PDBx ontology The OWL ontology for PDB/RDF, generated from the 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 PDBML. 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 related PDB entry. link to associated wwPDB validation report. 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 KEGG Compound. external link to KEGG Drug. external link to Novel Antibiotics Data Base. external link to ORCiD (Open Researcher and Contributor ID). 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 parental 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 ChemDB. datablock The datablock class holds all categories of PDB data. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 PDBML Schema translated from the PDBx/mmCIF Dictionary v5.399: 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 array_data Data items in the ARRAY_DATA category are the containers for the array data items described in the category ARRAY_STRUCTURE. It is recognized that the data in this category need to be used in two distinct ways. During a data collection the lack of ancillary data and timing constraints in processing data may dictate the need to make a 'miniCBF', nothing more than an essential minimum of information to record the results of the data collection. In that case it is proper to use the ARRAY_DATA category as a container for just a single image and a compacted, beamline-dependent list of data collection parameter values. In such a case, only the tags '_array_data.header_convention', '_array_data.header_contents' and '_array_data.data' need be populated. For full processing and archiving, most of the tags in this dictionary will need to be populated. Example 1. This example shows two binary data blocks. The first one was compressed by the CBF_CANONICAL compression algorithm and is presented as hexadecimal data. The first character 'H' on the data lines means hexadecimal. It could have been 'O' for octal or 'D' for decimal. The second character on the line shows the number of bytes in each word (in this case '4'), which then requires eight hexadecimal digits per word. The third character gives the order of octets within a word, in this case '<' for the ordering 4321 (i.e. 'big-endian'). Alternatively, the character '>' could have been used for the ordering 1234 (i.e. 'little-endian'). The block has a 'message digest' to check the integrity of the data. The second block is similar, but uses CBF_PACKED compression and BASE64 encoding. Note that the size and the digest are different. <PDBx:array_dataCategory> <PDBx:array_data array_id="image_1" binary_id="1"> <PDBx:data> --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions=&quot;X-CBF_CANONICAL&quot; Content-Transfer-Encoding: X-BASE16 X-Binary-Size: 3927126 X-Binary-ID: 1 Content-MD5: u2sTJEovAHkmkDjPi+gWsg== # Hexadecimal encoding, byte 0, byte order ...21 # H4&lt; 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ... .... --CIF-BINARY-FORMAT-SECTION----</PDBx:data> </PDBx:array_data> <PDBx:array_data array_id="image_2" binary_id="2"> <PDBx:data> --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions=&quot;X-CBF-PACKED&quot; Content-Transfer-Encoding: BASE64 X-Binary-Size: 3745758 X-Binary-ID: 2 Content-MD5: 1zsJjWPfol2GYl2V+QSXrw== ELhQAAAAAAAA... ... --CIF-BINARY-FORMAT-SECTION----</PDBx:data> </PDBx:array_data> </PDBx:array_dataCategory> 1 1 0 1 0 1 0 1 1 1 array_dataCategory This property indicates that datablock has a category holder array_dataCategory. array_dataCategory This property indicates that array_dataCategory. has a category array_data. array_dataItem Abstract datatype property for array_data items. reference_to_array_data cross-reference to array_data. referenced_by_array_data cross-reference from array_data. array_data.data The value of attribute data in category array_data contains the array data encapsulated in a STAR string. The value of this item is required unless a value is given for attribute external_data_id in category array_data instead, in which case, a null value of '.' should be given here. The representation used is a variant on the Multipurpose Internet Mail Extensions (MIME) specified in RFC 2045-2049 by N. Freed et al. The boundary delimiter used in writing an imgCIF or CBF is \n--CIF-BINARY-FORMAT-SECTION-- (including the required initial \n--, where \n represents the system newline character(s)). The Content-Type may be any of the discrete types permitted in RFC 2045; 'application/octet-stream' is recommended for diffraction images in the ARRAY_DATA category. Note: When appropriate in other categories, e.g. for photographs of crystals, more precise types, such as 'image/jpeg', 'image/tiff', 'image/png', etc. should be used. If an octet stream was compressed, the compression should be specified by the parameter conversions="X-CBF_PACKED" or the parameter conversions="X-CBF_CANONICAL" or the parameter conversions="X-CBF_BYTE_OFFSET" or the parameter conversions="X-CBF_BACKGROUND_OFFSET_DELTA" If the parameter conversions="X-CBF_PACKED" is given it may be further modified with the parameters uncorrelated_sections or flat (e.g. conversions="X-CBF_PACKED flat"). In such cases the attribute compression_type_flag in category array_structure should also be present with the corresponding value. If the "uncorrelated_sections" parameter is given, each section will be compressed without using the prior section for averaging. If the "flat" parameter is given, each image will be treated as one long row. Note that X-CBF_CANONICAL and X-CBF_PACKED are slower but more efficient compressions than the others. The X-CBF_BYTE_OFFSET compression is a good compromise between speed and efficiency for ordinary diffraction images. The X-CBF_BACKGROUND_OFFSET_DELTA compression is oriented towards sparse data, such as masks and tables of replacement pixel values for images with overloaded spots. The Content-Transfer-Encoding may be 'BASE64', 'Quoted-Printable', 'X-BASE8', 'X-BASE10', 'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY' for a CBF. The octal, decimal and hexadecimal transfer encodings are provided for convenience in debugging and are not recommended for archiving and data interchange. In a CIF, one of the parameters 'charset=us-ascii', 'charset=utf-8' or 'charset=utf-16' may be used on the Content-Transfer-Encoding to specify the character set used for the external presentation of the encoded data. If no charset parameter is given, the character set of the enclosing CIF is assumed. In any case, if a BOM flag is detected (FE FF for big-endian UTF-16, FF FE for little-endian UTF-16 or EF BB BF for UTF-8) is detected, the indicated charset will be assumed until the end of the encoded data or the detection of a different BOM. The charset of the Content-Transfer-Encoding is not the character set of the encoded data, only the character set of the presentation of the encoded data and should be respecified for each distinct STAR string. In an imgCIF file, the encoded binary data begin after the empty line terminating the header. In an imgCIF file, the encoded binary data ends with the terminating boundary delimiter '\n--CIF-BINARY-FORMAT-SECTION----' in the currently effective charset or with the '\n;' that terminates the STAR string. In a CBF, the raw binary data begin after an empty line terminating the header and after the sequence: Octet Hex Decimal Purpose 0 0C 12 Ctrl-L: page break 1 1A 26 Ctrl-Z: stop listings, MS-DOS 2 04 04 Ctrl-D: stop listings, UNIX 3 D5 213 binary section begins None of these octets are included in the calculation of the message size or in the calculation of the message digest. The X-Binary-Size header specifies the size of the equivalent binary data in octets. If compression was used, this size is the size after compression, including any book-keeping fields. An adjustment is made for the deprecated binary formats in which eight bytes of binary header are used for the compression type. In this case, the eight bytes used for the compression type are subtracted from the size, so that the same size will be reported if the compression type is supplied in the MIME header. Use of the MIME header is the recommended way to supply the compression type. In general, no portion of the binary header is included in the calculation of the size. The X-Binary-Element-Type header specifies the type of binary data in the octets, using the same descriptive phrases as in attribute encoding_type in category array_structure. The default value is 'unsigned 32-bit integer'. An MD5 message digest may, optionally, be used. The 'RSA Data Security, Inc. MD5 Message-Digest Algorithm' should be used. No portion of the header is included in the calculation of the message digest. If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or 'X-BASE16', the data are presented as octal, decimal or hexadecimal data organized into lines or words. Each word is created by composing octets of data in fixed groups of 2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big- endian') or 1234... ('little-endian'). If there are fewer than the specified number of octets to fill the last word, then the missing octets are presented as '==' for each missing octet. Exactly two equal signs are used for each missing octet even for octal and decimal encoding. The format of lines is: rnd xxxxxx xxxxxx xxxxxx where r is 'H', 'O' or 'D' for hexadecimal, octal or decimal, n is the number of octets per word and d is '<' or '>' for the '...4321' and '1234...' octet orderings, respectively. The '==' padding for the last word should be on the appropriate side to correspond to the missing octets, e.g. H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000 or H3> FF0700 00==== For these hexadecimal, octal and decimal formats only, comments beginning with '#' are permitted to improve readability. BASE64 encoding follows MIME conventions. Octets are in groups of three: c1, c2, c3. The resulting 24 bits are broken into four six-bit quantities, starting with the high-order six bits (c1 >> 2) of the first octet, then the low-order two bits of the first octet followed by the high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)], then the bottom four bits of the second octet followed by the high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)], then the bottom six bits of the last octet (c3 & 63). Each of these four quantities is translated into an ASCII character using the mapping: 1 2 3 4 5 6 0123456789012345678901234567890123456789012345678901234567890123 | | | | | | | ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/ with short groups of octets padded on the right with one '=' if c3 is missing, and with '==' if both c2 and c3 are missing. X-BASE32K encoding is similar to BASE64 encoding, except that sets of 15 octets are encoded as sets of 8 16-bit Unicode characters, by breaking the 120 bits into 8 15-bit quantities. 256 is added to each 15-bit quantity to bring it into a printable Unicode range. When encoding, zero padding is used to fill out the last 15-bit quantity. If 8 or more bits of padding are used, a single equals sign (hexadecimal 003D) is appended. Embedded whitespace and newlines are introduced to produce lines of no more than 80 characters each. On decoding, all printable ASCII characters and ASCII whitespace characters are ignored except for any trailing equals signs. The number of trailing equals signs indicated the number of trailing octets to be trimmed from the end of the decoded data (see Darakev et al., 2006). QUOTED-PRINTABLE encoding also follows MIME conventions, copying octets without translation if their ASCII values are 32...38, 42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';' in column 1. All other characters are translated to =nn, where nn is the hexadecimal encoding of the octet. All lines are 'wrapped' with a terminating '=' (i.e. the MIME conventions for an implicit line terminator are never used). The 'X-Binary-Element-Byte-Order' can specify either 'BIG_ENDIAN' or 'LITTLE_ENDIAN' byte order of the image data. Only LITTLE_ENDIAN is recommended. Processors may treat BIG_ENDIAN as a warning of data that can only be processed by special software. The 'X-Binary-Number-of-Elements' specifies the number of elements (not the number of octets) in the decompressed, decoded image. The optional 'X-Binary-Size-Fastest-Dimension' specifies the number of elements (not the number of octets) in one row of the fastest changing dimension of the binary data array. This information must be in the MIME header for proper operation of some of the decompression algorithms. The optional 'X-Binary-Size-Second-Dimension' specifies the number of elements (not the number of octets) in one column of the second-fastest changing dimension of the binary data array. This information must be in the MIME header for proper operation of some of the decompression algorithms. The optional 'X-Binary-Size-Third-Dimension' specifies the number of sections for the third-fastest changing dimension of the binary data array. The optional 'X-Binary-Size-Padding' specifies the size in octets of an optional padding after the binary array data and before the closing flags for a binary section. Reference: Darakev, G., Litchev, V., Mitev, K. Z. & Bernstein, H. J. (2006). 'Efficient Support of Binary Data in the XML Implementation of the NeXus File Format', abstract W0165, ACA Summer Meeting, Honolulu, HI, USA, July 2006. array_data.external_data_id This item is a pointer to attribute id in category array_data_external_data in the ARRAY_DATA_EXTERNAL_DATA category. If not given, then the actual array data should be specified as the value of attribute data in category array_data. If both values are given, the value on attribute data in category array_data takes precedence, and a warning of a possible conflict should be issued. array_data.header_contents This item is a text field for use in minimal CBF files to carry essential header information to be kept with image data in attribute data in category array_data when the tags that normally carry the structured metadata for the image have not been populated. Normally this data item should not appear when the full set of tags has been populated and attribute details in category diffrn_data_frame appears. array_data.header_convention This item is an identifier for the convention followed in constructing the contents of attribute header_contents in category array_data The permitted values are of an image creator identifier followed by an underscore and a version string. To avoid confusion about conventions, all creator identifiers should be registered with the IUCr and the conventions for all identifiers and versions should be posted on the MEDSBIO.org web site. array_data.array_id This item is a pointer to attribute id in category array_structure in the ARRAY_STRUCTURE category. If not given, it defaults to 1. array_data.binary_id This item is an integer identifier which, along with attribute array_id in category array_data, should uniquely identify the particular block of array data. If attribute binary_id in category array_data is not explicitly given, it defaults to 1. The value of attribute binary_id in category array_data distinguishes among multiple sets of data with the same array structure. If the MIME header of the data array specifies a value for X-Binary-ID, the value of attribute binary_id in category array_data should be equal to the value given for X-Binary-ID. 0 array_intensities Data items in the ARRAY_INTENSITIES category record the information required to recover the intensity data from the set of data values stored in the ARRAY_DATA category. The detector may have a complex relationship between the raw intensity values and the number of incident photons. In most cases, the number stored in the final array will have a simple linear relationship to the actual number of incident photons, given by attribute gain in category array_intensities. If raw, uncorrected values are presented (e.g. for calibration experiments), the value of attribute linearity in category array_intensities will be 'raw' and attribute gain in category array_intensities will not be used. Example 1 <PDBx:array_intensitiesCategory> <PDBx:array_intensities array_id="image_1"> <PDBx:gain>1.2</PDBx:gain> <PDBx:linearity>linear</PDBx:linearity> <PDBx:overload>655535</PDBx:overload> <PDBx:pixel_binning_method>hardware</PDBx:pixel_binning_method> <PDBx:pixel_fast_bin_size>2</PDBx:pixel_fast_bin_size> <PDBx:pixel_slow_bin_size>2</PDBx:pixel_slow_bin_size> <PDBx:undefined_value>0</PDBx:undefined_value> </PDBx:array_intensities> </PDBx:array_intensitiesCategory> 0 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 array_intensitiesCategory This property indicates that datablock has a category holder array_intensitiesCategory. array_intensitiesCategory This property indicates that array_intensitiesCategory. has a category array_intensities. array_intensitiesItem Abstract datatype property for array_intensities items. reference_to_array_intensities cross-reference to array_intensities. referenced_by_array_intensities cross-reference from array_intensities. array_intensities.details A description of special aspects of the calculation of array intensities. Gain_setting: low gain (vrf = -0.300) array_intensities.gain Detector 'gain'. The factor by which linearized intensity count values should be divided to produce true photon counts. array_intensities.gain_esd The standard uncertainty (estimated standard deviation, e.s.d.) of detector 'gain'. linear offset scaling scaling_offset sqrt_scaled logarithmic_scaled raw The intensity linearity scaling method used to convert from the raw intensity to the stored element value: 'linear' is linear. 'offset' means that the value defined by attribute offset in category array_intensities should be added to each element value. 'scaling' means that the value defined by attribute scaling in category array_intensities should be multiplied with each element value. 'scaling_offset' is the combination of the two previous cases, with the scale factor applied before the offset value. 'sqrt_scaled' means that the square root of raw intensities multiplied by attribute scaling in category array_intensities is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by attribute scaling in category array_intensities and squaring the result. 'logarithmic_scaled' means that the logarithm base 10 of raw intensities multiplied by attribute scaling in category array_intensities is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by attribute scaling in category array_intensities and calculating 10 to the power of this number. 'raw' means that the data are a set of raw values straight from the detector. array_intensities.offset Offset value to add to array element values in the manner described by the item attribute linearity in category array_intensities. array_intensities.overload The saturation intensity level for this data array, i.e. the value above which correct intensities may not be recorded. The valid pixel values are those less than attribute overload in category array_intensities and greater than or equal to attribute underload in category array_intensities hardware software combined none unspecified The value of attribute pixel_binning_method in category array_intensities specifies the method used to derive array elements from multiple pixels. array_intensities.pixel_fast_bin_size The value of attribute pixel_fast_bin_size in category array_intensities specifies the number of pixels that compose one element in the direction of the most rapidly varying array dimension. Typical values are 1, 2, 4 or 8. When there is 1 pixel per array element in both directions, the value given for attribute pixel_binning_method in category array_intensities normally should be 'none'. It is specified as a float to allow for binning algorithms that create array elements that are not integer multiples of the detector pixel size. array_intensities.pixel_slow_bin_size The value of attribute pixel_slow_bin_size in category array_intensities specifies the number of pixels that compose one element in the direction of the second most rapidly varying array dimension. Typical values are 1, 2, 4 or 8. When there is 1 pixel per array element in both directions, the value given for attribute pixel_binning_method in category array_intensities normally should be 'none'. It is specified as a float to allow for binning algorithms that create array elements that are not integer multiples of the detector pixel size. array_intensities.scaling Multiplicative scaling value to be applied to array data in the manner described by the item attribute linearity in category array_intensities. array_intensities.undefined_value A value to be substituted for undefined values in the data array. array_intensities.underload The lowest value at which pixels for this detector are measured. The valid pixel values are those less than attribute overload in category array_intensities and greater than or equal to attribute underload in category array_intensities array_intensities.array_id This item is a pointer to attribute id in category array_structure in the ARRAY_STRUCTURE category. array_intensities.binary_id This item is a pointer to attribute binary_id in category array_data in the ARRAY_DATA category. 0 array_structure Data items in the ARRAY_STRUCTURE category record the organization and encoding of array data that may be stored in the ARRAY_DATA category. Example 1. <PDBx:array_structureCategory> <PDBx:array_structure id="image_1"> <PDBx:byte_order>little_endian</PDBx:byte_order> <PDBx:compression_type>none</PDBx:compression_type> <PDBx:encoding_type>unsigned 16-bit integer</PDBx:encoding_type> </PDBx:array_structure> </PDBx:array_structureCategory> 1 1 0 1 0 1 1 1 1 array_structureCategory This property indicates that datablock has a category holder array_structureCategory. array_structureCategory This property indicates that array_structureCategory. has a category array_structure. array_structureItem Abstract datatype property for array_structure items. reference_to_array_structure cross-reference to array_structure. referenced_by_array_structure cross-reference from array_structure. big_endian little_endian The order of bytes for integer values which require more than 1 byte. (IBM-PCs and compatibles, and DEC VAXs use low-byte-first ordered integers, whereas Hewlett Packard 700 series, Sun-4 and Silicon Graphics use high-byte-first ordered integers. DEC Alphas can produce/use either depending on a compiler switch.) byte_offset canonical nibble_offset none packed packed_v2 Type of data-compression method used to compress the array data. uncorrelated_sections flat Flags modifying the type of data-compression method used to compress the arraydata. unsigned 1-bit integer unsigned 8-bit integer signed 8-bit integer unsigned 16-bit integer signed 16-bit integer unsigned 32-bit integer signed 32-bit integer signed 32-bit real IEEE signed 64-bit real IEEE signed 32-bit complex IEEE Data encoding of a single element of array data. The type 'unsigned 1-bit integer' is used for packed Boolean arrays for masks. Each element of the array corresponds to a single bit packed in unsigned 8-bit data. In several cases, the IEEE format is referenced. See IEEE Standard 754-1985 (IEEE, 1985). Reference: IEEE (1985). IEEE Standard for Binary Floating-Point Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of Electrical and Electronics Engineers. array_structure.id The value of attribute id in category array_structure must uniquely identify each item of array data. This item has been made implicit and given a default value of 1 as a convenience in writing miniCBF files. Normally an explicit name with useful content should be used. 0 array_structure_list Data items in the ARRAY_STRUCTURE_LIST category record the size and organization of each array dimension. The relationship to physical axes may be given. Example 1. An image array of 1300 x 1200 elements. The raster order of the image is left to right (increasing) in the first dimension and bottom to top (decreasing) in the second dimension. <PDBx:array_structure_listCategory> <PDBx:array_structure_list array_id="image_1" index="1"> <PDBx:axis_set_id>ELEMENT_X</PDBx:axis_set_id> <PDBx:dimension>1300</PDBx:dimension> <PDBx:direction>increasing</PDBx:direction> <PDBx:precedence>1</PDBx:precedence> </PDBx:array_structure_list> <PDBx:array_structure_list array_id="image_1" index="2"> <PDBx:axis_set_id>ELEMENY_Y</PDBx:axis_set_id> <PDBx:dimension>1200</PDBx:dimension> <PDBx:direction>decreasing</PDBx:direction> <PDBx:precedence>2</PDBx:precedence> </PDBx:array_structure_list> </PDBx:array_structure_listCategory> 0 1 1 1 1 1 1 1 1 1 1 1 array_structure_listCategory This property indicates that datablock has a category holder array_structure_listCategory. array_structure_listCategory This property indicates that array_structure_listCategory. has a category array_structure_list. array_structure_listItem Abstract datatype property for array_structure_list items. reference_to_array_structure_list cross-reference to array_structure_list. referenced_by_array_structure_list cross-reference from array_structure_list. array_structure_list.array_section_id This item is a pointer to attribute id in category array_structure_list_section in the ARRAY_STRUCTURE_LIST_SECTION category. array_structure_list.axis_set_id This is a descriptor for the physical axis or set of axes corresponding to an array index. This data item is related to the axes of the detector itself given in DIFFRN_DETECTOR_AXIS, but usually differs in that the axes in this category are the axes of the coordinate system of reported data points, while the axes in DIFFRN_DETECTOR_AXIS are the physical axes of the detector describing the 'poise' of the detector as an overall physical object. If there is only one axis in the set, the identifier of that axis should be used as the identifier of the set. array_structure_list.dimension The number of elements stored in the array structure in this dimension. increasing decreasing Identifies the direction in which this array index changes. array_structure_list.precedence Identifies the rank order in which this array index changes with respect to other array indices. The precedence of 1 indicates the index which changes fastest. array_structure_list.array_id This item is a pointer to attribute id in category array_structure in the ARRAY_STRUCTURE category. array_structure_list.index Identifies the one-based index of the row or column in the array structure. 0 array_structure_list_axis Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe the physical settings of sets of axes for the centres of pixels that correspond to data points described in the ARRAY_STRUCTURE_LIST category. In the simplest cases, the physical increments of a single axis correspond to the increments of a single array index. More complex organizations, e.g. spiral scans, may require coupled motions along multiple axes. Note that a spiral scan uses two coupled axes: one for the angular direction and one for the radial direction. This differs from a cylindrical scan for which the two axes are not coupled into one set. Axes may be specified either for an entire array or for just a section of an array. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 array_structure_list_axisCategory This property indicates that datablock has a category holder array_structure_list_axisCategory. array_structure_list_axisCategory This property indicates that array_structure_list_axisCategory. has a category array_structure_list_axis. array_structure_list_axisItem Abstract datatype property for array_structure_list_axis items. reference_to_array_structure_list_axis cross-reference to array_structure_list_axis. referenced_by_array_structure_list_axis cross-reference from array_structure_list_axis. array_structure_list_axis.angle The setting of the specified axis in degrees for the first data point of the array index with the corresponding value of attribute axis_set_id in category array_structure_list. If the index is specified as 'increasing', this will be the centre of the pixel with index value 1. If the index is specified as 'decreasing', this will be the centre of the pixel with maximum index value. array_structure_list_axis.angle_increment The pixel-centre-to-pixel-centre increment in the angular setting of the specified axis in degrees. This is not meaningful in the case of 'constant velocity' spiral scans and should not be specified for this case. See attribute angular_pitch in category array_structure_list_axis. array_structure_list_axis.angular_pitch The pixel-centre-to-pixel-centre distance for a one-step change in the setting of the specified axis in millimetres. This is meaningful only for 'constant velocity' spiral scans or for uncoupled angular scans at a constant radius (cylindrical scans) and should not be specified for cases in which the angle between pixels (rather than the distance between pixels) is uniform. See attribute angle_increment in category array_structure_list_axis. array_structure_list_axis.displacement The setting of the specified axis in millimetres for the first data point of the array index with the corresponding value of attribute axis_set_id in category array_structure_list. If the index is specified as 'increasing', this will be the centre of the pixel with index value 1. If the index is specified as 'decreasing', this will be the centre of the pixel with maximum index value. array_structure_list_axis.displacement_increment The pixel-centre-to-pixel-centre increment for the displacement setting of the specified axis in millimetres. array_structure_list_axis.fract_displacement The setting of the specified axis as a decimal fraction of the axis unit vector for the first data point of the array index with the corresponding value of attribute axis_set_id. in category array_structure_list If the index is specified as 'increasing', this will be the centre of the pixel with index value 1. If the index is specified as 'decreasing', this will be the centre of the pixel with maximum index value. array_structure_list_axis.fract_displacement_increment The pixel-centre-to-pixel-centre increment for the displacement setting of the specified axis as a decimal fraction of the axis unit vector. array_structure_list_axis.radial_pitch The radial distance from one 'cylinder' of pixels to the next in millimetres. If the scan is a 'constant velocity' scan with differing angular displacements between pixels, the value of this item may differ significantly from the value of attribute displacement_increment in category array_structure_list_axis. array_structure_list_axis.reference_angle The value of attribute reference_angle in category array_structure_list_axis specifies the setting of the angle of this axis used for determining a reference beam centre and a reference detector distance. It is normally expected to be identical to the value of attribute angle in category array_structure_list_axis. array_structure_list_axis.reference_displacement The value of attribute reference_displacement in category array_structure_list_axis specifies the setting of the displacement of this axis used for determining a reference beam centre and a reference detector distance. It is normally expected to be identical to the value of attribute displacement in category array_structure_list_axis. array_structure_list_axis.axis_id The value of this data item is the identifier of one of the axes in the set of axes for which settings are being specified. Multiple axes may be specified for the same value of attribute axis_set_id. in category array_structure_list_axis This item is a pointer to attribute id in category axis in the AXIS category. array_structure_list_axis.axis_set_id The value of this data item is the identifier of the set of axes for which axis settings are being specified. Multiple axes may be specified for the same value of attribute axis_set_id. in category array_structure_list_axis This item is a pointer to attribute axis_set_id in category array_structure_list in the ARRAY_STRUCTURE_LIST category. If this item is not specified, it defaults to the corresponding axis identifier. 