P 21 3 P 21 21 2 P 21 21 2 A P 21 21 21 P 3 P 3 1 2 P 3 2 1 P 31 P 31 1 2 P 31 2 1 P 32 P 32 1 2 P 32 2 1 P 4 P 4 2 2 P 4 3 2 P 4 21 2 P 41 P 41 2 2 P 41 3 2 P 41 21 2 P 42 P 42 2 2 P 42 3 2 P 42 21 2 P 43 P 43 2 2 P 43 3 2 P 43 21 2 P 6 P 6 2 2 P 61 P 61 2 2 P 62 P 62 2 2 P 63 P 63 2 2 P 64 P 64 2 2 P 65 P 65 2 2 H 3 R 3 H 3 2 R 3 2 symmetry.space_group_name_Hall Space-group symbol as described by Hall (1981). This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981) A37, 921. -P 2ac 2n -R 3 2" P 61 2 2 (0 0 -1) symmetry.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 symmetry_equiv Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <VRPTx:symmetry_equivCategory> <VRPTx:symmetry_equiv id="1"> <VRPTx:pos_as_xyz>+x,+y,+z</VRPTx:pos_as_xyz> </VRPTx:symmetry_equiv> <VRPTx:symmetry_equiv id="2"> <VRPTx:pos_as_xyz>-x,-y,z</VRPTx:pos_as_xyz> </VRPTx:symmetry_equiv> <VRPTx:symmetry_equiv id="3"> <VRPTx:pos_as_xyz>1/2+x,1/2-y,-z</VRPTx:pos_as_xyz> </VRPTx:symmetry_equiv> <VRPTx:symmetry_equiv id="4"> <VRPTx:pos_as_xyz>1/2-x,1/2+y,-z</VRPTx:pos_as_xyz> </VRPTx:symmetry_equiv> </VRPTx:symmetry_equivCategory> 0 1 1 symmetry_equivCategory This property indicates that datablock has a category holder symmetry_equivCategory. symmetry_equivCategory This property indicates that symmetry_equivCategory. has a category symmetry_equiv. symmetry_equivItem Abstract datatype property for symmetry_equiv items. reference_to_symmetry_equiv cross-reference to symmetry_equiv. referenced_by_symmetry_equiv cross-reference from symmetry_equiv. symmetry_equiv.pos_as_xyz Symmetry-equivalent position in the 'xyz' representation. Except for the space group P1, these data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography Vol. A (2002). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. -y+x,-y,1/3+z symmetry_equiv.id The value of attribute id in category symmetry_equiv must uniquely identify a record in the SYMMETRY_EQUIV category. Note that this item need not be a number; it can be any unique identifier.