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 VRPT PDBML Schema translated from wwPDB Validation Information Dictionary v4.389, 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. diffrn.pdbx_serial_crystal_experiment 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 entity_assembly_id="1" id="1"> <VRPTx:units>MEGADALTONS</VRPTx:units> <VRPTx:value>30.5</VRPTx:value> </VRPTx:em_entity_assembly_molwt> </VRPTx:em_entity_assembly_molwtCategory> 0 1 0 1 0 1 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. 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.entity_assembly_id A reference to em_entity_assembly.id which uniquely identifies one sample or sample subcomponent of the imaged specimen. 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 entity_assembly_id="8333" id="1"> <VRPTx:cellular_location xsi:nil="true" /> <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 0 1 0 1 1 1 0 1 0 1 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.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.entity_assembly_id Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category. 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 entity_assembly_id="1" id="1"> <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 0 1 0 1 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.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.entity_assembly_id Pointer to the expressed component described in the EM ENTITY ASSEMBLY category. 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