0 array_structure_list_section Data items in the ARRAY_STRUCTURE_LIST_SECTION category identify the dimension-by-dimension start, end and stride of each section of an array that is to be referenced. For any array with identifier ARRAYID, array section ids of the form ARRAYID(start1:end1:stride1,start2:end2:stride2, ...) are defined by default. For the given index, the elements in the section are of indices: attribute start, in category array_structure_list_section _array_structure_list_section.start + _array_structure_list_section.stride, attribute start in category array_structure_list_section + 2*_array_structure_list_section.stride, ... stopping either when the indices leave the limits of the indices of that dimension or [min(_array_structure_list_section.start, attribute end), in category array_structure_list_section max(_array_structure_list_section.start, attribute end)]. in category array_structure_list_section The ordering of these elements is determined by the overall ordering of attribute array_id in category array_structure_list_section and not by the ordering implied by the stride. Example 1. An image array, myarray, of 1300 x 1200 elements, and 700 frames is defined in ARRAY_STRUCTURE_LIST, and the array section identifier "myarray(101:1200,101:1100,1:700:10)" is explicitly defined taking every 10th frame and removing a 100 pixel border. Note that even though the slow index high is 700, the last frame that will actually be included is only 691. <PDBx:array_structure_listCategory> <PDBx:array_structure_list array_id="myarray" index="1"> <PDBx:axis_set_id>ELEMENT_X</PDBx:axis_set_id> <PDBx:dimension>1300</PDBx:dimension> <PDBx:direction>increasing</PDBx:direction> <PDBx:precedence>1</PDBx:precedence> </PDBx:array_structure_list> <PDBx:array_structure_list array_id="myarray" index="2"> <PDBx:axis_set_id>ELEMENT_Y</PDBx:axis_set_id> <PDBx:dimension>1200</PDBx:dimension> <PDBx:direction>increasing</PDBx:direction> <PDBx:precedence>2</PDBx:precedence> </PDBx:array_structure_list> <PDBx:array_structure_list array_id="myarray" index="3"> <PDBx:axis_set_id>FRAME_NO</PDBx:axis_set_id> <PDBx:dimension>700</PDBx:dimension> <PDBx:direction>increasing</PDBx:direction> <PDBx:precedence>3</PDBx:precedence> </PDBx:array_structure_list> </PDBx:array_structure_listCategory> <PDBx:array_structure_list_sectionCategory> <PDBx:array_structure_list_section array_id="myarray" id="myarray(101:1200,101:1100,1:700:10)" index="1"> <PDBx:end>1200</PDBx:end> <PDBx:start>101</PDBx:start> <PDBx:stride xsi:nil="true" /> </PDBx:array_structure_list_section> <PDBx:array_structure_list_section array_id="myarray" id="myarray(101:1200,101:1100,1:700:10)" index="2"> <PDBx:end>1100</PDBx:end> <PDBx:start>101</PDBx:start> <PDBx:stride xsi:nil="true" /> </PDBx:array_structure_list_section> <PDBx:array_structure_list_section array_id="myarray" id="myarray(101:1200,101:1100,1:700:10)" index="3"> <PDBx:end>700</PDBx:end> <PDBx:start>1</PDBx:start> <PDBx:stride>10</PDBx:stride> </PDBx:array_structure_list_section> </PDBx:array_structure_list_sectionCategory> 0 1 0 1 0 1 1 1 1 array_structure_list_sectionCategory This property indicates that datablock has a category holder array_structure_list_sectionCategory. array_structure_list_sectionCategory This property indicates that array_structure_list_sectionCategory. has a category array_structure_list_section. array_structure_list_sectionItem Abstract datatype property for array_structure_list_section items. reference_to_array_structure_list_section cross-reference to array_structure_list_section. referenced_by_array_structure_list_section cross-reference from array_structure_list_section. array_structure_list_section.end Identifies the ending ordinal, numbered from 1, for an array element of index attribute index in category array_structure_list_section in the section. The value defaults to the dimension for index attribute index in category array_structure_list_section of the array. Note that this agrees with the Fortran convention, rather than the Python convention in that, if compatible with the stride, the end element is included in the section as in Fortran, rather than being one beyond the section as in Python. array_structure_list_section.start Identifies the starting ordinal, numbered from 1, for an array element of index attribute index in category array_structure_list_section in the section. The value defaults to 1. For the given index, the elements in the section are of indices: attribute start, in category array_structure_list_section attribute start in category array_structure_list_section + attribute stride, in category array_structure_list_section attribute start in category array_structure_list_section + 2*_array_structure_list_section.stride, ... stopping either when the indices leave the limits of the indices of that dimension or [min(_array_structure_list_section.start, attribute end in category array_structure_list_section ), max(_array_structure_list_section.start, attribute end in category array_structure_list_section )]. The ordering of these elements is determined by the overall ordering of attribute array_id in category array_structure_list_section and not by the ordering implied by the stride. array_structure_list_section.stride Identifies the incremental steps to be taken when moving element to element in the section in that particular dimension. The value of attribute stride in category array_structure_list_section may be positive or negative. If the stride is zero, the section is just defined by attribute start in category array_structure_list_section. array_structure_list_section.array_id This item is a pointer to attribute id in category array_structure in the ARRAY_STRUCTURE category. array_structure_list_section.id Uniquely identifies the array section chosen. To avoid confusion array section IDs that contain parentheses should conform to the default syntax ARRAYID(start1:end1:stride1,start2:end2:stride2, ...) array_structure_list_section.index This item is a pointer to attribute index in category array_structure_list in the ARRAY_STRUCTURE_LIST category. Identifies the one-based index of the row, column, sheet ... the ARRAY_STRUCTURE_LIST category. For a multidimensional array, a value must be explicitly given. If an index is omitted from a section then all elements for that index are assumed to be included in the section. 0 atom_site Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. wwPDB recommends wwPDB-assigned residue number, residue ID, and chain ID, _atom_site.auth_seq_id _atom_site.auth_comp_id, and attribute auth_asym_id in category atom_site, respectively, to be used for publication materials. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_siteCategory> <PDBx:atom_site id="1"> <PDBx:B_iso_or_equiv>17.93</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.369</PDBx:Cartn_x> <PDBx:Cartn_y>30.691</PDBx:Cartn_y> <PDBx:Cartn_z>11.795</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="2"> <PDBx:B_iso_or_equiv>17.75</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.970</PDBx:Cartn_x> <PDBx:Cartn_y>31.965</PDBx:Cartn_y> <PDBx:Cartn_z>12.332</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="3"> <PDBx:B_iso_or_equiv>17.83</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.569</PDBx:Cartn_x> <PDBx:Cartn_y>32.010</PDBx:Cartn_y> <PDBx:Cartn_z>13.808</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="4"> <PDBx:B_iso_or_equiv>17.53</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.735</PDBx:Cartn_x> <PDBx:Cartn_y>31.190</PDBx:Cartn_y> <PDBx:Cartn_z>14.167</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="5"> <PDBx:B_iso_or_equiv>17.66</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.379</PDBx:Cartn_x> <PDBx:Cartn_y>33.146</PDBx:Cartn_y> <PDBx:Cartn_z>11.540</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="6"> <PDBx:B_iso_or_equiv>18.86</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.584</PDBx:Cartn_x> <PDBx:Cartn_y>33.034</PDBx:Cartn_y> <PDBx:Cartn_z>10.030</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="7"> <PDBx:B_iso_or_equiv>17.12</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.933</PDBx:Cartn_x> <PDBx:Cartn_y>33.309</PDBx:Cartn_y> <PDBx:Cartn_z>11.872</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="8"> <PDBx:B_iso_or_equiv>18.97</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.095</PDBx:Cartn_x> <PDBx:Cartn_y>32.930</PDBx:Cartn_y> <PDBx:Cartn_z>14.590</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="9"> <PDBx:B_iso_or_equiv>19.80</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.734</PDBx:Cartn_x> <PDBx:Cartn_y>32.995</PDBx:Cartn_y> <PDBx:Cartn_z>16.032</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="10"> <PDBx:B_iso_or_equiv>20.92</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.695</PDBx:Cartn_x> <PDBx:Cartn_y>34.106</PDBx:Cartn_y> <PDBx:Cartn_z>16.113</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="11"> <PDBx:B_iso_or_equiv>21.84</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.869</PDBx:Cartn_x> <PDBx:Cartn_y>35.118</PDBx:Cartn_y> <PDBx:Cartn_z>15.421</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="12"> <PDBx:B_iso_or_equiv>20.51</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.911</PDBx:Cartn_x> <PDBx:Cartn_y>33.346</PDBx:Cartn_y> <PDBx:Cartn_z>17.018</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="13"> <PDBx:B_iso_or_equiv>20.29</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.946</PDBx:Cartn_x> <PDBx:Cartn_y>33.921</PDBx:Cartn_y> <PDBx:Cartn_z>16.183</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="14"> <PDBx:B_iso_or_equiv>20.59</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.769</PDBx:Cartn_x> <PDBx:Cartn_y>32.142</PDBx:Cartn_y> <PDBx:Cartn_z>17.103</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="15"> <PDBx:B_iso_or_equiv>20.47</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.418</PDBx:Cartn_x> <PDBx:Cartn_y>32.181</PDBx:Cartn_y> <PDBx:Cartn_z>17.878</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="16"> <PDBx:B_iso_or_equiv>20.00</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.489</PDBx:Cartn_x> <PDBx:Cartn_y>33.778</PDBx:Cartn_y> <PDBx:Cartn_z>18.426</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="17"> <PDBx:B_iso_or_equiv>22.08</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.664</PDBx:Cartn_x> <PDBx:Cartn_y>33.855</PDBx:Cartn_y> <PDBx:Cartn_z>16.884</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="18"> <PDBx:B_iso_or_equiv>23.44</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>22.623</PDBx:Cartn_x> <PDBx:Cartn_y>34.850</PDBx:Cartn_y> <PDBx:Cartn_z>17.093</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="19"> <PDBx:B_iso_or_equiv>25.77</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>22.657</PDBx:Cartn_x> <PDBx:Cartn_y>35.113</PDBx:Cartn_y> <PDBx:Cartn_z>18.610</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="20"> <PDBx:B_iso_or_equiv>26.28</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.123</PDBx:Cartn_x> <PDBx:Cartn_y>34.250</PDBx:Cartn_y> <PDBx:Cartn_z>19.406</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="21"> <PDBx:B_iso_or_equiv>22.67</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>21.236</PDBx:Cartn_x> <PDBx:Cartn_y>34.463</PDBx:Cartn_y> <PDBx:Cartn_z>16.492</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="22"> <PDBx:B_iso_or_equiv>22.14</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>20.478</PDBx:Cartn_x> <PDBx:Cartn_y>33.469</PDBx:Cartn_y> <PDBx:Cartn_z>17.371</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="23"> <PDBx:B_iso_or_equiv>21.75</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>21.357</PDBx:Cartn_x> <PDBx:Cartn_y>33.986</PDBx:Cartn_y> <PDBx:Cartn_z>15.016</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="101"> <PDBx:B_iso_or_equiv>17.27</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.171</PDBx:Cartn_x> <PDBx:Cartn_y>29.012</PDBx:Cartn_y> <PDBx:Cartn_z>7.116</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C1</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="102"> <PDBx:B_iso_or_equiv>16.95</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.949</PDBx:Cartn_x> <PDBx:Cartn_y>27.758</PDBx:Cartn_y> <PDBx:Cartn_z>6.793</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C2</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="103"> <PDBx:B_iso_or_equiv>16.85</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.800</PDBx:Cartn_x> <PDBx:Cartn_y>26.678</PDBx:Cartn_y> <PDBx:Cartn_z>7.393</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>O3</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="104"> <PDBx:B_iso_or_equiv>16.43</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>5.930</PDBx:Cartn_x> <PDBx:Cartn_y>27.841</PDBx:Cartn_y> <PDBx:Cartn_z>5.869</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>N4</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> </PDBx:atom_siteCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 atom_siteCategory This property indicates that datablock has a category holder atom_siteCategory. atom_siteCategory This property indicates that atom_siteCategory. has a category atom_site. atom_siteItem Abstract datatype property for atom_site items. reference_to_atom_site cross-reference to atom_site. referenced_by_atom_site cross-reference from atom_site. atom_site.B_equiv_geom_mean Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.B_equiv_geom_mean_esd The standard uncertainty (estimated standard deviation) of attribute B_equiv_geom_mean in category atom_site. atom_site.B_iso_or_equiv Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. Note - The particular type of ADP stored in this item is qualified by item attribute pdbx_adp_type in category refine. atom_site.B_iso_or_equiv_esd The standard uncertainty (estimated standard deviation) of attribute B_iso_or_equiv in category atom_site. atom_site.Cartn_x The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. atom_site.Cartn_x_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_x in category atom_site. atom_site.Cartn_y The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. atom_site.Cartn_y_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_y in category atom_site. atom_site.Cartn_z The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. atom_site.Cartn_z_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_z in category atom_site. atom_site.U_equiv_geom_mean Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ atom_site.U_equiv_geom_mean_esd The standard uncertainty (estimated standard deviation) of attribute U_equiv_geom_mean in category atom_site. atom_site.U_iso_or_equiv Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. atom_site.U_iso_or_equiv_esd The standard uncertainty (estimated standard deviation) of attribute U_iso_or_equiv in category atom_site. atom_site.Wyckoff_symbol The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002). Uani Uiso Uovl Umpe Bani Biso Bovl A standard code used to describe the type of atomic displacement parameters used for the site. atom_site.aniso_B11 The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B11_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][1] in category atom_site. atom_site.aniso_B12 The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B12_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][2] in category atom_site. atom_site.aniso_B13 The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B13_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][3] in category atom_site. atom_site.aniso_B22 The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B22_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][2] in category atom_site. atom_site.aniso_B23 The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B23_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][3] in category atom_site. atom_site.aniso_B33 The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B33_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[3][3] in category atom_site. atom_site.aniso_U11 The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U11_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][1] in category atom_site. atom_site.aniso_U12 The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U12_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][2] in category atom_site. atom_site.aniso_U13 The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U13_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][3] in category atom_site. atom_site.aniso_U22 The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U22_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][2] in category atom_site. atom_site.aniso_U23 The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U23_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][3] in category atom_site. atom_site.aniso_U33 The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U33_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[3][3] in category atom_site. atom_site.aniso_ratio Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. atom_site.attached_hydrogens The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given. water oxygen 2 hydroxyl oxygen 1 ammonium nitrogen 4 atom_site.auth_asym_id An alternative identifier for attribute label_asym_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. atom_site.auth_atom_id An alternative identifier for attribute label_atom_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. atom_site.auth_comp_id An alternative identifier for attribute label_comp_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. atom_site.auth_seq_id An alternative identifier for attribute label_seq_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of attribute label_seq_id in category atom_site. The value of attribute label_seq_id in category atom_site is required to be a sequential list of positive integers. The author may assign values to attribute auth_seq_id in category atom_site in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. atom_site.calc_attached_atom The attribute id in category atom_site of the atom site to which the 'geometry-calculated' atom site is attached. d calc c dum A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'. atom_site.chemical_conn_number This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. atom_site.constraints A description of the constraints applied to parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_constraints in category refine. pop=1.0-pop(Zn3) atom_site.details A description of special aspects of this site. See also attribute refinement_flags in category atom_site. Ag/Si disordered atom_site.disorder_assembly A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, attribute disorder_group in category atom_site is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** atom_site.disorder_group A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** atom_site.footnote_id The value of attribute footnote_id in category atom_site must match an ID specified by attribute id in category atom_sites_footnote in the ATOM_SITES_FOOTNOTE list. atom_site.fract_x The x coordinate of the atom-site position specified as a fraction of attribute length_a in category cell. atom_site.fract_x_esd The standard uncertainty (estimated standard deviation) of attribute fract_x in category atom_site. atom_site.fract_y The y coordinate of the atom-site position specified as a fraction of attribute length_b in category cell. atom_site.fract_y_esd The standard uncertainty (estimated standard deviation) of attribute fract_y in category atom_site. atom_site.fract_z The z coordinate of the atom-site position specified as a fraction of attribute length_c in category cell. atom_site.fract_z_esd The standard uncertainty (estimated standard deviation) of attribute fract_z in category atom_site. ATOM HETATM The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. atom_site.label_alt_id A place holder to indicate alternate conformation. The alternate conformation can be an entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. atom_site.label_asym_id A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. atom_site.label_atom_id A component of the identifier for this atom site. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. atom_site.label_comp_id A component of the identifier for this atom site. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. atom_site.label_entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. atom_site.label_seq_id This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not exceed 1.0 unless it is a dummy site. atom_site.occupancy_esd The standard uncertainty (estimated standard deviation) of attribute occupancy in category atom_site. atom_site.pdbx_PDB_atom_name PDB atom name. atom_site.pdbx_PDB_ins_code PDB insertion code. atom_site.pdbx_PDB_model_num PDB model number. atom_site.pdbx_PDB_residue_name PDB residue name. atom_site.pdbx_PDB_residue_no PDB residue number. atom_site.pdbx_PDB_strand_id PDB strand id. atom_site.pdbx_atom_ambiguity The optional value of attribute pdbx_atom_ambiguity in category atom_site atoms that differ only by stereochemistry but are not stereospecifically assigned by the experiment. HDx% HDy% H5x H5y atom_site.pdbx_atom_group The ATOM group code used by the NDB. atom_site.pdbx_auth_alt_id Author's alternate location identifier. atom_site.pdbx_auth_asym_id Author's strand id. atom_site.pdbx_auth_atom_name Author's atom name. atom_site.pdbx_auth_comp_id Author's residue name. atom_site.pdbx_auth_seq_id Author's sequence identifier. atom_site.pdbx_formal_charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 atom_site.pdbx_group_NDB The ATOM group code used by the NDB. atom_site.pdbx_label_index This data item is an ordinal which identifies distinct chemical components in the atom_site category, both polymeric and non-polymeric. atom_site.pdbx_label_seq_num Sequential residue number used by NDB. atom_site.pdbx_ncs_dom_id The NCS domain to which the atom position is assigned. The NCS group is defined in category struct_ncs_dom. This item is a reference to attribute id in category struct_ncs_dom. atom_site.pdbx_not_in_asym Will identify with a 'Y' that this strand got generated. atom_site.pdbx_sifts_xref_db_acc The accession code related to the additional external database entry. atom_site.pdbx_sifts_xref_db_name The name of additional external databases with residue level mapping. atom_site.pdbx_sifts_xref_db_num The sequence position of the external database entry that corresponds to the residue mapping defined by the SIFTS process. atom_site.pdbx_sifts_xref_db_res Describes the residue type of the given UniProt match alanine A arginine R asparagine N aspartic acid D cysteine C glutamine Q glutamic acid E glycine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P selenocysteine U serine S threonine T tryptophan W tyrosine Y valine V pyrrolysine O other X atom_site.pdbx_struct_group_id The value of attribute pdbx_struct_group_id in category atom_site identifies the group or groups assigned to this atom. This is a reference to the identifier for group definition in category PDBX_STRUCT_GROUP_LIST. Multiple groups identifiers are encoded as a comma separated list. atom assigned to individual group C1 C1 atom assigned to multiple groups C1, C2 and C3 C1,C2,C3 atom_site.pdbx_tls_group_id The TLS group to which the atom position is assigned. The TLS group is defined in category pdbx_refine_tls. This item is a reference to attribute id in category pdbx_refine_tls. S G R D T U P A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by attribute refinement_flags_posn in category atom_site, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs. T U TU A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site. P A code which indicates that refinement restraints or constraints were applied to the occupancy of this site. D G R S DG DR DS GR GS RS DGR DGS DRS GRS DGRS A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site. atom_site.restraints A description of restraints applied to specific parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_restraints in category refine. restrained to planar ring atom_site.symmetry_multiplicity The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002). Uani Uiso Uovl Umpe Bani Biso Bovl A standard code used to describe the type of atomic displacement parameters used for the site. atom_site.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. atom_site.id The value of attribute id in category atom_site must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and attribute label_seq_id in category atom_site. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to attribute id. in category atom_site In general, this aggregate identifier does not uniquely identify an atom site as for non-polymers attribute label_seq_id in category atom_site is '.'. 5 C12 Ca3g28 Fe3+17 H*251 boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0 0 atom_site_anisotrop Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [Acta Cryst. (1985), B41, 255-262]. <PDBx:atom_site_anisotropCategory> <PDBx:atom_site_anisotrop id="1"> <PDBx:U11>8642</PDBx:U11> <PDBx:U12>4866</PDBx:U12> <PDBx:U13>7299</PDBx:U13> <PDBx:U22>-342</PDBx:U22> <PDBx:U23>-258</PDBx:U23> <PDBx:U33>-1427</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="2"> <PDBx:U11>5174</PDBx:U11> <PDBx:U12>4871</PDBx:U12> <PDBx:U13>6243</PDBx:U13> <PDBx:U22>-1885</PDBx:U22> <PDBx:U23>-2051</PDBx:U23> <PDBx:U33>-1377</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="3"> <PDBx:U11>6202</PDBx:U11> <PDBx:U12>5020</PDBx:U12> <PDBx:U13>4395</PDBx:U13> <PDBx:U22>-1130</PDBx:U22> <PDBx:U23>-556</PDBx:U23> <PDBx:U33>-632</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="4"> <PDBx:U11>4224</PDBx:U11> <PDBx:U12>4700</PDBx:U12> <PDBx:U13>5046</PDBx:U13> <PDBx:U22>1105</PDBx:U22> <PDBx:U23>-161</PDBx:U23> <PDBx:U33>345</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="5"> <PDBx:U11>8684</PDBx:U11> <PDBx:U12>4688</PDBx:U12> <PDBx:U13>4171</PDBx:U13> <PDBx:U22>-1850</PDBx:U22> <PDBx:U23>-433</PDBx:U23> <PDBx:U33>-292</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="6"> <PDBx:U11>11226</PDBx:U11> <PDBx:U12>5255</PDBx:U12> <PDBx:U13>3532</PDBx:U13> <PDBx:U22>-341</PDBx:U22> <PDBx:U23>2685</PDBx:U23> <PDBx:U33>1328</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="7"> <PDBx:U11>10214</PDBx:U11> <PDBx:U12>2428</PDBx:U12> <PDBx:U13>5614</PDBx:U13> <PDBx:U22>-2610</PDBx:U22> <PDBx:U23>-1940</PDBx:U23> <PDBx:U33>902</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="8"> <PDBx:U11>4590</PDBx:U11> <PDBx:U12>3488</PDBx:U12> <PDBx:U13>5827</PDBx:U13> <PDBx:U22>751</PDBx:U22> <PDBx:U23>-770</PDBx:U23> <PDBx:U33>986</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="9"> <PDBx:U11>5014</PDBx:U11> <PDBx:U12>4434</PDBx:U12> <PDBx:U13>3447</PDBx:U13> <PDBx:U22>-17</PDBx:U22> <PDBx:U23>-1593</PDBx:U23> <PDBx:U33>539</PDBx:U33> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site_anisotrop> </PDBx:atom_site_anisotropCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 atom_site_anisotropCategory This property indicates that datablock has a category holder atom_site_anisotropCategory. atom_site_anisotropCategory This property indicates that atom_site_anisotropCategory. has a category atom_site_anisotrop. atom_site_anisotropItem Abstract datatype property for atom_site_anisotrop items. reference_to_atom_site_anisotrop cross-reference to atom_site_anisotrop. referenced_by_atom_site_anisotrop cross-reference from atom_site_anisotrop. atom_site_anisotrop.B11 The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B11_esd The standard uncertainty (estimated standard deviation) of attribute B[1][1] in category atom_site_anisotrop. atom_site_anisotrop.B12 The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B12_esd The standard uncertainty (estimated standard deviation) of attribute B[1][2] in category atom_site_anisotrop. atom_site_anisotrop.B13 The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B13_esd The standard uncertainty (estimated standard deviation) of attribute B[1][3] in category atom_site_anisotrop. atom_site_anisotrop.B22 The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B22_esd The standard uncertainty (estimated standard deviation) of attribute B[2][2] in category atom_site_anisotrop. atom_site_anisotrop.B23 The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B23_esd The standard uncertainty (estimated standard deviation) of attribute B[2][3] in category atom_site_anisotrop. atom_site_anisotrop.B33 The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B33_esd The standard uncertainty (estimated standard deviation) of attribute B[3][3] in category atom_site_anisotrop. atom_site_anisotrop.U11 The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U11_esd The standard uncertainty (estimated standard deviation) of attribute U[1][1] in category atom_site_anisotrop. atom_site_anisotrop.U12 The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U12_esd The standard uncertainty (estimated standard deviation) of attribute U[1][2] in category atom_site_anisotrop. atom_site_anisotrop.U13 The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U13_esd The standard uncertainty (estimated standard deviation) of attribute U[1][3] in category atom_site_anisotrop. atom_site_anisotrop.U22 The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U22_esd The standard uncertainty (estimated standard deviation) of attribute U[2][2] in category atom_site_anisotrop. atom_site_anisotrop.U23 The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U23_esd The standard uncertainty (estimated standard deviation) of attribute U[2][3] in category atom_site_anisotrop. atom_site_anisotrop.U33 The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U33_esd The standard uncertainty (estimated standard deviation) of attribute U[3][3] in category atom_site_anisotrop. atom_site_anisotrop.pdbx_PDB_atom_name PDB atom name. atom_site_anisotrop.pdbx_PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site atom_site_anisotrop.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site atom_site_anisotrop.pdbx_PDB_residue_name PDB residue name. atom_site_anisotrop.pdbx_PDB_residue_no PDB residue number. atom_site_anisotrop.pdbx_PDB_strand_id PDB strand id. atom_site_anisotrop.pdbx_auth_alt_id Pointer to attribute pdbx_auth_alt_id in category atom_site. atom_site_anisotrop.pdbx_auth_asym_id Pointer to attribute auth_asym_id in category atom_site atom_site_anisotrop.pdbx_auth_atom_id Pointer to attribute auth_atom_id in category atom_site atom_site_anisotrop.pdbx_auth_atom_name Author's atom name. atom_site_anisotrop.pdbx_auth_comp_id Pointer to attribute auth_comp_id in category atom_site atom_site_anisotrop.pdbx_auth_seq_id Pointer to attribute auth_seq_id in category atom_site atom_site_anisotrop.pdbx_label_alt_id Pointer to attribute label_alt_id in category atom_site. atom_site_anisotrop.pdbx_label_asym_id Pointer to attribute label_asym_id in category atom_site atom_site_anisotrop.pdbx_label_atom_id Pointer to attribute label_atom_id in category atom_site atom_site_anisotrop.pdbx_label_comp_id Pointer to attribute label_comp_id in category atom_site atom_site_anisotrop.pdbx_label_ins_code NDB INSERTION CODE atom_site_anisotrop.pdbx_label_seq_id Pointer to attribute label_seq_id in category atom_site atom_site_anisotrop.pdbx_not_in_asym Will identify with a 'Y' that this strand got generated. atom_site_anisotrop.ratio Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. atom_site_anisotrop.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. atom_site_anisotrop.id This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. 0 atom_sites Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sitesCategory> <PDBx:atom_sites entry_id="5HVP"> <PDBx:Cartn_transf_matrix11>58.39</PDBx:Cartn_transf_matrix11> <PDBx:Cartn_transf_matrix12>0.00</PDBx:Cartn_transf_matrix12> <PDBx:Cartn_transf_matrix13>0.00</PDBx:Cartn_transf_matrix13> <PDBx:Cartn_transf_matrix21>0.00</PDBx:Cartn_transf_matrix21> <PDBx:Cartn_transf_matrix22>86.70</PDBx:Cartn_transf_matrix22> <PDBx:Cartn_transf_matrix23>0.00</PDBx:Cartn_transf_matrix23> <PDBx:Cartn_transf_matrix31>0.00</PDBx:Cartn_transf_matrix31> <PDBx:Cartn_transf_matrix32>0.00</PDBx:Cartn_transf_matrix32> <PDBx:Cartn_transf_matrix33>46.27</PDBx:Cartn_transf_matrix33> <PDBx:Cartn_transf_vector1>0.00</PDBx:Cartn_transf_vector1> <PDBx:Cartn_transf_vector2>0.00</PDBx:Cartn_transf_vector2> <PDBx:Cartn_transf_vector3>0.00</PDBx:Cartn_transf_vector3> <PDBx:Cartn_transform_axes>c along z, astar along x, b along y</PDBx:Cartn_transform_axes> </PDBx:atom_sites> </PDBx:atom_sitesCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 atom_sitesCategory This property indicates that datablock has a category holder atom_sitesCategory. atom_sitesCategory This property indicates that atom_sitesCategory. has a category atom_sites. atom_sitesItem Abstract datatype property for atom_sites items. reference_to_atom_sites cross-reference to atom_sites. referenced_by_atom_sites cross-reference from atom_sites. atom_sites.Cartn_transf_matrix11 The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix12 The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix13 The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix21 The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix22 The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix23 The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix31 The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix32 The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix33 The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_vector1 The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_vector2 The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_vector3 The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transform_axes A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix attribute Cartn_transf_matrix[][] in category atom_sites. a parallel to x; b in the plane of y and z atom_sites.fract_transf_matrix11 The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix12 The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix13 The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix21 The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix22 The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix23 The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix31 The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix32 The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix33 The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_vector1 The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_vector2 The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_vector3 The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| difmap vecmap heavy direct geom disper isomor This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. *** difmap vecmap heavy direct geom disper isomor This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. *** difmap vecmap heavy direct geom disper isomor This code identifies the method used to locate the non-hydrogen-atom sites not found by attribute solution_primary. in category atom_sites *** This data item would not in general be used in a macromolecular data block. *** atom_sites.special_details Additional information about the atomic coordinates not coded elsewhere in the CIF. atom_sites.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 atom_sites_alt Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_altCategory> <PDBx:atom_sites_alt id="1"> <PDBx:details> Atom sites with the alternative ID set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 2. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 1 correlate with the conformation of the inhibitor marked with alternative ID 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="2"> <PDBx:details> Atom sites with the alternative ID set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 1. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 2 correlate with the conformation of the inhibitor marked with alternative ID 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="3"> <PDBx:details> Atom sites with the alternative ID set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative ID 4. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="4"> <PDBx:details> Atom sites with the alternative ID set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative ID 3. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> </PDBx:atom_sites_altCategory> 0 1 1 atom_sites_altCategory This property indicates that datablock has a category holder atom_sites_altCategory. atom_sites_altCategory This property indicates that atom_sites_altCategory. has a category atom_sites_alt. atom_sites_altItem Abstract datatype property for atom_sites_alt items. reference_to_atom_sites_alt cross-reference to atom_sites_alt. referenced_by_atom_sites_alt cross-reference from atom_sites_alt. atom_sites_alt.details A description of special aspects of the modelling of atoms in alternative conformations. atom_sites_alt.id The value of attribute id in category atom_sites_alt must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier. orientation 1 molecule abc 0 atom_sites_alt_ens Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_alt_ensCategory> <PDBx:atom_sites_alt_ens id="Ensemble 1-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 1-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> </PDBx:atom_sites_alt_ensCategory> 0 1 1 atom_sites_alt_ensCategory This property indicates that datablock has a category holder atom_sites_alt_ensCategory. atom_sites_alt_ensCategory This property indicates that atom_sites_alt_ensCategory. has a category atom_sites_alt_ens. atom_sites_alt_ensItem Abstract datatype property for atom_sites_alt_ens items. reference_to_atom_sites_alt_ens cross-reference to atom_sites_alt_ens. referenced_by_atom_sites_alt_ens cross-reference from atom_sites_alt_ens. atom_sites_alt_ens.details A description of special aspects of the ensemble structure generated from atoms with various alternative IDs. atom_sites_alt_ens.id The value of attribute id in category atom_sites_alt_ens must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier. 0 atom_sites_alt_gen Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_alt_genCategory> <PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen> </PDBx:atom_sites_alt_genCategory> 1 1 atom_sites_alt_genCategory This property indicates that datablock has a category holder atom_sites_alt_genCategory. atom_sites_alt_genCategory This property indicates that atom_sites_alt_genCategory. has a category atom_sites_alt_gen. atom_sites_alt_genItem Abstract datatype property for atom_sites_alt_gen items. reference_to_atom_sites_alt_gen cross-reference to atom_sites_alt_gen. referenced_by_atom_sites_alt_gen cross-reference from atom_sites_alt_gen. atom_sites_alt_gen.alt_id This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. atom_sites_alt_gen.ens_id This data item is a pointer to attribute id in category atom_sites_alt_ens in the ATOM_SITES_ALT_ENS category. 0 atom_sites_footnote Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_footnoteCategory> <PDBx:atom_sites_footnote id="1"> <PDBx:text> The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative IDs *1* and *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="2"> <PDBx:text> Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="3"> <PDBx:text> The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="4"> <PDBx:text> Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="5"> <PDBx:text> The positions of these water molecules correlate with alternative orientations of amino-acid side chains that do not correlate with alternative orientations of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> </PDBx:atom_sites_footnoteCategory> 0 1 1 atom_sites_footnoteCategory This property indicates that datablock has a category holder atom_sites_footnoteCategory. atom_sites_footnoteCategory This property indicates that atom_sites_footnoteCategory. has a category atom_sites_footnote. atom_sites_footnoteItem Abstract datatype property for atom_sites_footnote items. reference_to_atom_sites_footnote cross-reference to atom_sites_footnote. referenced_by_atom_sites_footnote cross-reference from atom_sites_footnote. atom_sites_footnote.text The text of the footnote. Footnotes are used to describe an atom site or a group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled. atom_sites_footnote.id A code that identifies the footnote. a b 1 2 0 atom_type Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>2.31000</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>1.58860</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>1.02000</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>0.865000</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>20.8439</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.568700</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>10.2075</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>51.6512</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.21560</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>12.2126</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>3.13220</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>2.01250</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>1.166300</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>0.005700</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>9.893300</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>28.9975</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>0.582600</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-11.529</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>3.04850</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>2.28680</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>1.54630</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>0.867000</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>13.2771</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>5.70110</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.323900</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>32.9089</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.250800</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="S"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>6.90530</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>5.20340</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>1.58630</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>1.43790</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.46790</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>22.2151</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>56.1720</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>0.253600</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.866900</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="CL"> <PDBx:oxidation_number>-1</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>18.2915</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>7.20840</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>6.53370</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>2.33860</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>0.006600</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>1.17170</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>19.5424</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>60.4486</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-16.378</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> </PDBx:atom_typeCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:number_in_cell>72</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.009</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.017</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="H"> <PDBx:number_in_cell>100</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>0</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>0</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:number_in_cell>12</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.032</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.047</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:number_in_cell>4</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.018</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.029</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> </PDBx:atom_typeCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 atom_typeCategory This property indicates that datablock has a category holder atom_typeCategory. atom_typeCategory This property indicates that atom_typeCategory. has a category atom_type. atom_typeItem Abstract datatype property for atom_type items. reference_to_atom_type cross-reference to atom_type. referenced_by_atom_type cross-reference from atom_type. atom_type.analytical_mass_percent Mass percentage of this atom type derived from chemical analysis. atom_type.description A description of the atom(s) designated by this atom type. In most cases, this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. deuterium 0.34Fe+0.66Ni atom_type.number_in_cell Total number of atoms of this atom type in the unit cell. atom_type.oxidation_number Formal oxidation state of this atom type in the structure. atom_type.pdbx_N_electrons Number of electrons in atom used in scattering factor atom_type.pdbx_scat_Cromer_Mann_a5 Scattering-factor coefficient a5, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.pdbx_scat_Cromer_Mann_a6 Scattering-factor coefficient a6, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.pdbx_scat_Cromer_Mann_b5 Scattering-factor coefficient b5, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.pdbx_scat_Cromer_Mann_b6 Scattering-factor coefficient b6, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.pdbx_scat_Z Atomic number of atom in scattering amplitude. atom_type.radius_bond The effective intramolecular bonding radius in angstroms of this atom type. atom_type.radius_contact The effective intermolecular bonding radius in angstroms of this atom type. atom_type.scat_Cromer_Mann_a1 The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_a2 The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_a3 The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_a4 The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b1 The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b2 The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b3 The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b4 The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_c The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_dispersion_imag The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. atom_type.scat_dispersion_real The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. atom_type.scat_dispersion_source Reference to the source of the real and imaginary dispersion corrections for scattering factors used for this atom type. International Tables Vol. IV Table 2.3.1 atom_type.scat_length_neutron The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. atom_type.scat_source Reference to the source of the scattering factors or scattering lengths used for this atom type. International Tables Vol. IV Table 2.4.6B atom_type.scat_versus_stol_list A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. atom_type.symbol The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. C Cu2+ H(SDS) dummy FeNi 0 audit Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:auditCategory> <PDBx:audit revision_id="1"> <PDBx:creation_date>1992-12-08</PDBx:creation_date> <PDBx:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records</PDBx:creation_method> <PDBx:update_record> 1992-12-09 adjusted to reflect comments from B. McKeever 1992-12-10 adjusted to reflect comments from H. Berman 1992-12-12 adjusted to reflect comments from K. Watenpaugh</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:auditCategory> <PDBx:audit revision_id="2"> <PDBx:creation_date>1991-03-20</PDBx:creation_date> <PDBx:creation_method>from_xtal_archive_file_using_CIFIO</PDBx:creation_method> <PDBx:update_record> 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec&apos;d by co-editor as manuscript HL0007. 1991-04-17 adjustments based on first referee report. 1991-04-18 adjustments based on second referee report.</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> 0 1 0 1 0 1 1 auditCategory This property indicates that datablock has a category holder auditCategory. auditCategory This property indicates that auditCategory. has a category audit. auditItem Abstract datatype property for audit items. reference_to_audit cross-reference to audit. referenced_by_audit cross-reference from audit. audit.creation_date A date that the data block was created. The date format is yyyy-mm-dd. 1990-07-12 audit.creation_method A description of how data were entered into the data block. spawned by the program QBEE audit.update_record A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. 1990-07-15 Updated by the Co-editor audit.revision_id The value of attribute revision_id in category audit must uniquely identify a record in the AUDIT list. rev1 0 audit_author Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:audit_authorCategory> <PDBx:audit_author pdbx_ordinal="1"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Fitzgerald, Paula M.D.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="2"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>McKeever, Brian M.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="3"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Van Middlesworth, J.F.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="4"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Springer, James P.</PDBx:name> </PDBx:audit_author> </PDBx:audit_authorCategory> 0 1 0 1 1 1 1 audit_authorCategory This property indicates that datablock has a category holder audit_authorCategory. audit_authorCategory This property indicates that audit_authorCategory. has a category audit_author. audit_authorItem Abstract datatype property for audit_author items. reference_to_audit_author cross-reference to audit_author. referenced_by_audit_author cross-reference from audit_author. audit_author.address The address of an author of this data block. If there are multiple authors, attribute address in category audit_author is looped with attribute name in category audit_author. Department Institute Street City and postcode COUNTRY audit_author.identifier_ORCID The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X audit_author.name The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A audit_author.pdbx_ordinal This data item defines the order of the author's name in the list of audit authors. 1 2 3 0 audit_conform Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. Example 1 - any file conforming to the current CIF core dictionary. <PDBx:audit_conformCategory> <PDBx:audit_conform dict_name="cif_core.dic" dict_version="2.3.1"> <PDBx:dict_location>ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic</PDBx:dict_location> </PDBx:audit_conform> </PDBx:audit_conformCategory> 0 1 1 1 audit_conformCategory This property indicates that datablock has a category holder audit_conformCategory. audit_conformCategory This property indicates that audit_conformCategory. has a category audit_conform. audit_conformItem Abstract datatype property for audit_conform items. reference_to_audit_conform cross-reference to audit_conform. referenced_by_audit_conform cross-reference from audit_conform. audit_conform.dict_location A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. audit_conform.dict_name The string identifying the highest-level dictionary defining data names used in this file. audit_conform.dict_version The version number of the dictionary to which the current data block conforms. 0 audit_contact_author Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:audit_contact_authorCategory> <PDBx:audit_contact_author name="Fitzgerald, Paula M.D."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:email>paula_fitzgerald@merck.com</PDBx:email> <PDBx:fax>1(908)5946645</PDBx:fax> <PDBx:phone>1(908)5945510</PDBx:phone> </PDBx:audit_contact_author> </PDBx:audit_contact_authorCategory> 0 1 0 1 0 1 0 1 1 audit_contact_authorCategory This property indicates that datablock has a category holder audit_contact_authorCategory. audit_contact_authorCategory This property indicates that audit_contact_authorCategory. has a category audit_contact_author. audit_contact_authorItem Abstract datatype property for audit_contact_author items. reference_to_audit_contact_author cross-reference to audit_contact_author. referenced_by_audit_contact_author cross-reference from audit_contact_author. audit_contact_author.address The mailing address of the author of the data block to whom correspondence should be addressed. Department Institute Street City and postcode COUNTRY audit_contact_author.email The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. name@host.domain.country bm@iucr.org audit_contact_author.fax The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. 12(34)9477334 12()349477334 audit_contact_author.phone The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. 12(34)9477330 12()349477330 12(34)9477330x5543 audit_contact_author.name The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A 0 audit_link Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF. Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. <PDBx:audit_linkCategory> <PDBx:audit_link block_code="morA_pub" block_description="discursive text of paper with two structures"></PDBx:audit_link> <PDBx:audit_link block_code="morA_(1)" block_description="structure 1 of 2"></PDBx:audit_link> <PDBx:audit_link block_code="morA_(2)" block_description="structure 2 of 2"></PDBx:audit_link> </PDBx:audit_linkCategory> Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:audit_linkCategory> <PDBx:audit_link block_code="KSE_PUB" block_description="publication details"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_COM" block_description="experimental data common to ref./mod. structures"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_REF" block_description="reference structure"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_MOD" block_description="modulated structure"></PDBx:audit_link> </PDBx:audit_linkCategory> 1 1 audit_linkCategory This property indicates that datablock has a category holder audit_linkCategory. audit_linkCategory This property indicates that audit_linkCategory. has a category audit_link. audit_linkItem Abstract datatype property for audit_link items. reference_to_audit_link cross-reference to audit_link. referenced_by_audit_link cross-reference from audit_link. audit_link.block_code The value of attribute code in category audit_block associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness. audit_link.block_description A textual description of the relationship of the referenced data block to the current one. 0 cell Data items in the CELL category record details about the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:cellCategory> <PDBx:cell entry_id="5HVP"> <PDBx:angle_alpha>90.00</PDBx:angle_alpha> <PDBx:angle_beta>90.00</PDBx:angle_beta> <PDBx:angle_gamma>90.00</PDBx:angle_gamma> <PDBx:details> The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean.</PDBx:details> <PDBx:length_a>58.39</PDBx:length_a> <PDBx:length_a_esd>0.05</PDBx:length_a_esd> <PDBx:length_b>86.70</PDBx:length_b> <PDBx:length_b_esd>0.12</PDBx:length_b_esd> <PDBx:length_c>46.27</PDBx:length_c> <PDBx:length_c_esd>0.06</PDBx:length_c_esd> <PDBx:volume>234237</PDBx:volume> </PDBx:cell> </PDBx:cellCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:cellCategory> <PDBx:cell entry_id="1TOZ"> <PDBx:angle_alpha>90.0</PDBx:angle_alpha> <PDBx:angle_beta>90.0</PDBx:angle_beta> <PDBx:angle_gamma>90.0</PDBx:angle_gamma> <PDBx:length_a>5.959</PDBx:length_a> <PDBx:length_a_esd>0.001</PDBx:length_a_esd> <PDBx:length_b>14.956</PDBx:length_b> <PDBx:length_b_esd>0.001</PDBx:length_b_esd> <PDBx:length_c>19.737</PDBx:length_c> <PDBx:length_c_esd>0.003</PDBx:length_c_esd> <PDBx:volume>1759.0</PDBx:volume> <PDBx:volume_esd>0.3</PDBx:volume_esd> </PDBx:cell> </PDBx:cellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 cellCategory This property indicates that datablock has a category holder cellCategory. cellCategory This property indicates that cellCategory. has a category cell. cellItem Abstract datatype property for cell items. reference_to_cell cross-reference to cell. referenced_by_cell cross-reference from cell. cell.Z_PDB The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. cell.angle_alpha Unit-cell angle alpha of the reported structure in degrees. cell.angle_alpha_esd The standard uncertainty (estimated standard deviation) of attribute angle_alpha in category cell. cell.angle_beta Unit-cell angle beta of the reported structure in degrees. cell.angle_beta_esd The standard uncertainty (estimated standard deviation) of attribute angle_beta in category cell. cell.angle_gamma Unit-cell angle gamma of the reported structure in degrees. cell.angle_gamma_esd The standard uncertainty (estimated standard deviation) of attribute angle_gamma in category cell. cell.details A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c cell.formula_units_Z The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or attribute sum in category chemical_formula. cell.length_a Unit-cell length a corresponding to the structure reported in angstroms. cell.length_a_esd The standard uncertainty (estimated standard deviation) of attribute length_a in category cell. cell.length_b Unit-cell length b corresponding to the structure reported in angstroms. cell.length_b_esd The standard uncertainty (estimated standard deviation) of attribute length_b in category cell. cell.length_c Unit-cell length c corresponding to the structure reported in angstroms. cell.length_c_esd The standard uncertainty (estimated standard deviation) of attribute length_c in category cell. single crystal window scan varying propagated population refined How the estimated standard deviation was determined. cell.pdbx_unique_axis To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field. cell.reciprocal_angle_alpha The angle (recip-alpha) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_angle_alpha_esd The estimated standard deviation of attribute reciprocal_angle_alpha in category cell. cell.reciprocal_angle_beta The angle (recip-beta) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_angle_beta_esd The estimated standard deviation of attribute reciprocal_angle_beta in category cell. cell.reciprocal_angle_gamma The angle (recip-gamma) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_angle_gamma_esd The estimated standard deviation of attribute reciprocal_angle_gamma in category cell. cell.reciprocal_length_a The reciprocal cell length (recip-a) in inverse angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_length_a_esd The estimated standard deviation of attribute reciprocal_length_a in category cell. cell.reciprocal_length_b The reciprocal cell length (recip-b) in inverse angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_length_b_esd The estimated standard deviation of attribute reciprocal_length_b in category cell. cell.reciprocal_length_c The reciprocal cell length (recip-c) in inverse angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_length_c_esd The estimated standard deviation of attribute reciprocal_length_c in category cell. cell.volume Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = attribute length_a in category cell b = attribute length_b in category cell c = attribute length_c in category cell alpha = attribute angle_alpha in category cell beta = attribute angle_beta in category cell gamma = attribute angle_gamma in category cell cell.volume_esd The standard uncertainty (estimated standard deviation) of attribute volume in category cell. cell.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 cell_measurement Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="5HVP"> <PDBx:temp>293</PDBx:temp> <PDBx:temp_esd>3</PDBx:temp_esd> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:theta_min>11</PDBx:theta_min> <PDBx:wavelength>1.54</PDBx:wavelength> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="1TOZ"> <PDBx:reflns_used>25</PDBx:reflns_used> <PDBx:temp>293</PDBx:temp> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:theta_min>25</PDBx:theta_min> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 cell_measurementCategory This property indicates that datablock has a category holder cell_measurementCategory. cell_measurementCategory This property indicates that cell_measurementCategory. has a category cell_measurement. cell_measurementItem Abstract datatype property for cell_measurement items. reference_to_cell_measurement cross-reference to cell_measurement. referenced_by_cell_measurement cross-reference from cell_measurement. cell_measurement.pressure The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). cell_measurement.pressure_esd The standard uncertainty (estimated standard deviation) of attribute pressure in category cell_measurement. cell_measurement.radiation Description of the radiation used to measure the unit-cell data. See also attribute wavelength in category cell_measurement. neutron Cu K\a synchrotron cell_measurement.reflns_used The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. cell_measurement.temp The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). cell_measurement.temp_esd The standard uncertainty (estimated standard deviation) of attribute temp in category cell_measurement. cell_measurement.theta_max The maximum theta angle of reflections used to measure the unit cell in degrees. cell_measurement.theta_min The minimum theta angle of reflections used to measure the unit cell in degrees. cell_measurement.wavelength The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH. cell_measurement.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 cell_measurement_refln Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (unpublished). <PDBx:cell_measurement_reflnCategory> <PDBx:cell_measurement_refln index_h="-2" index_k="4" index_l="1"> <PDBx:theta>8.67</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="3" index_l="2"> <PDBx:theta>9.45</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="3" index_k="0" index_l="2"> <PDBx:theta>9.46</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-3" index_k="4" index_l="1"> <PDBx:theta>8.93</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-2" index_k="1" index_l="-2"> <PDBx:theta>7.53</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="10" index_k="0" index_l="0"> <PDBx:theta>23.77</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="10" index_l="0"> <PDBx:theta>23.78</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-5" index_k="4" index_l="1"> <PDBx:theta>11.14</PDBx:theta> </PDBx:cell_measurement_refln> </PDBx:cell_measurement_reflnCategory> 0 1 1 1 1 cell_measurement_reflnCategory This property indicates that datablock has a category holder cell_measurement_reflnCategory. cell_measurement_reflnCategory This property indicates that cell_measurement_reflnCategory. has a category cell_measurement_refln. cell_measurement_reflnItem Abstract datatype property for cell_measurement_refln items. reference_to_cell_measurement_refln cross-reference to cell_measurement_refln. referenced_by_cell_measurement_refln cross-reference from cell_measurement_refln. cell_measurement_refln.theta Theta angle for a reflection used for measurement of the unit cell in degrees. cell_measurement_refln.index_h Miller index h of a reflection used for measurement of the unit cell. cell_measurement_refln.index_k Miller index k of a reflection used for measurement of the unit cell. cell_measurement_refln.index_l Miller index l of a reflection used for measurement of the unit cell. 0 chem_comp Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_compCategory> <PDBx:chem_comp id="phe"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>phenylalanine</PDBx:name> </PDBx:chem_comp> <PDBx:chem_comp id="val"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>alanine</PDBx:name> </PDBx:chem_comp> </PDBx:chem_compCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 chem_compCategory This property indicates that datablock has a category holder chem_compCategory. chem_compCategory This property indicates that chem_compCategory. has a category chem_comp. chem_compItem Abstract datatype property for chem_comp items. reference_to_chem_comp cross-reference to chem_comp. referenced_by_chem_comp cross-reference from chem_comp. chem_comp.formula The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S chem_comp.formula_weight Formula mass in daltons of the chemical component. chem_comp.model_details A description of special aspects of the generation of the coordinates for the model of the component. geometry idealized but not minimized chem_comp.model_erf A pointer to an external reference file from which the atomic description of the component is taken. chem_comp.model_source The source of the coordinates for the model of the component. CSD entry ABCDEF built using Quanta/Charmm chem_comp.mon_nstd_class A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer. iodinated base phosphorylated amino acid brominated base modified amino acid glycosylated amino acid chem_comp.mon_nstd_details A description of special details of a nonstandard monomer. no n yes y 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and attribute mon_nstd_details in category chem_comp data items. chem_comp.mon_nstd_parent The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. tyrosine cytosine chem_comp.mon_nstd_parent_comp_id The identifier for the parent component of the nonstandard component. May be be a comma separated list if this component is derived from multiple components. Items in this indirectly point to attribute id in category chem_comp in the CHEM_COMP category. chem_comp.name The full name of the component. alanine valine adenine cytosine chem_comp.number_atoms_all The total number of atoms in the component. chem_comp.number_atoms_nh The number of non-hydrogen atoms in the component. chem_comp.one_letter_code For standard polymer components, the one-letter code for the component. For non-standard polymer components, the one-letter code for parent component if this exists; otherwise, the one-letter code should be given as 'X'. Components that derived from multiple parents components are described by a sequence of one-letter-codes. alanine or adenine A ambiguous asparagine/aspartic acid B arginine R asparagine N aspartic acid D cysteine or cystine or cytosine C glutamine Q glutamic acid E ambiguous glutamine/glutamic acid Z glycine or guanine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P serine S threonine or thymine T tryptophan W tyrosine Y valine V uracil U water O other X chem_comp.pdbx_ambiguous_flag A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous. Software tools may not be able to process this component definition. chem_comp.pdbx_casnum Chemical Abstract Service identifier. chem_comp.pdbx_class_1 Internal classifier used to organize ligand dictionary (broad chemical class). HETEROCYCLIC AROMATIC COMPOUNDS chem_comp.pdbx_class_2 Internal classifier used to organize ligand dictionary (notable chemical features). COMPOUNDS WITH THIAZOLIDINE solvent organic ligand inorganic ligand organometalic ligand metal cation A type classification of this chemical component. chem_comp.pdbx_component_no A serial number used by PDB in the FORMUL record. 3 chem_comp.pdbx_formal_charge The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams. chem_comp.pdbx_ideal_coordinates_details This data item identifies the source of the ideal coordinates in the component definition. Y N This data item identifies if ideal coordinates are missing in this definition. chem_comp.pdbx_initial_date Date component was added to database. chem_comp.pdbx_model_coordinates_db_code This data item identifies the PDB database code from which the heavy atom model coordinates were obtained. chem_comp.pdbx_model_coordinates_details This data item provides additional details about the model coordinates in the component definition. Y N This data item identifies if model coordinates are missing in this definition. chem_comp.pdbx_modification_details For nonstandard components a text description of modification of the parent component. ATP chem_comp.pdbx_modified_date Date component was last modified. chem_comp.pdbx_nscnum NSC identifier for component. chem_comp.pdbx_number_subcomponents The number of subcomponents represented in this component. Y N A flag to indicate if the CCD can be used to represent a protein modification. Y PDBE EBI PDBJ PDBC RCSB This data item identifies the deposition site that processed this chemical component defintion. REL HOLD HPUB OBS DEL REF_ONLY This data item holds the current release status for the component. chem_comp.pdbx_replaced_by Identifies the attribute id in category chem_comp of the component that has replaced this component. q11 tvx chem_comp.pdbx_replaces Identifies the attribute id's in category chem_comp of the components which have been replaced by this component. Multiple id codes should be separated by commas. q11 tvx,atv chem_comp.pdbx_reserved_name Previous chemical name used for this component if a name correction has been made. chem_comp.pdbx_smiles SMILES code for component. chem_comp.pdbx_status Release status of component chem_comp.pdbx_subcomponent_list The list of subcomponents contained in this component. TSM DPH HIS CHF EMR chem_comp.pdbx_synonyms Synonym list for the component. ATP chem_comp.pdbx_type A preliminary classification used by PDB. chem_comp.pdbx_type_modified Modification flag. chem_comp.three_letter_code For standard polymer components, the common three-letter code for the component. Non-standard polymer components and non-polymer components are also assigned three-letter-codes. For ambiguous polymer components three-letter code should be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'. Ambiguous non-polymer components are assigned the code 'UNL'. alanine ALA arginine ARG asparagine ASN aspartic acid ASP ambiguous asparagine/aspartic acid ASX cysteine CYS glutamine GLN glutamic acid GLU glycine GLY ambiguous glutamine/glutamic acid GLX histidine HIS isoleucine ILE leucine LEU lysine LYS methionine MET phenylalanine PHE proline PRO serine SER threonine THR tryptophan TRP tyrosine TYR valine VAL 1-methyladenosine 1MA 5-methylcytosine 5MC 2(prime)-O-methylcytodine OMC 1-methylguanosine 1MG N(2)-methylguanosine 2MG N(2)-dimethylguanosine M2G 7-methylguanosine 7MG 2(prime)-O-methylguanosine 0MG dihydrouridine H2U ribosylthymidine 5MU pseudouridine PSU acetic acid ACE formic acid FOR water HOH other UNK D-peptide linking L-peptide linking D-peptide NH3 amino terminus L-peptide NH3 amino terminus D-peptide COOH carboxy terminus L-peptide COOH carboxy terminus DNA linking RNA linking L-RNA linking L-DNA linking DNA OH 5 prime terminus RNA OH 5 prime terminus DNA OH 3 prime terminus RNA OH 3 prime terminus D-saccharide, beta linking D-saccharide, alpha linking L-saccharide, beta linking L-saccharide, alpha linking L-saccharide D-saccharide saccharide non-polymer peptide linking peptide-like L-gamma-peptide, C-delta linking D-gamma-peptide, C-delta linking L-beta-peptide, C-gamma linking D-beta-peptide, C-gamma linking other For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. chem_comp.id The value of attribute id in category chem_comp must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. ALA VAL DG C 0 chem_comp_angle Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_angleCategory> <PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="PHE"> <PDBx:value_angle>110.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="CB" comp_id="PHE"> <PDBx:value_angle>110.1</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="CB" comp_id="PHE"> <PDBx:value_angle>110.3</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="HA" comp_id="PHE"> <PDBx:value_angle>108.3</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="PHE"> <PDBx:value_angle>118.4</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="OXT" comp_id="PHE"> <PDBx:value_angle>117.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG" comp_id="PHE"> <PDBx:value_angle>114.0</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="O" atom_id_2="C" atom_id_3="OXT" comp_id="PHE"> <PDBx:value_angle>123.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1" comp_id="PHE"> <PDBx:value_angle>120.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2" comp_id="PHE"> <PDBx:value_angle>120.5</PDBx:value_angle> </PDBx:chem_comp_angle> </PDBx:chem_comp_angleCategory> 0 1 0 1 0 1 0 1 1 1 1 1 chem_comp_angleCategory This property indicates that datablock has a category holder chem_comp_angleCategory. chem_comp_angleCategory This property indicates that chem_comp_angleCategory. has a category chem_comp_angle. chem_comp_angleItem Abstract datatype property for chem_comp_angle items. reference_to_chem_comp_angle cross-reference to chem_comp_angle. referenced_by_chem_comp_angle cross-reference from chem_comp_angle. chem_comp_angle.value_angle The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. chem_comp_angle.value_angle_esd The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_comp_angle. chem_comp_angle.value_dist The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. chem_comp_angle.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. chem_comp_angle.atom_id_1 The ID of the first of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_angle.atom_id_2 The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_angle.atom_id_3 The ID of the third of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_angle.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_atom Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_atomCategory> <PDBx:chem_comp_atom atom_id="N" comp_id="phe"> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CA" comp_id="phe"> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="C" comp_id="phe"> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="O" comp_id="phe"> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CB" comp_id="phe"> <PDBx:model_Cartn_x>0.00662</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-1.03603</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.11081</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG" comp_id="phe"> <PDBx:model_Cartn_x>0.03254</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.49711</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.50951</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CD1" comp_id="phe"> <PDBx:model_Cartn_x>-1.15813</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.12084</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.13467</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CE1" comp_id="phe"> <PDBx:model_Cartn_x>-1.15720</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.38038</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.42732</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CZ" comp_id="phe"> <PDBx:model_Cartn_x>0.05385</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.51332</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>5.11032</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CE2" comp_id="phe"> <PDBx:model_Cartn_x>1.26137</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.11613</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.50975</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CD2" comp_id="phe"> <PDBx:model_Cartn_x>1.23668</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.38351</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.20288</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="N" comp_id="val"> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CA" comp_id="val"> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="C" comp_id="val"> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="O" comp_id="val"> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CB" comp_id="val"> <PDBx:model_Cartn_x>0.05260</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.99339</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.17429</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG1" comp_id="val"> <PDBx:model_Cartn_x>-0.13288</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.31545</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.52668</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG2" comp_id="val"> <PDBx:model_Cartn_x>-0.94265</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-2.12930</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.99811</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> </PDBx:chem_comp_atomCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 chem_comp_atomCategory This property indicates that datablock has a category holder chem_comp_atomCategory. chem_comp_atomCategory This property indicates that chem_comp_atomCategory. has a category chem_comp_atom. chem_comp_atomItem Abstract datatype property for chem_comp_atom items. reference_to_chem_comp_atom cross-reference to chem_comp_atom. referenced_by_chem_comp_atom cross-reference from chem_comp_atom. chem_comp_atom.alt_atom_id An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. chem_comp_atom.charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 chem_comp_atom.model_Cartn_x The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. chem_comp_atom.model_Cartn_x_esd The standard uncertainty (estimated standard deviation) of attribute model_Cartn_x in category chem_comp_atom. chem_comp_atom.model_Cartn_y The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. chem_comp_atom.model_Cartn_y_esd The standard uncertainty (estimated standard deviation) of attribute model_Cartn_y in category chem_comp_atom. chem_comp_atom.model_Cartn_z The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. chem_comp_atom.model_Cartn_z_esd The standard uncertainty (estimated standard deviation) of attribute model_Cartn_z in category chem_comp_atom. chem_comp_atom.partial_charge The partial charge assigned to this atom. chem_comp_atom.pdbx_align Atom name alignment offset in PDB atom field. chem_comp_atom.pdbx_alt_atom_id An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. chem_comp_atom.pdbx_alt_comp_id An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. Y N A flag indicating an aromatic atom. Y N A flag indicating the backbone atoms in polypeptide units. Y N A flag indicating the C-terminal group atoms in polypeptide units. chem_comp_atom.pdbx_component_atom_id The atom identifier in the subcomponent where a larger component has been divided subcomponents. CB CA CG chem_comp_atom.pdbx_component_comp_id The component identifier for the subcomponent where a larger component has been divided subcomponents. HIS PRO chem_comp_atom.pdbx_component_entity_id A reference to entity identifier in data category pdbx_chem_comp_subcomponent_entity_list. chem_comp_atom.pdbx_component_id A reference to attribute component_id in category pdbx_reference_entity_list Y N A flag indicating a leaving atom. chem_comp_atom.pdbx_model_Cartn_x_ideal An alternative x component of the coordinates for this atom in this component specified as orthogonal angstroms. chem_comp_atom.pdbx_model_Cartn_y_ideal An alternative y component of the coordinates for this atom in this component specified as orthogonal angstroms. chem_comp_atom.pdbx_model_Cartn_z_ideal An alternative z component of the coordinates for this atom in this component specified as orthogonal angstroms. Y N A flag indicating the N-terminal group atoms in polypeptide units. chem_comp_atom.pdbx_ordinal Ordinal index for the component atom list. polymer non-polymer Is the atom in a polymer or non-polymer subcomponent in the BIRD definition. chem_comp_atom.pdbx_ref_id A reference to attribute ref_entity_id in category pdbx_reference_entity_list chem_comp_atom.pdbx_residue_numbering Preferred residue numbering in the BIRD definition. R S N The chiral configuration of the atom that is a chiral center. chem_comp_atom.pdbx_stnd_atom_id A standard identifier for the atom. This data item is used when IUPAC/IUBMB nomenclature exists for labeling atoms. main side base phos sugar none This data item assigns the atom to a substructure of the component, if appropriate. chem_comp_atom.type_symbol The code used to identify the atom species representing this atom type. Normally this code is the element symbol. C N O chem_comp_atom.atom_id The value of attribute atom_id in category chem_comp_atom must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. chem_comp_atom.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_bond Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_bondCategory> <PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="phe"> <PDBx:value_order>doub</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CG" atom_id_2="CD1" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CD1" atom_id_2="CE1" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CE1" atom_id_2="CZ" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CZ" atom_id_2="CE2" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CE2" atom_id_2="CD2" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CD2" atom_id_2="CG" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="val"> <PDBx:value_order>doub</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG1" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG2" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> </PDBx:chem_comp_bondCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 chem_comp_bondCategory This property indicates that datablock has a category holder chem_comp_bondCategory. chem_comp_bondCategory This property indicates that chem_comp_bondCategory. has a category chem_comp_bond. chem_comp_bondItem Abstract datatype property for chem_comp_bond items. reference_to_chem_comp_bond cross-reference to chem_comp_bond. referenced_by_chem_comp_bond cross-reference from chem_comp_bond. Y N A flag indicating an aromatic bond. chem_comp_bond.pdbx_ordinal Ordinal index for the component bond list. E Z N Stereochemical configuration across a double bond. chem_comp_bond.value_dist The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. chem_comp_bond.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_bond. sing doub trip quad arom poly delo pi The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. chem_comp_bond.atom_id_1 The ID of the first of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_bond.atom_id_2 The ID of the second of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_bond.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_chir Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_chirCategory> <PDBx:chem_comp_chir comp_id="phe" id="phe1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> <PDBx:chem_comp_chir comp_id="val" id="val1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> </PDBx:chem_comp_chirCategory> 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 chem_comp_chirCategory This property indicates that datablock has a category holder chem_comp_chirCategory. chem_comp_chirCategory This property indicates that chem_comp_chirCategory. has a category chem_comp_chir. chem_comp_chirItem Abstract datatype property for chem_comp_chir items. reference_to_chem_comp_chir cross-reference to chem_comp_chir. referenced_by_chem_comp_chir cross-reference from chem_comp_chir. R S The chiral configuration of the atom that is a chiral centre. chem_comp_chir.atom_id The ID of the atom that is a chiral centre. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_chir.number_atoms_all The total number of atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. chem_comp_chir.number_atoms_nh The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. sign nosign A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. chem_comp_chir.volume_three The chiral volume, V~c~, for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product chem_comp_chir.volume_three_esd The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_comp_chir. chem_comp_chir.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_chir.id The value of attribute id in category chem_comp_chir must uniquely identify a record in the CHEM_COMP_CHIR list. 0 chem_comp_chir_atom Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_chir_atomCategory> <PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> </PDBx:chem_comp_chir_atomCategory> 0 1 1 1 1 chem_comp_chir_atomCategory This property indicates that datablock has a category holder chem_comp_chir_atomCategory. chem_comp_chir_atomCategory This property indicates that chem_comp_chir_atomCategory. has a category chem_comp_chir_atom. chem_comp_chir_atomItem Abstract datatype property for chem_comp_chir_atom items. reference_to_chem_comp_chir_atom cross-reference to chem_comp_chir_atom. referenced_by_chem_comp_chir_atom cross-reference from chem_comp_chir_atom. chem_comp_chir_atom.dev The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. chem_comp_chir_atom.atom_id The ID of an atom bonded to the chiral atom. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_chir_atom.chir_id This data item is a pointer to attribute id in category chem_comp_chir in the CHEM_COMP_CHIR category. chem_comp_chir_atom.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_link Data items in the CHEM_COMP_LINK category give details about the links between chemical components. 0 1 1 1 1 1 1 chem_comp_linkCategory This property indicates that datablock has a category holder chem_comp_linkCategory. chem_comp_linkCategory This property indicates that chem_comp_linkCategory. has a category chem_comp_link. chem_comp_linkItem Abstract datatype property for chem_comp_link items. reference_to_chem_comp_link cross-reference to chem_comp_link. referenced_by_chem_comp_link cross-reference from chem_comp_link. chem_comp_link.details A description of special aspects of a link between chemical components in the structure. chem_comp_link.type_comp_1 The type of the first of the two components joined by the link. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. chem_comp_link.type_comp_2 The type of the second of the two components joined by the link. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. chem_comp_link.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_comp_plane Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_planeCategory> <PDBx:chem_comp_plane comp_id="phe" id="phe1"></PDBx:chem_comp_plane> </PDBx:chem_comp_planeCategory> 0 1 0 1 1 1 chem_comp_planeCategory This property indicates that datablock has a category holder chem_comp_planeCategory. chem_comp_planeCategory This property indicates that chem_comp_planeCategory. has a category chem_comp_plane. chem_comp_planeItem Abstract datatype property for chem_comp_plane items. reference_to_chem_comp_plane cross-reference to chem_comp_plane. referenced_by_chem_comp_plane cross-reference from chem_comp_plane. chem_comp_plane.number_atoms_all The total number of atoms in the plane. chem_comp_plane.number_atoms_nh The number of non-hydrogen atoms in the plane. chem_comp_plane.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_plane.id The value of attribute id in category chem_comp_plane must uniquely identify a record in the CHEM_COMP_PLANE list. 0 chem_comp_plane_atom Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_plane_atomCategory> <PDBx:chem_comp_plane_atom atom_id="CB" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CG" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CD1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CE1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CZ" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CE2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CD2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> </PDBx:chem_comp_plane_atomCategory> 0 1 1 1 1 chem_comp_plane_atomCategory This property indicates that datablock has a category holder chem_comp_plane_atomCategory. chem_comp_plane_atomCategory This property indicates that chem_comp_plane_atomCategory. has a category chem_comp_plane_atom. chem_comp_plane_atomItem Abstract datatype property for chem_comp_plane_atom items. reference_to_chem_comp_plane_atom cross-reference to chem_comp_plane_atom. referenced_by_chem_comp_plane_atom cross-reference from chem_comp_plane_atom. chem_comp_plane_atom.dist_esd This data item is the standard deviation of the out-of-plane distance for this atom. chem_comp_plane_atom.atom_id The ID of an atom involved in the plane. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_plane_atom.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_plane_atom.plane_id This data item is a pointer to attribute id in category chem_comp_plane in the CHEM_COMP_PLANE category. 0 chem_comp_tor Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_torCategory> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi1"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>CA</PDBx:atom_id_2> <PDBx:atom_id_3>CB</PDBx:atom_id_3> <PDBx:atom_id_4>CG</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi2"> <PDBx:atom_id_1>CA</PDBx:atom_id_1> <PDBx:atom_id_2>CB</PDBx:atom_id_2> <PDBx:atom_id_3>CG</PDBx:atom_id_3> <PDBx:atom_id_4>CD1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring1"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD1</PDBx:atom_id_3> <PDBx:atom_id_4>CE1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring2"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD2</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring3"> <PDBx:atom_id_1>CG</PDBx:atom_id_1> <PDBx:atom_id_2>CD1</PDBx:atom_id_2> <PDBx:atom_id_3>CE1</PDBx:atom_id_3> <PDBx:atom_id_4>CZ</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring4"> <PDBx:atom_id_1>CD1</PDBx:atom_id_1> <PDBx:atom_id_2>CE1</PDBx:atom_id_2> <PDBx:atom_id_3>CZ</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring5"> <PDBx:atom_id_1>CE1</PDBx:atom_id_1> <PDBx:atom_id_2>CZ</PDBx:atom_id_2> <PDBx:atom_id_3>CE2</PDBx:atom_id_3> <PDBx:atom_id_4>CD2</PDBx:atom_id_4> </PDBx:chem_comp_tor> </PDBx:chem_comp_torCategory> 1 1 1 1 1 1 1 1 1 1 chem_comp_torCategory This property indicates that datablock has a category holder chem_comp_torCategory. chem_comp_torCategory This property indicates that chem_comp_torCategory. has a category chem_comp_tor. chem_comp_torItem Abstract datatype property for chem_comp_tor items. reference_to_chem_comp_tor cross-reference to chem_comp_tor. referenced_by_chem_comp_tor cross-reference from chem_comp_tor. chem_comp_tor.atom_id_1 The ID of the first of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.atom_id_2 The ID of the second of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.atom_id_3 The ID of the third of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.atom_id_4 The ID of the fourth of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_tor.id The value of attribute id in category chem_comp_tor must uniquely identify a record in the CHEM_COMP_TOR list. 0 chem_comp_tor_value Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_tor_valueCategory> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>-60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.72</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <PDBx:angle>90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <PDBx:angle>-90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring1"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring2"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring3"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring4"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring5"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> </PDBx:chem_comp_tor_valueCategory> 1 1 1 1 0 1 0 1 1 1 chem_comp_tor_valueCategory This property indicates that datablock has a category holder chem_comp_tor_valueCategory. chem_comp_tor_valueCategory This property indicates that chem_comp_tor_valueCategory. has a category chem_comp_tor_value. chem_comp_tor_valueItem Abstract datatype property for chem_comp_tor_value items. reference_to_chem_comp_tor_value cross-reference to chem_comp_tor_value. referenced_by_chem_comp_tor_value cross-reference from chem_comp_tor_value. chem_comp_tor_value.angle A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. chem_comp_tor_value.angle_esd The standard uncertainty (estimated standard deviation) of attribute angle in category chem_comp_tor_value. chem_comp_tor_value.dist A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. chem_comp_tor_value.dist_esd The standard uncertainty (estimated standard deviation) of attribute dist in category chem_comp_tor_value. chem_comp_tor_value.comp_id This data item is a pointer to attribute comp_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor_value.tor_id This data item is a pointer to attribute id in category chem_comp_tor in the CHEM_COMP_TOR category. 0 chem_link Data items in the CHEM_LINK category give details about the links between chemical components. 0 1 1 chem_linkCategory This property indicates that datablock has a category holder chem_linkCategory. chem_linkCategory This property indicates that chem_linkCategory. has a category chem_link. chem_linkItem Abstract datatype property for chem_link items. reference_to_chem_link cross-reference to chem_link. referenced_by_chem_link cross-reference from chem_link. chem_link.details A description of special aspects of a link between chemical components in the structure. chem_link.id The value of attribute id in category chem_link must uniquely identify each item in the CHEM_LINK list. peptide oligosaccharide 1,4 DNA 0 chem_link_angle Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <PDBx:chem_link_angleCategory> <PDBx:chem_link_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> <PDBx:value_angle>111.2</PDBx:value_angle> <PDBx:value_angle_esd>2.8</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> <PDBx:value_angle>120.8</PDBx:value_angle> <PDBx:value_angle_esd>1.7</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>116.2</PDBx:value_angle> <PDBx:value_angle_esd>2.0</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="O" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>123.0</PDBx:value_angle> <PDBx:value_angle_esd>1.6</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="C" atom_id_2="N" atom_id_3="CA" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>121.7</PDBx:value_angle> <PDBx:value_angle_esd>1.8</PDBx:value_angle_esd> </PDBx:chem_link_angle> </PDBx:chem_link_angleCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 chem_link_angleCategory This property indicates that datablock has a category holder chem_link_angleCategory. chem_link_angleCategory This property indicates that chem_link_angleCategory. has a category chem_link_angle. chem_link_angleItem Abstract datatype property for chem_link_angle items. reference_to_chem_link_angle cross-reference to chem_link_angle. referenced_by_chem_link_angle cross-reference from chem_link_angle. 1 2 This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. chem_link_angle.value_angle The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. chem_link_angle.value_angle_esd The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_link_angle. chem_link_angle.value_dist The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. chem_link_angle.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. chem_link_angle.atom_id_1 The ID of the first of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_1_comp_id) in category chem_comp_angle. chem_link_angle.atom_id_2 The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_2_comp_id) in category chem_comp_angle. chem_link_angle.atom_id_3 The ID of the third of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_3_comp_id) in category chem_comp_angle. chem_link_angle.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_bond Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <PDBx:chem_link_bondCategory> <PDBx:chem_link_bond atom_id_1="N" atom_id_2="CA" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.458</PDBx:value_dist> <PDBx:value_dist_esd>0.019</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="CA" atom_id_2="C" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.525</PDBx:value_dist> <PDBx:value_dist_esd>0.021</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="C" atom_id_2="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:value_dist>1.329</PDBx:value_dist> <PDBx:value_dist_esd>0.014</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="C" atom_id_2="O" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.231</PDBx:value_dist> <PDBx:value_dist_esd>0.020</PDBx:value_dist_esd> </PDBx:chem_link_bond> </PDBx:chem_link_bondCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 chem_link_bondCategory This property indicates that datablock has a category holder chem_link_bondCategory. chem_link_bondCategory This property indicates that chem_link_bondCategory. has a category chem_link_bond. chem_link_bondItem Abstract datatype property for chem_link_bond items. reference_to_chem_link_bond cross-reference to chem_link_bond. referenced_by_chem_link_bond cross-reference from chem_link_bond. 1 2 This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link. chem_link_bond.value_dist The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. chem_link_bond.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_link_bond. sing doub trip quad arom poly delo pi The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. chem_link_bond.atom_id_1 The ID of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_bond.atom_id_2 The ID of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. chem_link_bond.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_chir Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 chem_link_chirCategory This property indicates that datablock has a category holder chem_link_chirCategory. chem_link_chirCategory This property indicates that chem_link_chirCategory. has a category chem_link_chir. chem_link_chirItem Abstract datatype property for chem_link_chir items. reference_to_chem_link_chir cross-reference to chem_link_chir. referenced_by_chem_link_chir cross-reference from chem_link_chir. 1 2 This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link. R S The chiral configuration of the atom that is a chiral centre. chem_link_chir.atom_id The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_chir.number_atoms_all The total number of atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. chem_link_chir.number_atoms_nh The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. sign nosign A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. chem_link_chir.volume_three The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product chem_link_chir.volume_three_esd The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_link_chir. chem_link_chir.id The value of attribute id in category chem_link_chir must uniquely identify a record in the CHEM_LINK_CHIR list. chem_link_chir.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_chir_atom Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components. 0 1 0 1 1 1 chem_link_chir_atomCategory This property indicates that datablock has a category holder chem_link_chir_atomCategory. chem_link_chir_atomCategory This property indicates that chem_link_chir_atomCategory. has a category chem_link_chir_atom. chem_link_chir_atomItem Abstract datatype property for chem_link_chir_atom items. reference_to_chem_link_chir_atom cross-reference to chem_link_chir_atom. referenced_by_chem_link_chir_atom cross-reference from chem_link_chir_atom. 1 2 This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the link. chem_link_chir_atom.dev The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. chem_link_chir_atom.atom_id The ID of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_chir_atom.chir_id This data item is a pointer to attribute id in category chem_link_chir in the CHEM_LINK_CHIR category. 0 chem_link_plane Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. 0 1 0 1 1 1 chem_link_planeCategory This property indicates that datablock has a category holder chem_link_planeCategory. chem_link_planeCategory This property indicates that chem_link_planeCategory. has a category chem_link_plane. chem_link_planeItem Abstract datatype property for chem_link_plane items. reference_to_chem_link_plane cross-reference to chem_link_plane. referenced_by_chem_link_plane cross-reference from chem_link_plane. chem_link_plane.number_atoms_all The total number of atoms in the plane. chem_link_plane.number_atoms_nh The number of non-hydrogen atoms in the plane. chem_link_plane.id The value of attribute id in category chem_link_plane must uniquely identify a record in the CHEM_LINK_PLANE list. chem_link_plane.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_plane_atom Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components. 0 1 1 1 chem_link_plane_atomCategory This property indicates that datablock has a category holder chem_link_plane_atomCategory. chem_link_plane_atomCategory This property indicates that chem_link_plane_atomCategory. has a category chem_link_plane_atom. chem_link_plane_atomItem Abstract datatype property for chem_link_plane_atom items. reference_to_chem_link_plane_atom cross-reference to chem_link_plane_atom. referenced_by_chem_link_plane_atom cross-reference from chem_link_plane_atom. 1 2 This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the link. chem_link_plane_atom.atom_id The ID of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_plane_atom.plane_id This data item is a pointer to attribute id in category chem_link_plane in the CHEM_LINK_PLANE category. 0 chem_link_tor Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 chem_link_torCategory This property indicates that datablock has a category holder chem_link_torCategory. chem_link_torCategory This property indicates that chem_link_torCategory. has a category chem_link_tor. chem_link_torItem Abstract datatype property for chem_link_tor items. reference_to_chem_link_tor cross-reference to chem_link_tor. referenced_by_chem_link_tor cross-reference from chem_link_tor. 1 2 This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link. chem_link_tor.atom_id_1 The ID of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.atom_id_2 The ID of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.atom_id_3 The ID of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.atom_id_4 The ID of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.id The value of attribute id in category chem_link_tor must uniquely identify a record in the CHEM_LINK_TOR list. chem_link_tor.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_tor_value Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. 1 1 1 1 0 1 0 1 1 chem_link_tor_valueCategory This property indicates that datablock has a category holder chem_link_tor_valueCategory. chem_link_tor_valueCategory This property indicates that chem_link_tor_valueCategory. has a category chem_link_tor_value. chem_link_tor_valueItem Abstract datatype property for chem_link_tor_value items. reference_to_chem_link_tor_value cross-reference to chem_link_tor_value. referenced_by_chem_link_tor_value cross-reference from chem_link_tor_value. chem_link_tor_value.angle A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. chem_link_tor_value.angle_esd The standard uncertainty (estimated standard deviation) of attribute angle in category chem_link_tor_value. chem_link_tor_value.dist A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. chem_link_tor_value.dist_esd The standard uncertainty (estimated standard deviation) of attribute dist in category chem_link_tor_value. chem_link_tor_value.tor_id This data item is a pointer to attribute id in category chem_link_tor in the CHEM_LINK_TOR category. 0 chemical Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. <PDBx:chemicalCategory> <PDBx:chemical entry_id="9597gaus"> <PDBx:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</PDBx:name_systematic> </PDBx:chemical> </PDBx:chemicalCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 chemicalCategory This property indicates that datablock has a category holder chemicalCategory. chemicalCategory This property indicates that chemicalCategory. has a category chemical. chemicalItem Abstract datatype property for chemical items. reference_to_chemical cross-reference to chemical. referenced_by_chemical cross-reference from chemical. rm ad rmad syn unk Necessary conditions for the assignment of attribute absolute_configuration in category chemical are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021) chemical.compound_source Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. From Norilsk (USSR) Extracted from the bark of Cinchona Naturalis chemical.melting_point The temperature in kelvins at which the crystalline solid changes to a liquid. chemical.melting_point_gt A temperature in kelvins above which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. attribute melting_point in category chemical should always be used in preference to these two items whenever possible. chemical.melting_point_lt A temperature in kelvins below which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. attribute melting_point in category chemical should always be used in preference to these two items whenever possible. chemical.name_common Trivial name by which the compound is commonly known. 1-bromoestradiol chemical.name_mineral Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also attribute compound_source in category chemical. chalcopyrite chemical.name_structure_type Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. perovskite sphalerite A15 chemical.name_systematic IUPAC or Chemical Abstracts full name of the compound. 1-bromoestra-1,3,5(10)-triene-3,17\b-diol chemical.optical_rotation The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent. [\a]^25^~D~ = +108 (c = 3.42, CHCl~3~) chemical.properties_biological A free-text description of the biological properties of the material. diverse biological activities including use as a laxative and strong antibacterial activity against S. aureus and weak activity against cyclooxygenase-1 (COX-1) antibiotic activity against Bacillus subtilis (ATCC 6051) but no significant activity against Candida albicans (ATCC 14053), Aspergillus flavus (NRRL 6541) and Fusarium verticillioides (NRRL 25457) weakly potent lipoxygenase nonredox inhibitor no influenza A virus sialidase inhibitory and plaque reduction activities low toxicity against Drosophila melanogaster chemical.properties_physical A free-text description of the physical properties of the material. air-sensitive moisture-sensitive hygroscopic deliquescent oxygen-sensitive photo-sensitive pyrophoric semiconductor ferromagnetic at low temperature paramagnetic and thermochromic chemical.temperature_decomposition The temperature in kelvins at which the solid decomposes. 350 chemical.temperature_decomposition_esd The estimated standard deviation of attribute temperature_decomposition in category chemical. chemical.temperature_decomposition_gt A temperature in kelvins above which the solid is known to decompose. attribute temperature_decomposition_gt in category chemical and attribute temperature_decomposition_lt in category chemical allow a range of temperatures to be given. attribute temperature_decomposition in category chemical should always be used in preference to these two items whenever possible. 350 chemical.temperature_decomposition_lt A temperature in kelvins below which the solid is known to decompose. attribute temperature_decomposition_gt in category chemical and attribute temperature_decomposition_lt in category chemical allow a range of temperatures to be given. attribute temperature_decomposition in category chemical should always be used in preference to these two items whenever possible. 350 chemical.temperature_sublimation The temperature in kelvins at which the solid sublimes. 350 chemical.temperature_sublimation_esd The estimated standard deviation of attribute temperature_sublimation in category chemical. chemical.temperature_sublimation_gt A temperature in kelvins above which the solid is known to sublime. attribute temperature_sublimation_gt in category chemical and attribute temperature_sublimation_lt in category chemical allow a range of temperatures to be given. attribute temperature_sublimation in category chemical should always be used in preference to these two items whenever possible. 350 chemical.temperature_sublimation_lt A temperature in kelvins below which the solid is known to sublime. attribute temperature_sublimation_gt in category chemical and attribute temperature_sublimation_lt in category chemical allow a range of temperatures to be given. attribute temperature_sublimation in category chemical should always be used in preference to these two items whenever possible. 350 chemical.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 chemical_conn_atom Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. <PDBx:chemical_conn_atomCategory> <PDBx:chemical_conn_atom number="1"> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="2"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="3"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.14</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="4"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.33</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="5"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="6"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="7"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="8"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="9"> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="10"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="11"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.80</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="12"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.60</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="13"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="14"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="15"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="16"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> </PDBx:chemical_conn_atomCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 chemical_conn_atomCategory This property indicates that datablock has a category holder chemical_conn_atomCategory. chemical_conn_atomCategory This property indicates that chemical_conn_atomCategory. has a category chemical_conn_atom. chemical_conn_atomItem Abstract datatype property for chemical_conn_atom items. reference_to_chemical_conn_atom cross-reference to chemical_conn_atom. referenced_by_chemical_conn_atom cross-reference from chemical_conn_atom. chemical_conn_atom.NCA The number of connected atoms excluding terminal hydrogen atoms. chemical_conn_atom.NH The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as attribute attached_hydrogens in category atom_site only if none of the hydrogen atoms appear in the ATOM_SITE list. chemical_conn_atom.charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 chemical_conn_atom.display_x The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. chemical_conn_atom.display_y The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. chemical_conn_atom.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. chemical_conn_atom.number The chemical sequence number to be associated with this atom. Within an ATOM_SITE list, this number must match one of the attribute chemical_conn_number in category atom_site values. 0 chemical_conn_bond Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. <PDBx:chemical_conn_bondCategory> <PDBx:chemical_conn_bond atom_1="4" atom_2="1"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="5" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="6" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="7" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="10" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="9"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="10"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="13" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="14" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="15" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="17" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="18" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="19" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="20" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="21" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="22" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="23" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="24" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="25" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="26" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="27" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="28" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="29" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="30" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="31" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="32" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> </PDBx:chemical_conn_bondCategory> 0 1 1 1 chemical_conn_bondCategory This property indicates that datablock has a category holder chemical_conn_bondCategory. chemical_conn_bondCategory This property indicates that chemical_conn_bondCategory. has a category chemical_conn_bond. chemical_conn_bondItem Abstract datatype property for chemical_conn_bond items. reference_to_chemical_conn_bond cross-reference to chemical_conn_bond. referenced_by_chemical_conn_bond cross-reference from chemical_conn_bond. sing doub trip quad arom poly delo pi The chemical bond type associated with the connection between the two sites attribute atom_1 in category chemical_conn_bond and attribute atom_2 in category chemical_conn_bond. chemical_conn_bond.atom_1 This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. chemical_conn_bond.atom_2 This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. 0 chemical_formula Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and attribute sum in category chemical_formula. For the data item attribute moiety in category chemical_formula, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see attribute moiety). in category chemical_formula (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for attribute moiety in category chemical_formula formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in attribute structural in category chemical_formula, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:chemical_formulaCategory> <PDBx:chemical_formula entry_id="TOZ"> <PDBx:moiety>C18 H25 N O3</PDBx:moiety> <PDBx:sum>C18 H25 N O3</PDBx:sum> <PDBx:weight>303.40</PDBx:weight> </PDBx:chemical_formula> </PDBx:chemical_formulaCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 chemical_formulaCategory This property indicates that datablock has a category holder chemical_formulaCategory. chemical_formulaCategory This property indicates that chemical_formulaCategory. has a category chemical_formula. chemical_formulaItem Abstract datatype property for chemical_formula items. reference_to_chemical_formula cross-reference to chemical_formula. referenced_by_chemical_formula cross-reference from chemical_formula. chemical_formula.analytical Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (estimated standard deviations). Fe2.45(2) Ni1.60(3) S4 chemical_formula.iupac Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. [Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H chemical_formula.moiety Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the CHEMICAL_FORMULA category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. C7 H4 Cl Hg N O3 S C12 H17 N4 O S 1+, C6 H2 N3 O7 1- C12 H16 N2 O6, 5(H2 O1) (Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O) chemical_formula.structural See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site data should not be included in this formula (see also attribute analytical) in category chemical_formula. Ca ((Cl O3)2 O)2 (H2 O)6 (Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2 chemical_formula.sum See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the CHEMICAL_FORMULA category description. Parentheses are not normally used. C18 H19 N7 O8 S chemical_formula.weight Formula mass in daltons. This mass should correspond to the formulae given under attribute structural, in category chemical_formula _chemical_formula.moiety or _chemical_formula.sum and, together with the Z value and cell parameters, should yield the density given as attribute density_diffrn in category exptl_crystal. chemical_formula.weight_meas Formula mass in daltons measured by a non-diffraction experiment. chemical_formula.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 citation Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:citationCategory> <PDBx:citation id="primary"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>yes</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> The publication that directly relates to this coordinate set.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>265</PDBx:journal_volume> <PDBx:page_first>14209</PDBx:page_first> <PDBx:page_last>14219</PDBx:page_last> <PDBx:title> Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.</PDBx:title> <PDBx:year>1990</PDBx:year> </PDBx:citation> <PDBx:citation id="2"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>UK</PDBx:country> <PDBx:details> Determination of the structure of the unliganded enzyme.</PDBx:details> <PDBx:journal_abbrev>Nature</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>NATUAS</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>006</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0028-0836</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>337</PDBx:journal_volume> <PDBx:page_first>615</PDBx:page_first> <PDBx:page_last>619</PDBx:page_last> <PDBx:title> Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> <PDBx:citation id="3"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> Crystallization of the unliganded enzyme.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>1919</PDBx:page_first> <PDBx:page_last>1921</PDBx:page_last> <PDBx:title> Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> <PDBx:citation id="4"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> Expression and purification of the enzyme.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>2307</PDBx:page_first> <PDBx:page_last>2312</PDBx:page_last> <PDBx:title> Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> </PDBx:citationCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 citationCategory This property indicates that datablock has a category holder citationCategory. citationCategory This property indicates that citationCategory. has a category citation. citationItem Abstract datatype property for citation items. reference_to_citation cross-reference to citation. referenced_by_citation cross-reference from citation. citation.abstract Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. citation.abstract_id_CAS The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. citation.book_id_ISBN The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. citation.book_publisher The name of the publisher of the citation; relevant for books or book chapters. John Wiley and Sons citation.book_publisher_city The location of the publisher of the citation; relevant for books or book chapters. London citation.book_title The title of the book in which the citation appeared; relevant for books or book chapters. no n yes y attribute coordinate_linkage in category citation states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. citation.country The country/region of publication; relevant for books and book chapters. citation.database_id_CSD Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. LEKKUH citation.database_id_Medline Accession number used by Medline to categorize a specific bibliographic entry. 89064067 citation.details A description of special aspects of the relationship of the contents of the data block to the literature item cited. citation relates to this precise coordinate set citation relates to earlier low-resolution structure citation relates to further refinement of structure reported in citation 2 citation.journal_abbrev Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. J. Mol. Biol. citation.journal_full Full name of the cited journal; relevant for journal articles. Journal of Molecular Biology citation.journal_id_ASTM The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. citation.journal_id_CSD The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). 0070 citation.journal_id_ISSN The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. citation.journal_issue Issue number of the journal cited; relevant for journal articles. 2 citation.journal_volume Volume number of the journal cited; relevant for journal articles. 174 citation.language Language in which the cited article is written. German citation.page_first The first page of the citation; relevant for journal articles, books and book chapters. citation.page_last The last page of the citation; relevant for journal articles, books and book chapters. citation.pdbx_database_id_DOI Document Object Identifier used by doi.org to uniquely specify bibliographic entry. 10.2345/S1384107697000225 citation.pdbx_database_id_PubMed Ascession number used by PubMed to categorize a specific bibliographic entry. 12627512 citation.pdbx_database_id_patent If citation is a patent, the accession issued by a patent office. citation.title The title of the citation; relevant for journal articles, books and book chapters. Structure of diferric duck ovotransferrin at 2.35 Angstroms resolution. Y N Flag to indicate that this citation will not be published. citation.year The year of the citation; relevant for journal articles, books and book chapters. 1984 citation.id The value of attribute id in category citation must uniquely identify a record in the CITATION list. The attribute id in category citation 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. primary 1 2 0 citation_author Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:citation_authorCategory> <PDBx:citation_author citation_id="primary" name="Fitzgerald, P.M.D." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="McKeever, B.M." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Van Middlesworth, J.F." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Springer, J.P." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Leu, C.-T." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Herber, W.K." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Dixon, R.A.F." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Darke, P.L." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Navia, M.A." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Fitzgerald, P.M.D." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="McKeever, B.M." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Leu, C.-T." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Herber, W.K." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Sigal, I.S." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Darke, P.L." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Springer, J.P." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="McKeever, B.M." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Navia, M.A." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Fitzgerald, P.M.D." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Springer, J.P." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Leu, C.-T." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Heimbach, J.C." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Herber, W.K." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Sigal, I.S." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Darke, P.L." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Darke, P.L." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Leu, C.-T." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Davis, L.J." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Heimbach, J.C." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Diehl, R.E." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Hill, W.S." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Dixon, R.A.F." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Sigal, I.S." ordinal="8"></PDBx:citation_author> </PDBx:citation_authorCategory> 0 1 1 1 1 citation_authorCategory This property indicates that datablock has a category holder citation_authorCategory. citation_authorCategory This property indicates that citation_authorCategory. has a category citation_author. citation_authorItem Abstract datatype property for citation_author items. reference_to_citation_author cross-reference to citation_author. referenced_by_citation_author cross-reference from citation_author. citation_author.identifier_ORCID The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X citation_author.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. citation_author.name Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A citation_author.ordinal This data item defines the order of the author's name in the list of authors of a citation. 0 citation_editor Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list. Example 1 - hypothetical example. <PDBx:citation_editorCategory> <PDBx:citation_editor citation_id="5" name="McKeever, B.M."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Navia, M.A."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Springer, J.P."></PDBx:citation_editor> </PDBx:citation_editorCategory> 0 1 1 1 citation_editorCategory This property indicates that datablock has a category holder citation_editorCategory. citation_editorCategory This property indicates that citation_editorCategory. has a category citation_editor. citation_editorItem Abstract datatype property for citation_editor items. reference_to_citation_editor cross-reference to citation_editor. referenced_by_citation_editor cross-reference from citation_editor. citation_editor.ordinal This data item defines the order of the editor's name in the list of editors of a citation. citation_editor.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. citation_editor.name Names of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A 0 computing Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead. Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. <PDBx:computingCategory> <PDBx:computing entry_id="1ABC"> <PDBx:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</PDBx:cell_refinement> <PDBx:data_collection>CAD-4 (Enraf-Nonius, 1989)</PDBx:data_collection> <PDBx:data_reduction>CFEO (Solans, 1978)</PDBx:data_reduction> <PDBx:molecular_graphics>ORTEPII (Johnson, 1976)</PDBx:molecular_graphics> <PDBx:publication_material>PARST (Nardelli, 1983)</PDBx:publication_material> <PDBx:structure_refinement>SHELXL93 (Sheldrick, 1993)</PDBx:structure_refinement> <PDBx:structure_solution>SHELXS86 (Sheldrick, 1990)</PDBx:structure_solution> </PDBx:computing> </PDBx:computingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 computingCategory This property indicates that datablock has a category holder computingCategory. computingCategory This property indicates that computingCategory. has a category computing. computingItem Abstract datatype property for computing items. reference_to_computing cross-reference to computing. referenced_by_computing cross-reference from computing. computing.cell_refinement Software used for cell refinement. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) computing.data_collection Software used for data collection. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) computing.data_reduction Software used for data reduction. Give the program or package name and a brief reference. DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990) computing.molecular_graphics Software used for molecular graphics. Give the program or package name and a brief reference. FRODO (Jones, 1986), ORTEP (Johnson, 1965) computing.pdbx_data_reduction_ds Program/package name for data reduction/data scaling computing.pdbx_data_reduction_ii Program/package name for data reduction/intensity integration software computing.pdbx_structure_refinement_method Program/package name for structure refinement method. computing.publication_material Software used for generating material for publication. Give the program or package name and a brief reference. computing.structure_refinement Software used for refinement of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) X-PLOR (Brunger, 1992) computing.structure_solution Software used for solution of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) computing.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 database Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs. 0 1 0 1 0 1 0 1 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 databaseCategory This property indicates that datablock has a category holder databaseCategory. databaseCategory This property indicates that databaseCategory. has a category database. databaseItem Abstract datatype property for database items. reference_to_database cross-reference to database. referenced_by_database cross-reference from database. database.CSD_history A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD). database.code_CAS The code assigned by Chemical Abstracts. database.code_CSD The code assigned by the Cambridge Structural Database. database.code_ICSD The code assigned by the Inorganic Crystal Structure Database. database.code_MDF The code assigned by the Metals Data File. database.code_NBS The code assigned by the NBS (NIST) Crystal Data Database. database.code_PDB The code assigned by the Protein Data Bank. database.code_PDF The code assigned by the Powder Diffraction File (JCPDS/ICDD). database.code_depnum_ccdc_archive Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. database.code_depnum_ccdc_fiz Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). database.code_depnum_ccdc_journal Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). database.journal_ASTM The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service. database.journal_CSD The journal code used in the Cambridge Structural Database. database.pdbx_code_NDB The code assigned by the NDB. BDL001 database.pdbx_code_PDB The code assigned by the PDB. 1BNA database.pdbx_related_codes_PDB The codes of related PDB entries. 1NK1,1NK2 database.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 database_2 Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_2Category> <PDBx:database_2 database_code="5HVP" database_id="PDB"></PDBx:database_2> </PDBx:database_2Category> 0 1 0 1 1 1 database_2Category This property indicates that datablock has a category holder database_2Category. database_2Category This property indicates that database_2Category. has a category database_2. database_2Item Abstract datatype property for database_2 items. reference_to_database_2 cross-reference to database_2. referenced_by_database_2 cross-reference from database_2. database_2.pdbx_DOI Document Object Identifier (DOI) for this entry registered with http://crossref.org. 10.2210/pdb6lu7/pdb database_2.pdbx_database_accession Extended accession code issued for for attribute database_code in category database_2 assigned by the database identified in attribute database_id in category database_2. pdb_00006lu7 database_2.database_code The code assigned by the database identified in attribute database_id in category database_2. 1ABC ABCDEF AlphaFoldDB CAS CSD EMDB ICSD ModelArchive MDF MODBASE NDB NBS PDB PDB-Dev PDF RCSB SWISS-MODEL_REPOSITORY EBI PDBE BMRB WWPDB PDB_ACC An abbreviation that identifies the database. 0 database_PDB_caveat Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. Example 1 - hypothetical example. <PDBx:database_PDB_caveatCategory> <PDBx:database_PDB_caveat id="1"> <PDBx:text> THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</PDBx:text> </PDBx:database_PDB_caveat> <PDBx:database_PDB_caveat id="2"> <PDBx:text> UNCORRECTABLE AT THIS TIME</PDBx:text> </PDBx:database_PDB_caveat> </PDBx:database_PDB_caveatCategory> 0 1 1 database_PDB_caveatCategory This property indicates that datablock has a category holder database_PDB_caveatCategory. database_PDB_caveatCategory This property indicates that database_PDB_caveatCategory. has a category database_PDB_caveat. database_PDB_caveatItem Abstract datatype property for database_PDB_caveat items. reference_to_database_PDB_caveat cross-reference to database_PDB_caveat. referenced_by_database_PDB_caveat cross-reference from database_PDB_caveat. database_PDB_caveat.text The full text of the PDB caveat record. database_PDB_caveat.id A unique identifier for the PDB caveat record. 0 database_PDB_matrix The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 database_PDB_matrixCategory This property indicates that datablock has a category holder database_PDB_matrixCategory. database_PDB_matrixCategory This property indicates that database_PDB_matrixCategory. has a category database_PDB_matrix. database_PDB_matrixItem Abstract datatype property for database_PDB_matrix items. reference_to_database_PDB_matrix cross-reference to database_PDB_matrix. referenced_by_database_PDB_matrix cross-reference from database_PDB_matrix. database_PDB_matrix.origx11 The [1][1] element of the PDB ORIGX matrix. database_PDB_matrix.origx12 The [1][2] element of the PDB ORIGX matrix. database_PDB_matrix.origx13 The [1][3] element of the PDB ORIGX matrix. database_PDB_matrix.origx21 The [2][1] element of the PDB ORIGX matrix. database_PDB_matrix.origx22 The [2][2] element of the PDB ORIGX matrix. database_PDB_matrix.origx23 The [2][3] element of the PDB ORIGX matrix. database_PDB_matrix.origx31 The [3][1] element of the PDB ORIGX matrix. database_PDB_matrix.origx32 The [3][2] element of the PDB ORIGX matrix. database_PDB_matrix.origx33 The [3][3] element of the PDB ORIGX matrix. database_PDB_matrix.origx_vector1 The [1] element of the PDB ORIGX vector. database_PDB_matrix.origx_vector2 The [2] element of the PDB ORIGX vector. database_PDB_matrix.origx_vector3 The [3] element of the PDB ORIGX vector. database_PDB_matrix.scale11 The [1][1] element of the PDB SCALE matrix. database_PDB_matrix.scale12 The [1][2] element of the PDB SCALE matrix. database_PDB_matrix.scale13 The [1][3] element of the PDB SCALE matrix. database_PDB_matrix.scale21 The [2][1] element of the PDB SCALE matrix. database_PDB_matrix.scale22 The [2][2] element of the PDB SCALE matrix. database_PDB_matrix.scale23 The [2][3] element of the PDB SCALE matrix. database_PDB_matrix.scale31 The [3][1] element of the PDB SCALE matrix. database_PDB_matrix.scale32 The [3][2] element of the PDB SCALE matrix. database_PDB_matrix.scale33 The [3][3] element of the PDB SCALE matrix. database_PDB_matrix.scale_vector1 The [1] element of the PDB SCALE vector. database_PDB_matrix.scale_vector2 The [2] element of the PDB SCALE vector. database_PDB_matrix.scale_vector3 The [3] element of the PDB SCALE vector. database_PDB_matrix.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 database_PDB_remark Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. NOTE: These remark records in this category are not uniformly annotated by the PDB and may not be consistent with nomenclature or labeling used in the entry. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_PDB_remarkCategory> <PDBx:database_PDB_remark id="3"> <PDBx:text> REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE WEIGHTS OF THE CORRESPONDING RESTRAINTS) DISTANCE RESTRAINTS (ANGSTROMS) BOND DISTANCE 0.018(0.020) ANGLE DISTANCE 0.038(0.030) PLANAR 1-4 DISTANCE 0.043(0.040) PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) SINGLE TORSION CONTACT 0.216(0.500) MULTIPLE TORSION CONTACT 0.207(0.500) POSSIBLE HYDROGEN BOND 0.245(0.500) CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) PLANAR (OMEGA) 2.6(3.0) STAGGERED 17.4(15.0) ORTHONORMAL 18.1(20.0)</PDBx:text> </PDBx:database_PDB_remark> <PDBx:database_PDB_remark id="4"> <PDBx:text> THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE CHAIN INDICATORS *A* AND *B*.</PDBx:text> </PDBx:database_PDB_remark> </PDBx:database_PDB_remarkCategory> 0 1 1 database_PDB_remarkCategory This property indicates that datablock has a category holder database_PDB_remarkCategory. database_PDB_remarkCategory This property indicates that database_PDB_remarkCategory. has a category database_PDB_remark. database_PDB_remarkItem Abstract datatype property for database_PDB_remark items. reference_to_database_PDB_remark cross-reference to database_PDB_remark. referenced_by_database_PDB_remark cross-reference from database_PDB_remark. database_PDB_remark.text The full text of the PDB remark record. database_PDB_remark.id A unique identifier for the PDB remark record. 0 database_PDB_rev Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_PDB_revCategory> <PDBx:database_PDB_rev num="1"> <PDBx:author_name>Fitzgerald, Paula M.D</PDBx:author_name> <PDBx:date>1991-10-15</PDBx:date> <PDBx:date_original>1990-04-30</PDBx:date_original> <PDBx:mod_type>0</PDBx:mod_type> <PDBx:status>full release</PDBx:status> </PDBx:database_PDB_rev> </PDBx:database_PDB_revCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 database_PDB_revCategory This property indicates that datablock has a category holder database_PDB_revCategory. database_PDB_revCategory This property indicates that database_PDB_revCategory. has a category database_PDB_rev. database_PDB_revItem Abstract datatype property for database_PDB_rev items. reference_to_database_PDB_rev cross-reference to database_PDB_rev. referenced_by_database_PDB_rev cross-reference from database_PDB_rev. database_PDB_rev.author_name The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A database_PDB_rev.date Date the PDB revision took place. Taken from the REVDAT record. database_PDB_rev.date_original Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record. 1980-08-21 0 1 2 3 4 5 A code taken from the REVDAT record classifying common types of entry revisions. database_PDB_rev.pdbx_record_revised_1 The first PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE database_PDB_rev.pdbx_record_revised_2 The second PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE database_PDB_rev.pdbx_record_revised_3 The third PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE database_PDB_rev.pdbx_record_revised_4 The fourth PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE database_PDB_rev.replaced_by The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. database_PDB_rev.replaces The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. in preparation prerelease full release obsolete The status of this revision. database_PDB_rev.num The value of attribute num in category database_PDB_rev must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order. 0 database_PDB_rev_record Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - hypothetical example. <PDBx:database_PDB_rev_recordCategory> <PDBx:database_PDB_rev_record rev_num="1" type="CONECT"> <PDBx:details> Error fix - incorrect connection between atoms 2312 and 2317</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="2" type="MATRIX"> <PDBx:details>For consistency with 1995-08-04 style-guide</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="3" type="ORIGX"> <PDBx:details>Based on new data from author</PDBx:details> </PDBx:database_PDB_rev_record> </PDBx:database_PDB_rev_recordCategory> 0 1 1 1 database_PDB_rev_recordCategory This property indicates that datablock has a category holder database_PDB_rev_recordCategory. database_PDB_rev_recordCategory This property indicates that database_PDB_rev_recordCategory. has a category database_PDB_rev_record. database_PDB_rev_recordItem Abstract datatype property for database_PDB_rev_record items. reference_to_database_PDB_rev_record cross-reference to database_PDB_rev_record. referenced_by_database_PDB_rev_record cross-reference from database_PDB_rev_record. database_PDB_rev_record.details A description of special aspects of the revision of records in this PDB entry. Based on new data from author For consistency with 1995-08-04 style-guide For consistency with structural class database_PDB_rev_record.rev_num This data item is a pointer to attribute num in category database_PDB_rev in the DATABASE_PDB_REV category. database_PDB_rev_record.type The types of records that were changed in this revision to a PDB entry. CRYST1 SCALE MTRIX ATOM HETATM 0 database_PDB_tvect The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file. 0 1 0 1 0 1 0 1 1 database_PDB_tvectCategory This property indicates that datablock has a category holder database_PDB_tvectCategory. database_PDB_tvectCategory This property indicates that database_PDB_tvectCategory. has a category database_PDB_tvect. database_PDB_tvectItem Abstract datatype property for database_PDB_tvect items. reference_to_database_PDB_tvect cross-reference to database_PDB_tvect. referenced_by_database_PDB_tvect cross-reference from database_PDB_tvect. database_PDB_tvect.details A description of special aspects of this TVECT. database_PDB_tvect.vector1 The [1] element of the PDB TVECT vector. database_PDB_tvect.vector2 The [2] element of the PDB TVECT vector. database_PDB_tvect.vector3 The [3] element of the PDB TVECT vector. database_PDB_tvect.id The value of attribute id in category database_PDB_tvect must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. 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. <PDBx:diffrnCategory> <PDBx:diffrn id="Set1"> <PDBx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</PDBx:ambient_environment> <PDBx:ambient_temp>293.0</PDBx:ambient_temp> <PDBx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</PDBx:crystal_support> <PDBx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection</PDBx:crystal_treatment> </PDBx:diffrn> </PDBx:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrnCategory> <PDBx:diffrn id="d1"> <PDBx:ambient_temp>293</PDBx:ambient_temp> <PDBx: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.</PDBx:details> </PDBx:diffrn> </PDBx:diffrnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 1 diffrnCategory This property indicates that datablock has a category holder diffrnCategory. diffrnCategory This property indicates that diffrnCategory. has a category diffrn. diffrnItem Abstract datatype property for diffrn items. reference_to_diffrn cross-reference to diffrn. referenced_by_diffrn cross-reference from diffrn. diffrn.ambient_environment The gas or liquid surrounding the sample, if not air. diffrn.ambient_pressure The mean hydrostatic pressure in kilopascals at which the intensities were measured. diffrn.ambient_pressure_esd The estimated standard deviation of attribute ambient_pressure in category diffrn. diffrn.ambient_pressure_gt The mean hydrostatic pressure in kilopascals above which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_pressure_lt The mean hydrostatic pressure in kilopascals below which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_temp The mean temperature in kelvins at which the intensities were measured. diffrn.ambient_temp_details A description of special aspects of temperature control during data collection. diffrn.ambient_temp_esd The standard uncertainty (estimated standard deviation) of attribute ambient_temp in category diffrn. diffrn.ambient_temp_gt The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_temp_lt The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. diffrn.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. diffrn.crystal_support The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop diffrn.crystal_treatment Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. equilibrated in hutch for 24 hours flash frozen in liquid nitrogen slow cooled with direct air stream diffrn.details Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. Y N Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment. Y N diffrn.id This data item uniquely identifies a set of diffraction data. 0 diffrn_attenuator Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_attenuatorCategory> <PDBx:diffrn_attenuator code="1"> <PDBx:scale>16.976</PDBx:scale> </PDBx:diffrn_attenuator> </PDBx: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_data_frame Data items in the DIFFRN_DATA_FRAME category record the details about each frame of data. The items in this category were previously in a DIFFRN_FRAME_DATA category, which is now deprecated. The items from the old category are provided as aliases but should not be used for new work. Example 1. a frame containing data from four frame elements. Each frame element has a common array configuration 'array_1' described in ARRAY_STRUCTURE and related categories. The data for each detector element are stored in four groups of binary data in the ARRAY_DATA category, linked by the array_id and binary_id. <PDBx:diffrn_data_frameCategory> <PDBx:diffrn_data_frame detector_element_id="d1_ccd_1" id="frame_1"> <PDBx:array_id>array_1</PDBx:array_id> <PDBx:binary_id>1</PDBx:binary_id> </PDBx:diffrn_data_frame> <PDBx:diffrn_data_frame detector_element_id="d1_ccd_2" id="frame_1"> <PDBx:array_id>array_1</PDBx:array_id> <PDBx:binary_id>2</PDBx:binary_id> </PDBx:diffrn_data_frame> <PDBx:diffrn_data_frame detector_element_id="d1_ccd_3" id="frame_1"> <PDBx:array_id>array_1</PDBx:array_id> <PDBx:binary_id>3</PDBx:binary_id> </PDBx:diffrn_data_frame> <PDBx:diffrn_data_frame detector_element_id="d1_ccd_4" id="frame_1"> <PDBx:array_id>array_1</PDBx:array_id> <PDBx:binary_id>4</PDBx:binary_id> </PDBx:diffrn_data_frame> </PDBx:diffrn_data_frameCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 diffrn_data_frameCategory This property indicates that datablock has a category holder diffrn_data_frameCategory. diffrn_data_frameCategory This property indicates that diffrn_data_frameCategory. has a category diffrn_data_frame. diffrn_data_frameItem Abstract datatype property for diffrn_data_frame items. reference_to_diffrn_data_frame cross-reference to diffrn_data_frame. referenced_by_diffrn_data_frame cross-reference from diffrn_data_frame. diffrn_data_frame.array_id This item is a pointer to attribute id in category array_structure in the ARRAY_STRUCTURE category. diffrn_data_frame.array_section_id This item is a pointer to attribute id in category array_structure_list_section in the ARRAY_STRUCTURE_LIST_SECTION category. diffrn_data_frame.binary_id This item is a pointer to attribute binary_id in category array_data in the ARRAY_DATA category. diffrn_data_frame.center_derived The value of attribute center_derived in category diffrn_data_frame is assumed to be 'yes', i.e. that values of attribute center_fast in category diffrn_data_frame and attribute center_slow in category diffrn_data_frame are derived from the axis settings rather than measured. diffrn_data_frame.center_fast The value of attribute center_fast in category diffrn_data_frame is the fast index axis beam centre position relative to the detector element face in the units specified in the data item attribute center_units in category diffrn_data_frame along the fast axis of the detector from the centre of the first pixel to the point at which the Z axis (which should be collinear with the beam) intersects the face of the detector, if in fact it does. At the time of the measurement the current settings of the detector positioner for the given frame are used. It is important to note that for measurements in mm, the sense of the axis is used, rather than the sign of the pixel-to-pixel increments. diffrn_data_frame.center_slow The value of attribute center_slow in category diffrn_data_frame is the slow index axis beam centre position relative to the detector element face in the units specified in the data item attribute center_units in category diffrn_data_frame along the slow axis of the detector from the centre of the first pixel to the point at which the Z axis (which should be collinear with the beam) intersects the face of the detector, if in fact it does. At the time of the measurement the current settings of the detector positioner for the given frame are used. It is important to note that the sense of the axis is used, rather than the sign of the pixel-to-pixel increments. mm pixels bins The value of attribute center_units in category diffrn_data_frame specifies the units in which the values of attribute center_fast in category diffrn_data_frame and attribute center_slow in category diffrn_data_frame are presented. The default is 'mm' for millimetres. The alternatives are 'pixels' and 'bins'. In all cases the centre distances are measured from the centre of the first pixel, i.e. in a 2x2 binning, the measuring origin is offset from the centres of the bins by one half pixel towards the first pixel. If 'bins' is specified, the data in attribute pixel_fast_bin_size, in category array_intensities attribute pixel_slow_bin_size in category array_intensities, and attribute pixel_binning_method in category array_intensities are used to define the binning scheme. diffrn_data_frame.details The value of attribute details in category diffrn_data_frame should give a description of special aspects of each frame of data. This is an appropriate location in which to record information from vendor headers as presented in those headers, but it should never be used as a substitute for providing the fully parsed information within the appropriate imgCIF/CBF categories. Normally, when a conversion from a miniCBF has been done the data from attribute header_convention in category array_data should be transferred to this data item and attribute header_convention in category array_data should be removed. Example of header information extracted from an ADSC Quantum 315 detector header by CBFlib_0.7.6. Image provided by Chris Nielsen of ADSC from a data collection at SSRL beamline 1-5. HEADER_BYTES = 512; DIM = 2; BYTE_ORDER = big_endian; TYPE = unsigned_short; SIZE1 = 3072; SIZE2 = 3072; PIXEL_SIZE = 0.102588; BIN = 2x2; DETECTOR_SN = 901; TIME = 29.945155; DISTANCE = 200.000000; PHI = 85.000000; OSC_START = 85.000000; OSC_RANGE = 1.000000; WAVELENGTH = 0.979381; BEAM_CENTER_X = 157.500000; BEAM_CENTER_Y = 157.500000; PIXEL SIZE = 0.102588; OSCILLATION RANGE = 1; EXPOSURE TIME = 29.9452; TWO THETA = 0; BEAM CENTRE = 157.5 157.5; diffrn_data_frame.detector_element_id This item is a pointer to attribute id in category diffrn_detector_element in the DIFFRN_DETECTOR_ELEMENT category. diffrn_data_frame.id The value of attribute id in category diffrn_data_frame must uniquely identify each complete frame of data. 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. <PDBx:diffrn_detectorCategory> <PDBx:diffrn_detector diffrn_id="d1"> <PDBx:detector>multiwire</PDBx:detector> <PDBx:type>Siemens</PDBx:type> </PDBx:diffrn_detector> </PDBx:diffrn_detectorCategory> 0 1 0 1 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.id The value of attribute id in category diffrn_detector must uniquely identify each detector used to collect each diffraction data set. If the value of attribute id in category diffrn_detector is not given, it is implicitly equal to the value of attribute diffrn_id in category diffrn_detector. diffrn_detector.number_of_axes The value of attribute number_of_axes in category diffrn_detector gives the number of axes of the positioner for the detector identified by attribute id. in category diffrn_detector The word 'positioner' is a general term used in instrumentation design for devices that are used to change the positions of portions of apparatus by linear translation, rotation or combinations of such motions. Axes which are used to provide a coordinate system for the face of an area detector should not be counted for this data item. The description of each axis should be provided by entries in DIFFRN_DETECTOR_AXIS. 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_detector_axis Data items in the DIFFRN_DETECTOR_AXIS category associate axes with detectors. 1 1 diffrn_detector_axisCategory This property indicates that datablock has a category holder diffrn_detector_axisCategory. diffrn_detector_axisCategory This property indicates that diffrn_detector_axisCategory. has a category diffrn_detector_axis. diffrn_detector_axisItem Abstract datatype property for diffrn_detector_axis items. reference_to_diffrn_detector_axis cross-reference to diffrn_detector_axis. referenced_by_diffrn_detector_axis cross-reference from diffrn_detector_axis. diffrn_detector_axis.axis_id This data item is a pointer to attribute id in category axis in the AXIS category. diffrn_detector_axis.detector_id This data item is a pointer to attribute id in category diffrn_detector in the DIFFRN_DETECTOR category. This item was previously named attribute id in category diffrn_detector_axis which is now a deprecated name. The old name is provided as an alias but should not be used for new work. 0 diffrn_detector_element Data items in the DIFFRN_DETECTOR_ELEMENT category record the details about spatial layout and other characteristics of each element of a detector which may have multiple elements. In most cases, giving more detailed information in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS is preferable to simply providing the centre of the detector element. Example 1. Detector d1 is composed of four CCD detector elements, each 200 mm by 200 mm, arranged in a square, in the pattern 1 2 * 3 4 Note that the beam centre is slightly displaced from each of the detector elements, just beyond the lower right corner of 1, the lower left corner of 2, the upper right corner of 3 and the upper left corner of 4. For each element, the detector face coordinate system is assumed to have the fast axis running from left to right and the slow axis running from top to bottom with the origin at the top left corner. <PDBx:diffrn_detector_elementCategory> <PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_1"> <PDBx:reference_center_fast>201.5</PDBx:reference_center_fast> <PDBx:reference_center_slow>201.5</PDBx:reference_center_slow> <PDBx:reference_center_units>mm</PDBx:reference_center_units> </PDBx:diffrn_detector_element> <PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_2"> <PDBx:reference_center_fast>-1.8</PDBx:reference_center_fast> <PDBx:reference_center_slow>201.5</PDBx:reference_center_slow> <PDBx:reference_center_units>mm</PDBx:reference_center_units> </PDBx:diffrn_detector_element> <PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_3"> <PDBx:reference_center_fast>201.6</PDBx:reference_center_fast> <PDBx:reference_center_slow>-1.4</PDBx:reference_center_slow> <PDBx:reference_center_units>mm</PDBx:reference_center_units> </PDBx:diffrn_detector_element> <PDBx:diffrn_detector_element detector_id="d1" id="d1_ccd_4"> <PDBx:reference_center_fast>-1.7</PDBx:reference_center_fast> <PDBx:reference_center_slow>-1.5</PDBx:reference_center_slow> <PDBx:reference_center_units>mm</PDBx:reference_center_units> </PDBx:diffrn_detector_element> </PDBx:diffrn_detector_elementCategory> 0 1 0 1 0 1 1 1 diffrn_detector_elementCategory This property indicates that datablock has a category holder diffrn_detector_elementCategory. diffrn_detector_elementCategory This property indicates that diffrn_detector_elementCategory. has a category diffrn_detector_element. diffrn_detector_elementItem Abstract datatype property for diffrn_detector_element items. reference_to_diffrn_detector_element cross-reference to diffrn_detector_element. referenced_by_diffrn_detector_element cross-reference from diffrn_detector_element. diffrn_detector_element.reference_center_fast The value of attribute reference_center_fast in category diffrn_detector_element is the fast index axis beam centre position relative to the detector element face in the units specified in the data item attribute reference_center_units in category diffrn_detector_element along the fast axis of the detector from the centre of the first pixel to the point at which the Z-axis (which should be collinear with the beam) intersects the face of the detector, if in fact it does. At the time of the measurement all settings of the detector positioner should be at their reference settings. If more than one reference setting has been used the value given should be representative of the beam centre as determined from the ensemble of settings. It is important to note that for measurements in mm, the sense of the axis is used, rather than the sign of the pixel-to-pixel increments. diffrn_detector_element.reference_center_slow The value of attribute reference_center_slow in category diffrn_detector_element is the slow index axis beam centre position relative to the detector element face in the units specified in the data item attribute reference_center_units in category diffrn_detector_element along the slow axis of the detector from the centre of the first pixel to the point at which the Z-axis (which should be collinear with the beam) intersects the face of the detector, if in fact it does. At the time of the measurement all settings of the detector positioner should be at their reference settings. If more than one reference setting has been used the value given should be representative of the beam centre as determined from the ensemble of settings. It is important to note that the sense of the axis is used, rather than the sign of the pixel-to-pixel increments. mm pixels bins The value of attribute reference_center_units in category diffrn_detector_element specifies the units in which the values of attribute reference_center_fast in category diffrn_detector_element and attribute reference_center_slow in category diffrn_detector_element are presented. The default is 'mm' for millimetres. The alternatives are 'pixels' and 'bins'. In all cases the centre distances are measured from the centre of the first pixel, i.e. in a 2x2 binning, the measuring origin is offset from the centres of the bins by one half pixel towards the first pixel. If 'bins' is specified, the data in attribute pixel_fast_bin_size, in category array_intensities attribute pixel_slow_bin_size in category array_intensities, and attribute pixel_binning_method in category array_intensities are used to define the binning scheme. diffrn_detector_element.detector_id This item is a pointer to attribute id in category diffrn_detector in the DIFFRN_DETECTOR category. diffrn_detector_element.id The value of attribute id in category diffrn_detector_element must uniquely identify each element of a detector. 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. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="d1"> <PDBx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</PDBx:details> <PDBx:device>3-circle camera</PDBx:device> <PDBx:device_details>none</PDBx:device_details> <PDBx:device_type>Supper model x</PDBx:device_type> <PDBx:method>omega scan</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="s1"> <PDBx:device_type>Philips PW1100/20 diffractometer</PDBx:device_type> <PDBx:method>\q/2\q</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> 0 1 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.pdbx_date The date of data measurement yyyy-mm-dd 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. <PDBx:diffrn_orient_matrixCategory> <PDBx:diffrn_orient_matrix diffrn_id="set1"> <PDBx:UB11>-0.071479</PDBx:UB11> <PDBx:UB12>0.020208</PDBx:UB12> <PDBx:UB13>0.039076</PDBx:UB13> <PDBx:UB21>0.035372</PDBx:UB21> <PDBx:UB22>0.056209</PDBx:UB22> <PDBx:UB23>0.078324</PDBx:UB23> <PDBx:UB31>-0.007470</PDBx:UB31> <PDBx:UB32>0.067854</PDBx:UB32> <PDBx:UB33>-0.017832</PDBx:UB33> <PDBx:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</PDBx:type> </PDBx:diffrn_orient_matrix> </PDBx: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. <PDBx:diffrn_orient_reflnCategory> <PDBx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <PDBx:angle_chi>-28.45</PDBx:angle_chi> <PDBx:angle_kappa>-11.32</PDBx:angle_kappa> <PDBx:angle_omega>5.33</PDBx:angle_omega> <PDBx:angle_phi>101.78</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>10.66</PDBx:angle_theta> </PDBx:diffrn_orient_refln> </PDBx: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. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:collimation>0.3 mm double pinhole</PDBx:collimation> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx: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. <PDBx:diffrn_radiation_wavelengthCategory> <PDBx:diffrn_radiation_wavelength id="1"> <PDBx:wavelength>1.54</PDBx:wavelength> <PDBx:wt>1.0</PDBx:wt> </PDBx:diffrn_radiation_wavelength> </PDBx: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. <PDBx:diffrn_reflnCategory> <PDBx:diffrn_refln diffrn_id="set1" id="1102"> <PDBx:angle_chi>32.21</PDBx:angle_chi> <PDBx:angle_kappa>20.12</PDBx:angle_kappa> <PDBx:angle_omega>11.54</PDBx:angle_omega> <PDBx:angle_phi>176.02</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>23.08</PDBx:angle_theta> <PDBx:attenuator_code>Ni.005</PDBx:attenuator_code> <PDBx:counts_bg_1>22</PDBx:counts_bg_1> <PDBx:counts_bg_2>25</PDBx:counts_bg_2> <PDBx:counts_net>3450</PDBx:counts_net> <PDBx:counts_peak>321</PDBx:counts_peak> <PDBx:counts_total>3499</PDBx:counts_total> <PDBx:detect_slit_horiz>0.04</PDBx:detect_slit_horiz> <PDBx:detect_slit_vert>0.02</PDBx:detect_slit_vert> <PDBx:elapsed_time>1.00</PDBx:elapsed_time> <PDBx:index_h>4</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>2</PDBx:index_l> <PDBx:intensity_net>202.56</PDBx:intensity_net> <PDBx:intensity_sigma>2.18</PDBx:intensity_sigma> <PDBx:scale_group_code>A24</PDBx:scale_group_code> <PDBx:scan_mode>om</PDBx:scan_mode> <PDBx:scan_mode_backgd>mo</PDBx:scan_mode_backgd> <PDBx:scan_rate>1.2</PDBx:scan_rate> <PDBx:scan_time_backgd>900.00</PDBx:scan_time_backgd> <PDBx:scan_width>1.0</PDBx:scan_width> <PDBx:sint_over_lambda>0.25426</PDBx:sint_over_lambda> <PDBx:standard_code>1</PDBx:standard_code> <PDBx:wavelength>1.54184</PDBx:wavelength> <PDBx:wavelength_id>Cu1fixed</PDBx:wavelength_id> </PDBx:diffrn_refln> </PDBx: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 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 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.frame_id Pointer to attribute frame_id in category diffrn_scan_frame in the DIFFRN_SCAN_FRAME category. 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_batch_id Pointer to attribute id in category pdbx_diffrn_batch in the PDBX_DIFFRN_BATCH category. diffrn_refln.pdbx_detector_calc_fast Detector coordinate (in pixels) along the direction of the fast changing array index (of the 2D diffraction data) for this reflection. This is often the position where the calculated reflection is predicted to occur. The fast changing array index of the 2D diffraction array is often also defined as the detector X-coordinate, while the slow changing array index is defined as the Y-coordinate. This can vary depending on the convention of the detector and the facility, especially for multi-panel detectors. diffrn_refln.pdbx_detector_calc_slow Detector coordinate (in pixels) along the direction of the slow changing array index (of the 2D diffraction data) for this reflection. This is often the position where the calculated reflection is predicted to occur. The slow changing array index of the 2D diffraction array is often also defined as the detector Y-coordinate, while the fast changing array index is defined as the X-coordinate. This can vary depending on the convention of the detector and the facility, especially for multi-panel detectors. diffrn_refln.pdbx_detector_obs_fast Detector coordinate (in pixels) along the direction of the fast changing array index (of the 2D diffraction data) as observed for this reflection. This is often the position where the reflection centroid is observed. The fast changing array index of the 2D diffraction array is often also defined as the detector X-coordinate, while the slow changing array index is defined as the Y-coordinate. This can vary depending on the convention of the detector and the facility, especially for multi-panel detectors. diffrn_refln.pdbx_detector_obs_slow Detector coordinate (in pixels) along the direction of the slow changing array index (of the 2D diffraction data) as observed for this reflection. This is often the position where the reflection centroid is observed. The slow changing array index of the 2D diffraction array is often also defined as the detector Y-coordinate, while the fast changing array index is defined as the X-coordinate. This can vary depending on the convention of the detector and the facility, especially for multi-panel detectors. 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_panel_mapping_id Pointer to attribute id in category pdbx_diffrn_detector_panel_mapping in the PDBX_DIFFRN_DETECTOR_PANEL_MAPPING category 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. <PDBx:diffrn_reflns_classCategory> <PDBx:diffrn_reflns_class code="Main"> <PDBx:av_R_eq>0.015</PDBx:av_R_eq> <PDBx:d_res_high>0.551</PDBx:d_res_high> <PDBx:d_res_low>6.136</PDBx:d_res_low> <PDBx:description>m=0; main reflections</PDBx:description> <PDBx:number>1580</PDBx:number> </PDBx:diffrn_reflns_class> <PDBx:diffrn_reflns_class code="Sat1"> <PDBx:av_R_eq>0.010</PDBx:av_R_eq> <PDBx:d_res_high>0.551</PDBx:d_res_high> <PDBx:d_res_low>6.136</PDBx:d_res_low> <PDBx:description>m=1; first-order satellites</PDBx:description> <PDBx:number>1045</PDBx:number> </PDBx:diffrn_reflns_class> </PDBx: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. <PDBx:diffrn_scale_groupCategory> <PDBx:diffrn_scale_group code="A24"> <PDBx:I_net>1.021</PDBx:I_net> </PDBx:diffrn_scale_group> </PDBx: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_scan Data items in the DIFFRN_SCAN category describe the parameters of one or more scans, relating axis positions to frames. Example 1. derived from a suggestion by R. M. Sweet. The vector of each axis is not given here, because it is provided in the AXIS category. By making _diffrn_scan_axis.scan_id and _diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category, an arbitrary number of scanning and fixed axes can be specified for a scan. In this example, three rotation axes and one translation axis at nonzero values are specified, with one axis stepping. There is no reason why more axes could not have been specified to step. Range information has been specified, but note that it can be calculated from the number of frames and the increment, so the data item _diffrn_scan_axis.angle_range could be dropped. Both the sweep data and the data for a single frame are specified. Note that the information on how the axes are stepped is given twice, once in terms of the overall averages in the value of _diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS, and precisely for the given frame in the value for _diffrn_scan_frame.integration_time and the values for DIFFRN_SCAN_FRAME_AXIS . If dose-related adjustments are made to scan times and nonlinear stepping is done, these values may differ. Therefore, in interpreting the data for a particular frame it is important to use the frame-specific data. There are three date/times in this set: *.date_start and *. date_end_estimated, both of which are mandatory, because the former is data which can be logged at the start of collection and the latter is data that can be estimated at the same time, and *.date_end which can only be logged exactly if the data collection completes normally. <PDBx:diffrn_scanCategory> <PDBx:diffrn_scan id="1"> <PDBx:date_end>2001-11-18T03:36:45</PDBx:date_end> <PDBx:date_end_estimated>2001-11-18T03:36:45</PDBx:date_end_estimated> <PDBx:date_start>2001-11-18T03:26:42</PDBx:date_start> <PDBx:frame_id_end>mad_L2_200</PDBx:frame_id_end> <PDBx:frame_id_start>mad_L2_000</PDBx:frame_id_start> <PDBx:frames>201</PDBx:frames> <PDBx:integration_time>3.0</PDBx:integration_time> </PDBx:diffrn_scan> </PDBx:diffrn_scanCategory> <PDBx:diffrn_scan_axisCategory> <PDBx:diffrn_scan_axis axis_id="omega" scan_id="1"> <PDBx:angle_increment>0.1</PDBx:angle_increment> <PDBx:angle_range>20.0</PDBx:angle_range> <PDBx:angle_start>200.0</PDBx:angle_start> <PDBx:displacement_increment xsi:nil="true" /> <PDBx:displacement_range xsi:nil="true" /> <PDBx:displacement_start xsi:nil="true" /> </PDBx:diffrn_scan_axis> <PDBx:diffrn_scan_axis axis_id="kappa" scan_id="1"> <PDBx:angle_increment>0.0</PDBx:angle_increment> <PDBx:angle_range>0.0</PDBx:angle_range> <PDBx:angle_start>-40.0</PDBx:angle_start> <PDBx:displacement_increment xsi:nil="true" /> <PDBx:displacement_range xsi:nil="true" /> <PDBx:displacement_start xsi:nil="true" /> </PDBx:diffrn_scan_axis> <PDBx:diffrn_scan_axis axis_id="phi" scan_id="1"> <PDBx:angle_increment>0.0</PDBx:angle_increment> <PDBx:angle_range>0.0</PDBx:angle_range> <PDBx:angle_start>127.5</PDBx:angle_start> <PDBx:displacement_increment xsi:nil="true" /> <PDBx:displacement_range xsi:nil="true" /> <PDBx:displacement_start xsi:nil="true" /> </PDBx:diffrn_scan_axis> <PDBx:diffrn_scan_axis axis_id="tranz" scan_id="1"> <PDBx:angle_increment xsi:nil="true" /> <PDBx:angle_range xsi:nil="true" /> <PDBx:angle_start xsi:nil="true" /> <PDBx:displacement_increment>0.0</PDBx:displacement_increment> <PDBx:displacement_range>0.0</PDBx:displacement_range> <PDBx:displacement_start>2.3</PDBx:displacement_start> </PDBx:diffrn_scan_axis> </PDBx:diffrn_scan_axisCategory> <PDBx:diffrn_scan_frameCategory> <PDBx:diffrn_scan_frame frame_id="mad_L2_018" scan_id="1"> <PDBx:date>2001-11-18T03:27:33</PDBx:date> <PDBx:frame_number>18</PDBx:frame_number> <PDBx:integration_time>3.0</PDBx:integration_time> </PDBx:diffrn_scan_frame> </PDBx:diffrn_scan_frameCategory> <PDBx:diffrn_scan_frame_axisCategory> <PDBx:diffrn_scan_frame_axis axis_id="omega" frame_id="mad_L2_018"> <PDBx:angle>201.8</PDBx:angle> <PDBx:angle_increment>0.1</PDBx:angle_increment> <PDBx:displacement xsi:nil="true" /> <PDBx:displacement_increment xsi:nil="true" /> </PDBx:diffrn_scan_frame_axis> <PDBx:diffrn_scan_frame_axis axis_id="kappa" frame_id="mad_L2_018"> <PDBx:angle>-40.0</PDBx:angle> <PDBx:angle_increment>0.0</PDBx:angle_increment> <PDBx:displacement xsi:nil="true" /> <PDBx:displacement_increment xsi:nil="true" /> </PDBx:diffrn_scan_frame_axis> <PDBx:diffrn_scan_frame_axis axis_id="phi" frame_id="mad_L2_018"> <PDBx:angle>127.5</PDBx:angle> <PDBx:angle_increment>0.0</PDBx:angle_increment> <PDBx:displacement xsi:nil="true" /> <PDBx:displacement_increment xsi:nil="true" /> </PDBx:diffrn_scan_frame_axis> <PDBx:diffrn_scan_frame_axis axis_id="tranz" frame_id="mad_L2_018"> <PDBx:angle xsi:nil="true" /> <PDBx:angle_increment xsi:nil="true" /> <PDBx:displacement>2.3</PDBx:displacement> <PDBx:displacement_increment>0.0</PDBx:displacement_increment> </PDBx:diffrn_scan_frame_axis> </PDBx:diffrn_scan_frame_axisCategory> 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 1 diffrn_scanCategory This property indicates that datablock has a category holder diffrn_scanCategory. diffrn_scanCategory This property indicates that diffrn_scanCategory. has a category diffrn_scan. diffrn_scanItem Abstract datatype property for diffrn_scan items. reference_to_diffrn_scan cross-reference to diffrn_scan. referenced_by_diffrn_scan cross-reference from diffrn_scan. diffrn_scan.date_end The date and time of the end of the scan. Note that this may be an estimate generated during the scan, before the precise time of the end of the scan is known, in which case attribute date_end_estimated in category diffrn_scan should be used instead. diffrn_scan.date_end_estimated The estimated date and time of the end of the scan. Note that this may be generated at the start or during the scan, before the precise time of the end of the scan is known. diffrn_scan.date_start The date and time of the start of the scan. diffrn_scan.frame_id_end The value of this data item is the identifier of the last frame in the scan. This item is a pointer to attribute id in category diffrn_data_frame in the DIFFRN_DATA_FRAME category. diffrn_scan.frame_id_start The value of this data item is the identifier of the first frame in the scan. This item is a pointer to attribute id in category diffrn_data_frame in the DIFFRN_DATA_FRAME category. diffrn_scan.frames The value of this data item is the number of frames in the scan. diffrn_scan.integration_time Approximate average time in seconds to integrate each step of the scan. The precise time for integration of each particular step must be provided in attribute integration_time in category diffrn_scan_frame, even if all steps have the same integration time. diffrn_scan.time_period Approximate average time in seconds between the start of each step of the scan. The precise start-to-start time increment of each particular step may be provided in attribute time_period in category diffrn_scan_frame. diffrn_scan.time_rstrt_incr Approximate average time in seconds between the end of integration of each step of the scan and the start of integration of the next step. In general, this will agree with attribute time_rstrt_incr in category diffrn_scan_frame . The sum of the values of attribute integration_time in category diffrn_scan_frame and attribute time_rstrt_incr in category diffrn_scan_frame is the time from the start of integration of one frame and the start of integration for the next frame and should equal the value of attribute time_period in category diffrn_scan_frame for this frame. If the individual frame values vary, then the value of attribute time_rstrt_incr in category diffrn_scan will be representative of the ensemble of values of attribute time_rstrt_incr in category diffrn_scan_frame (e.g. the mean). diffrn_scan.id The value of attribute id in category diffrn_scan uniquely identifies each scan. The identifier is used to tie together all the information about the scan. 0 diffrn_scan_axis Data items in the DIFFRN_SCAN_AXIS category describe the settings of axes for particular scans. Unspecified axes are assumed to be at their zero points. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 diffrn_scan_axisCategory This property indicates that datablock has a category holder diffrn_scan_axisCategory. diffrn_scan_axisCategory This property indicates that diffrn_scan_axisCategory. has a category diffrn_scan_axis. diffrn_scan_axisItem Abstract datatype property for diffrn_scan_axis items. reference_to_diffrn_scan_axis cross-reference to diffrn_scan_axis. referenced_by_diffrn_scan_axis cross-reference from diffrn_scan_axis. diffrn_scan_axis.angle_increment The increment for each step for the specified axis in degrees. In general, this will agree with attribute angle_increment in category diffrn_scan_frame_axis . The sum of the values of attribute angle in category diffrn_scan_frame_axis and attribute angle_increment in category diffrn_scan_frame_axis is the angular setting of the axis at the end of the integration time for a given frame. If the individual frame values vary, then the value of attribute angle_increment in category diffrn_scan_axis will be representative of the ensemble of values of attribute angle_increment in category diffrn_scan_frame_axis (e.g. the mean). diffrn_scan_axis.angle_range The range from the starting position for the specified axis in degrees. diffrn_scan_axis.angle_rstrt_incr The increment after each step for the specified axis in degrees. In general, this will agree with attribute angle_rstrt_incr in category diffrn_scan_frame_axis . The sum of the values of attribute angle, in category diffrn_scan_frame_axis attribute angle_increment in category diffrn_scan_frame_axis and attribute angle_rstrt_incr in category diffrn_scan_frame_axis is the angular setting of the axis at the start of the integration time for the next frame relative to a given frame and should equal attribute angle in category diffrn_scan_frame_axis for this next frame. If the individual frame values vary, then the value of attribute angle_rstrt_incr in category diffrn_scan_axis will be representative of the ensemble of values of attribute angle_rstrt_incr in category diffrn_scan_frame_axis (e.g. the mean). diffrn_scan_axis.angle_start The starting position for the specified axis in degrees. diffrn_scan_axis.displacement_increment The increment for each step for the specified axis in millimetres. In general, this will agree with attribute displacement_increment. in category diffrn_scan_frame_axis The sum of the values of attribute displacement in category diffrn_scan_frame_axis and attribute displacement_increment in category diffrn_scan_frame_axis is the angular setting of the axis at the end of the integration time for a given frame. If the individual frame values vary, then the value of attribute displacement_increment in category diffrn_scan_axis will be representative of the ensemble of values of attribute displacement_increment in category diffrn_scan_frame_axis (e.g. the mean). diffrn_scan_axis.displacement_range The range from the starting position for the specified axis in millimetres. diffrn_scan_axis.displacement_rstrt_incr The increment for each step for the specified axis in millimetres. In general, this will agree with attribute displacement_rstrt_incr. in category diffrn_scan_frame_axis The sum of the values of attribute displacement, in category diffrn_scan_frame_axis attribute displacement_increment in category diffrn_scan_frame_axis and attribute displacement_rstrt_incr in category diffrn_scan_frame_axis is the angular setting of the axis at the start of the integration time for the next frame relative to a given frame and should equal attribute displacement in category diffrn_scan_frame_axis for this next frame. If the individual frame values vary, then the value of attribute displacement_rstrt_incr in category diffrn_scan_axis will be representative of the ensemble of values of attribute displacement_rstrt_incr in category diffrn_scan_frame_axis (e.g. the mean). diffrn_scan_axis.displacement_start The starting position for the specified axis in millimetres. diffrn_scan_axis.reference_angle The setting of the specified axis in degrees against which measurements of the reference beam centre and reference detector distance should be made. In general, this will agree with attribute reference_angle. in category diffrn_scan_frame_axis If the individual frame values vary, then the value of attribute reference_angle in category diffrn_scan_axis will be representative of the ensemble of values of attribute reference_angle in category diffrn_scan_frame_axis (e.g. the mean). If not specified, the value defaults to zero. diffrn_scan_axis.reference_displacement The setting of the specified axis in millimetres against which measurements of the reference beam centre and reference detector distance should be made. In general, this will agree with attribute reference_displacement. in category diffrn_scan_frame_axis If the individual frame values vary, then the value of attribute reference_displacement in category diffrn_scan_axis will be representative of the ensemble of values of attribute reference_displacement in category diffrn_scan_frame_axis (e.g. the mean). diffrn_scan_axis.axis_id The value of this data item is the identifier of one of the axes for the scan for which settings are being specified. Multiple axes may be specified for the same value of attribute id. in category diffrn_scan This item is a pointer to attribute id in category axis in the AXIS category. diffrn_scan_axis.scan_id The value of this data item is the identifier of the scan for which axis settings are being specified. Multiple axes may be specified for the same value of attribute id. in category diffrn_scan This item is a pointer to attribute id in category diffrn_scan in the DIFFRN_SCAN category. 0 diffrn_scan_collection Data items in the DIFFRN_SCAN_COLLECTION category describe the collection strategy for each scan. This category is a preliminary version being developed as synchrotron and XFEL collection strategies evolve. Example 1 - Describing a multi-wedge raster scan. <PDBx:diffrn_scan_collectionCategory> <PDBx:diffrn_scan_collection scan_id="multi_wedge"> <PDBx:details> scan 20 micrometre beam in 100 micrometre steps on 31 by 46 alternating raster of 20 degree wedges</PDBx:details> </PDBx:diffrn_scan_collection> </PDBx:diffrn_scan_collectionCategory> 0 1 0 1 0 1 1 diffrn_scan_collectionCategory This property indicates that datablock has a category holder diffrn_scan_collectionCategory. diffrn_scan_collectionCategory This property indicates that diffrn_scan_collectionCategory. has a category diffrn_scan_collection. diffrn_scan_collectionItem Abstract datatype property for diffrn_scan_collection items. reference_to_diffrn_scan_collection cross-reference to diffrn_scan_collection. referenced_by_diffrn_scan_collection cross-reference from diffrn_scan_collection. diffrn_scan_collection.details The value of attribute details in category diffrn_scan_collection should give a description of special aspects of each collection strategy. diffrn_scan_collection.translation_width The value of attribute translation_width in category diffrn_scan_collection gives the average single step translation in micrometres in collection strategies for which this information is appropriate, e.g. 'vector'. diffrn_scan_collection.type The value of attribute type in category diffrn_scan_collection identifies the strategy used in this scan, e.g. `rotation', 'raster', 'vector', 'still', etc. The default is 'rotation'. diffrn_scan_collection.scan_id The value of attribute scan_id in category diffrn_scan_collection identifies the scan containing this frame. This item is a pointer to attribute id in category diffrn_scan in the DIFFRN_SCAN category. In the case of a single-scan dataset, the value is implicit. 0 diffrn_scan_frame Data items in the DIFFRN_SCAN_FRAME category describe the relationships of particular frames to scans. 0 1 0 1 1 1 0 1 0 1 0 1 1 1 diffrn_scan_frameCategory This property indicates that datablock has a category holder diffrn_scan_frameCategory. diffrn_scan_frameCategory This property indicates that diffrn_scan_frameCategory. has a category diffrn_scan_frame. diffrn_scan_frameItem Abstract datatype property for diffrn_scan_frame items. reference_to_diffrn_scan_frame cross-reference to diffrn_scan_frame. referenced_by_diffrn_scan_frame cross-reference from diffrn_scan_frame. diffrn_scan_frame.date The date and time of the start of the frame being scanned. diffrn_scan_frame.frame_number The value of this data item is the number of the frame within the scan, starting with 1. It is not necessarily the same as the value of attribute frame_id, in category diffrn_scan_frame but it may be. diffrn_scan_frame.integration_time The time in seconds to integrate this step of the scan. This should be the precise time of integration of each particular frame. The value of this data item should be given explicitly for each frame and not inferred from the value of attribute integration_time in category diffrn_scan. diffrn_scan_frame.polarizn_Stokes_I The quantity Ip+In+Inp, where Ip is the intensity (amplitude squared) of the electric vector in the plane of polarization, In is the intensity (amplitude squared) of the electric vector in the plane of the normal to the plane of polarization, and Inp is the intensity (amplitude squared) of the non-polarized (incoherent) electric vector. This is an average or other representative sample of the frame. This is the first of the Stokes polarization parameters, I, Q, U, V [also known as I, M, C, S; see Berry et al. (1977)]. If the absolute intensity is not known, the value 1.0 is assumed for I, and all four Stokes parameters are dimensionless. When the absolute intensity is known, all four Stokes parameters are in units of watts per square metre. Note that, if the polarized intensity Ip+In is required, (Ip+In)^2^ is the sum of Q^2^+U^2^+V^2^. Reference: Berry, H. H., Gabrielse, G. & Livingston, A. E. (1977). 'Measurement of the Stokes parameters of light', Appl. Optics, 16:12, 3200--3205. diffrn_scan_frame.time_period The time in seconds between the start of this frame and the start of the next frame, if any. If there is no next frame, a null value should be given. diffrn_scan_frame.time_rstrt_incr The time in seconds between the end of integration of this step of the scan and the start of integration of the next step. The sum of the values of attribute integration_time in category diffrn_scan_frame and attribute time_rstrt_incr in category diffrn_scan_frame is the time from the start of integration of one frame and the start of integration for the next frame and should equal the value of attribute time_period in category diffrn_scan_frame for this frame. The value of attribute time_rstrt_incr in category diffrn_scan will be representative of the ensemble of values of attribute time_rstrt_incr in category diffrn_scan_frame (e.g. the mean). If there is no next frame, a null value should be given. diffrn_scan_frame.frame_id The value of this data item is the identifier of the frame being examined. This item is a pointer to attribute id in category diffrn_data_frame in the DIFFRN_DATA_FRAME category. diffrn_scan_frame.scan_id The value of attribute scan_id in category diffrn_scan_frame identifies the scan containing this frame. This item is a pointer to attribute id in category diffrn_scan in the DIFFRN_SCAN category. 0 diffrn_scan_frame_axis Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the settings of axes for particular frames. Unspecified axes are assumed to be at their zero points. If, for any given frame, nonzero values apply for any of the data items in this category, those values should be given explicitly in this category and not simply inferred from values in DIFFRN_SCAN_AXIS. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 diffrn_scan_frame_axisCategory This property indicates that datablock has a category holder diffrn_scan_frame_axisCategory. diffrn_scan_frame_axisCategory This property indicates that diffrn_scan_frame_axisCategory. has a category diffrn_scan_frame_axis. diffrn_scan_frame_axisItem Abstract datatype property for diffrn_scan_frame_axis items. reference_to_diffrn_scan_frame_axis cross-reference to diffrn_scan_frame_axis. referenced_by_diffrn_scan_frame_axis cross-reference from diffrn_scan_frame_axis. diffrn_scan_frame_axis.angle The setting of the specified axis in degrees for this frame. This is the setting at the start of the integration time. diffrn_scan_frame_axis.angle_increment The increment for this frame for the angular setting of the specified axis in degrees. The sum of the values of attribute angle in category diffrn_scan_frame_axis and attribute angle_increment in category diffrn_scan_frame_axis is the angular setting of the axis at the end of the integration time for this frame. diffrn_scan_frame_axis.angle_rstrt_incr The increment after this frame for the angular setting of the specified axis in degrees. The sum of the values of attribute angle, in category diffrn_scan_frame_axis attribute angle_increment in category diffrn_scan_frame_axis and attribute angle_rstrt_incr in category diffrn_scan_frame_axis is the angular setting of the axis at the start of the integration time for the next frame and should equal attribute angle in category diffrn_scan_frame_axis for this next frame. diffrn_scan_frame_axis.displacement The setting of the specified axis in millimetres for this frame. This is the setting at the start of the integration time. diffrn_scan_frame_axis.displacement_increment The increment for this frame for the displacement setting of the specified axis in millimetres. The sum of the values of attribute displacement in category diffrn_scan_frame_axis and attribute displacement_increment in category diffrn_scan_frame_axis is the angular setting of the axis at the end of the integration time for this frame. diffrn_scan_frame_axis.displacement_rstrt_incr The increment for this frame for the displacement setting of the specified axis in millimetres. The sum of the values of attribute displacement, in category diffrn_scan_frame_axis attribute displacement_increment in category diffrn_scan_frame_axis and attribute displacement_rstrt_incr in category diffrn_scan_frame_axis is the angular setting of the axis at the start of the integration time for the next frame and should equal attribute displacement in category diffrn_scan_frame_axis for this next frame. diffrn_scan_frame_axis.reference_angle The setting of the specified axis in degrees against which measurements of the reference beam centre and reference detector distance should be made. This is normally the same for all frames, but the option is provided here of making changes when needed. If not provided, it is assumed to be zero. diffrn_scan_frame_axis.reference_displacement The setting of the specified axis in millimetres for this frame against which measurements of the reference beam centre and reference detector distance should be made. This is normally the same for all frames, but the option is provided here of making changes when needed. If not provided, it is assumed to be equal to attribute displacement in category diffrn_scan_frame_axis. diffrn_scan_frame_axis.axis_id The value of this data item is the identifier of one of the axes for the frame for which settings are being specified. Multiple axes may be specified for the same value of attribute frame_id. in category diffrn_scan_frame This item is a pointer to attribute id in category axis in the AXIS category. diffrn_scan_frame_axis.frame_id The value of this data item is the identifier of the frame for which axis settings are being specified. Multiple axes may be specified for the same value of attribute frame_id. in category diffrn_scan_frame This item is a pointer to attribute id in category diffrn_data_frame in the DIFFRN_DATA_FRAME category. 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. <PDBx:diffrn_sourceCategory> <PDBx:diffrn_source diffrn_id="s1"> <PDBx:current>180</PDBx:current> <PDBx:power>50</PDBx:power> <PDBx:size>8mm x 0.4 mm broad-focus</PDBx:size> <PDBx:source>rotating anode</PDBx:source> <PDBx:type>Rigaku RU-200</PDBx:type> </PDBx:diffrn_source> </PDBx: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 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_source_specific_beamline Beamline for synchrotron source. 6A2 7.2 9.5 9.6 A-1 A1 BL-6A BW6 BW7B F-1 F1 PX7.2 PX9.6 UNDULATOR W32 WIGGLER X11 X12C X25 X26-C X31 X4A X8C diffrn_source.pdbx_synchrotron_beamline Synchrotron beamline. diffrn_source.pdbx_synchrotron_site Synchrotron site. diffrn_source.pdbx_synchrotron_y_n Yes/No if synchrotron source was used or not. Y N 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]. <PDBx:diffrn_standard_reflnCategory> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>2</PDBx:index_k> <PDBx:index_l>4</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>1</PDBx:index_h> <PDBx:index_k>9</PDBx:index_k> <PDBx:index_l>1</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>10</PDBx:index_l> </PDBx:diffrn_standard_refln> </PDBx: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]. <PDBx:diffrn_standardsCategory> <PDBx:diffrn_standards diffrn_id="s1"> <PDBx:decay_>0</PDBx:decay_> <PDBx:interval_time>120</PDBx:interval_time> <PDBx:number>3</PDBx:number> </PDBx:diffrn_standards> </PDBx:diffrn_standardsCategory> 0 1 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.scale_u The standard uncertainty 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 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.entity_assembly_id Corresponding key in _em_entity_assembly category. 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_2d_projection_selection Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 <PDBx:em_2d_projection_selectionCategory> <PDBx:em_2d_projection_selection entry_id="1ABC"> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_particles>52346</PDBx:num_particles> <PDBx:software_name>EMAN2 BOXER</PDBx:software_name> </PDBx:em_2d_projection_selection> </PDBx:em_2d_projection_selectionCategory> 0 1 0 1 1 1 0 1 0 1 0 1 1 em_2d_projection_selectionCategory This property indicates that datablock has a category holder em_2d_projection_selectionCategory. em_2d_projection_selectionCategory This property indicates that em_2d_projection_selectionCategory. has a category em_2d_projection_selection. em_2d_projection_selectionItem Abstract datatype property for em_2d_projection_selection items. reference_to_em_2d_projection_selection cross-reference to em_2d_projection_selection. referenced_by_em_2d_projection_selection cross-reference from em_2d_projection_selection. em_2d_projection_selection.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_2d_projection_selection.details Any additional details used for selecting observed assemblies. negative monitor contrast facilitated particle picking em_2d_projection_selection.id unique identifier for each projection selection description em_2d_projection_selection.method The method used for selecting observed assemblies. particles picked interactively from monitor em_2d_projection_selection.num_particles The number of particles selected from the projection set of images. 840 em_2d_projection_selection.software_name The software used to select 2d projections. em_2d_projection_selection.entry_id entry id 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 <PDBx:em_3d_fittingCategory> <PDBx:em_3d_fitting entry_id="1DYL" id="1"> <PDBx: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.</PDBx:details> <PDBx:method>AUTOMATIC</PDBx:method> <PDBx:overall_b_value xsi:nil="true" /> <PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol> <PDBx:ref_space>REAL</PDBx:ref_space> <PDBx:software_name>1</PDBx:software_name> <PDBx:target_criteria>R-FACTOR</PDBx:target_criteria> </PDBx:em_3d_fitting> </PDBx:em_3d_fittingCategory> 0 1 0 1 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.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.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.software_name The software used for fitting atomic coordinates to the map. Situs, NMFF, YUP.scx, etc. 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 <PDBx:em_3d_fitting_listCategory> <PDBx:em_3d_fitting_list _3d_fitting_id="l" id="1"> <PDBx:pdb_chain_id xsi:nil="true" /> <PDBx:pdb_entry_id>1VCQ</PDBx:pdb_entry_id> </PDBx:em_3d_fitting_list> </PDBx:em_3d_fitting_listCategory> 0 1 0 1 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.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. em_3d_fitting_list.chain_residue_range The residue ranges of the initial model used in this fitting. 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 <PDBx:em_3d_reconstructionCategory> <PDBx:em_3d_reconstruction id="1"> <PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size> <PDBx:ctf_correction_method xsi:nil="true" /> <PDBx:details xsi:nil="true" /> <PDBx:entry_id>1DYL</PDBx:entry_id> <PDBx:method>CROSS-COMMON LINES</PDBx:method> <PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size> <PDBx:resolution>9</PDBx:resolution> <PDBx:resolution_method xsi:nil="true" /> </PDBx:em_3d_reconstruction> </PDBx:em_3d_reconstructionCategory> 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 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.ctf_correction_method The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. The volumes were CTF-corrected in defocus groups, with an average of approximately 999 individual images per group 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 EVEN/ODD MAPS REFINED TOTALLY INDEPENDENT (GOLD STANDARD) EVEN/ODD MAPS REFINED AGAINST THE SAME MODEL (SEMI-INDEPENDENT) Half-set refinement protocol (semi-independent or gold standard) 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 em_3d_reconstruction.software software name 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 <PDBx:em_adminCategory> <PDBx:em_admin entry_id="D_100005"> <PDBx:current_status>REL</PDBx:current_status> <PDBx:deposition_date>2008-12-01</PDBx:deposition_date> <PDBx:details xsi:nil="true" /> <PDBx:last_update>2011-05-22</PDBx:last_update> <PDBx:map_release_date>2009-12-01</PDBx:map_release_date> </PDBx:em_admin> </PDBx:em_adminCategory> 0 1 1 1 1 1 1 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 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.header_release_date date of header information release for this entry em_admin.last_update date of last update to the file em_admin.map_hold_date Date when the map is due to be released after a specific hold period. em_admin.map_release_date date of map release for this entry em_admin.obsoleted_date date that map entry was obsoleted RCSB PDBE PDBJ PDBC The site where the file was deposited. RCSB PDBE PDBJ PDBC YES NO Please indicate whether the current entry is intended to supersede a previously released entry. Please contact wwPDB annotation staff using the "Communication" page if you have any questions regarding how to answer this question. em_admin.title Title for the EMDB entry. em_admin.entry_id This data item is a pointer to attribute id in category entry. 0 em_assembly Data items in the EM_ASSEMBLY category record details about the imaged EM sample. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_assemblyCategory> <PDBx:em_assembly entry_id="1DYL" id="1"> <PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state> <PDBx:composition>virus</PDBx:composition> <PDBx:details xsi:nil="true" /> <PDBx:mol_wt_exp xsi:nil="true" /> <PDBx:mol_wt_method xsi:nil="true" /> <PDBx:mol_wt_theo xsi:nil="true" /> <PDBx:name>virus</PDBx:name> <PDBx:num_components>1</PDBx:num_components> </PDBx:em_assembly> </PDBx:em_assemblyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_assemblyCategory This property indicates that datablock has a category holder em_assemblyCategory. em_assemblyCategory This property indicates that em_assemblyCategory. has a category em_assembly. em_assemblyItem Abstract datatype property for em_assembly items. reference_to_em_assembly cross-reference to em_assembly. referenced_by_em_assembly cross-reference from em_assembly. 2D CRYSTAL 3D CRYSTAL INDIVIDUAL STRUCTURE FILAMENT ICOSAHEDRAL PARTICLE TISSUE CELL A description of the aggregation state of the assembly. em_assembly.composition The composition of the assembly. Protein/DNA complex Virus em_assembly.details Any additional details describing the imaged sample. The sample was monodisperse em_assembly.mol_wt_exp The value (in megadaltons) of the experimentally determined molecular weight of the assembly. 3.5 em_assembly.mol_wt_method The method used to determine the molecular weight. em_assembly.mol_wt_theo The value (in megadaltons) of the theoretically determined molecular weight of the assembly. 3.5 em_assembly.name The name of the assembly of observed complexes. MaB1 Fab Fragment bound to Human Rhinovirus em_assembly.num_components The number of components of the biological assembly. 3 em_assembly.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_assembly.id The value of attribute id in category em_assembly must uniquely identify a collection of observed complexes. 0 em_author_list Category to collect the authors of this entry Example 1 <PDBx:em_author_listCategory> <PDBx:em_author_list ordinal="1"> <PDBx:author>Miller, A.</PDBx:author> </PDBx:em_author_list> <PDBx:em_author_list ordinal="2"> <PDBx:author>Smith, J.T.</PDBx:author> </PDBx:em_author_list> </PDBx:em_author_listCategory> 1 1 0 1 1 em_author_listCategory This property indicates that datablock has a category holder em_author_listCategory. em_author_listCategory This property indicates that em_author_listCategory. has a category em_author_list. em_author_listItem Abstract datatype property for em_author_list items. reference_to_em_author_list cross-reference to em_author_list. referenced_by_em_author_list cross-reference from em_author_list. em_author_list.author Author of the EMDB entry in PDB format: Taylor, T.J. Taylor, D.J. em_author_list.identifier_ORCID The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X em_author_list.ordinal ID 1 corresponds to the main author of the entry 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 <PDBx:em_ctf_correctionCategory> <PDBx:em_ctf_correction id="1"> <PDBx:em_image_processing_id>1</PDBx:em_image_processing_id> <PDBx:type>PHASE FLIPPING ONLY</PDBx:type> </PDBx:em_ctf_correction> </PDBx:em_ctf_correctionCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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. YES NO Yes if CTF amplitude correction was performed em_ctf_correction.amplitude_correction_factor Amplitude correction factor used in CTF correction REAL RECIPROCAL CTF amplitude correction space MULTIPLICATION DIVISION CTF correction operation 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 YES NO Yes if Phase reversal (flipping) was performed YES NO Yes if Anisotropic phase reversal (flipping) was performed REAL RECIPROCAL CTF phase reversal correction space em_ctf_correction.type Type of CTF correction applied em_ctf_correction.id PRIMARY KEY 0 em_db_reference Category holds links to raw data sources for the entry, e.g., held by a remote server. Example 1 <PDBx:em_db_referenceCategory> <PDBx:em_db_reference id="1"> <PDBx:access_code>1ABC</PDBx:access_code> <PDBx:db_name>PDB</PDBx:db_name> </PDBx:em_db_reference> </PDBx:em_db_referenceCategory> 1 1 1 1 0 1 0 1 1 em_db_referenceCategory This property indicates that datablock has a category holder em_db_referenceCategory. em_db_referenceCategory This property indicates that em_db_referenceCategory. has a category em_db_reference. em_db_referenceItem Abstract datatype property for em_db_reference items. reference_to_em_db_reference cross-reference to em_db_reference. referenced_by_em_db_reference cross-reference from em_db_reference. em_db_reference.access_code Unique identifier for a provided link. 1ABC EMD-5002 PDB EMDB The name of the database containing the related entry. em_db_reference.details A description of the related entry. map derived from same data with D7 symmetry imposed model derived from X-ray crystal structure 1ABC IN FRAME OTHER Indicates relationship of this entry with other entries in PDB and EMDB. em_db_reference.id PRIMARY KEY 0 em_db_reference_auxiliary Category holds links to raw data sources for the entry, e.g., held by a remote server. Example 1 <PDBx:em_db_reference_auxiliaryCategory> <PDBx:em_db_reference_auxiliary id="1"> <PDBx:link>http://www.ebi.ac.uk/pdbe/emdb/singleParticledir/SPIDER_FRANK_data</PDBx:link> <PDBx:link_type>2D EM DATA</PDBx:link_type> </PDBx:em_db_reference_auxiliary> </PDBx:em_db_reference_auxiliaryCategory> 1 1 1 1 1 em_db_reference_auxiliaryCategory This property indicates that datablock has a category holder em_db_reference_auxiliaryCategory. em_db_reference_auxiliaryCategory This property indicates that em_db_reference_auxiliaryCategory. has a category em_db_reference_auxiliary. em_db_reference_auxiliaryItem Abstract datatype property for em_db_reference_auxiliary items. reference_to_em_db_reference_auxiliary cross-reference to em_db_reference_auxiliary. referenced_by_em_db_reference_auxiliary cross-reference from em_db_reference_auxiliary. em_db_reference_auxiliary.link Hyperlink to the auxiliary data. 2D EM DATA CORRELATIVE LIGHT MICROSCOPY Type of auxiliary data stored at the indicated link. em_db_reference_auxiliary.id PRIMARY KEY 0 em_depositor_info Data items in the EM_DEPOSITOR INFO category record parameters for EM depositions that are provided by the depositor Example 1 <PDBx:em_depositor_infoCategory> <PDBx:em_depositor_info entry_id="D_10005049"> <PDBx:em_method_selection>yes</PDBx:em_method_selection> <PDBx:molecular_description_flag>yes</PDBx:molecular_description_flag> </PDBx:em_depositor_info> </PDBx:em_depositor_infoCategory> 1 1 0 1 1 em_depositor_infoCategory This property indicates that datablock has a category holder em_depositor_infoCategory. em_depositor_infoCategory This property indicates that em_depositor_infoCategory. has a category em_depositor_info. em_depositor_infoItem Abstract datatype property for em_depositor_info items. reference_to_em_depositor_info cross-reference to em_depositor_info. referenced_by_em_depositor_info cross-reference from em_depositor_info. Helical Single particle Subtomogram averaging Tomography Electron Diffraction The selected EM experimental method. yes no Records whether molecular/polymer entities of the EM sample will be described. em_depositor_info.entry_id This data item is a pointer to the ENTRY category. 0 em_depui Some internal items to power the deposition interface Example 1 <PDBx:em_depuiCategory> <PDBx:em_depui entry_id="1ABC"> <PDBx:depositor_hold_instructions>HOLD</PDBx:depositor_hold_instructions> <PDBx:macromolecule_description>YES</PDBx:macromolecule_description> <PDBx:obsolete_instructions xsi:nil="true" /> <PDBx:same_authors_as_pdb>NO</PDBx:same_authors_as_pdb> <PDBx:same_title_as_pdb>NO</PDBx:same_title_as_pdb> </PDBx:em_depui> </PDBx:em_depuiCategory> 0 1 1 1 1 1 0 1 1 1 1 1 1 em_depuiCategory This property indicates that datablock has a category holder em_depuiCategory. em_depuiCategory This property indicates that em_depuiCategory. has a category em_depui. em_depuiItem Abstract datatype property for em_depui items. reference_to_em_depui cross-reference to em_depui. referenced_by_em_depui cross-reference from em_depui. COMPOSITE MAP NO Indicates whether the authors have declared that this is a composite map deposition REL HOLD HOLD8W HPUB Choose the manner in which you would like the map and associated files (half maps, additional maps, masks, FSC curves, structure factors, layer lines, and images) to be released. Release of these files can be delayed either until publication of the associated primary citation or until one year after completion of the deposition. It is the responsibility of the depositor to notify the EMDB when the primary citation has been published. Please note that map-associated experimental information and metadata (header data) are made available to the public when an entry is placed on hold. YES NO Indicates whether the authors are providing a macromolecule level description of their sample em_depui.obsolete_instructions Instruction for annotators on why a previous released entry should be obsoleted. Example of valid request: * Author wants to replace a map that has already been released, following discovery of a processing error Examples of invalid requests: * Someone other than the author wants to obsolete a map. * Legal conflict of interest Obsoletion is not required for the following actions: * to change released metadata info. * to update the map of an HPUB entry. * to change the hand of a released map. * to deposit an improved version of a released map. YES NO Indicates whether the authors for the EMDB entry are the same as for the PDB entry in a joint map + model deposition YES NO Indicates whether the title for the EMDB entry is the same as for the PDB entry in a joint map + model deposition em_depui.entry_id PRIMARY KEY 0 em_detector Data items in the EM_DETECTOR category record details of the image detector type. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_detectorCategory> <PDBx:em_detector entry_id="1DYL" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:detective_quantum_efficiency xsi:nil="true" /> <PDBx:type>KODAK SO163 FILM</PDBx:type> </PDBx:em_detector> </PDBx:em_detectorCategory> 0 1 0 1 0 1 0 1 1 1 em_detectorCategory This property indicates that datablock has a category holder em_detectorCategory. em_detectorCategory This property indicates that em_detectorCategory. has a category em_detector. em_detectorItem Abstract datatype property for em_detector items. reference_to_em_detector cross-reference to em_detector. referenced_by_em_detector cross-reference from em_detector. em_detector.details Any additional information about the detection system. Any other details regarding the detector. em_detector.detective_quantum_efficiency The detective_quantum_efficiency (DQE)is defined as the square of the signal-to-noise ratio in the recording device divided by the square of the signal-to-ratio in the electron beam: (SIGNAL/NOISE)2 recording device DQE = ------------------------------- (SIGNAL/NOISE)2 electron beam A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas that the signal-to-noise ratio is reduced by half in the recording step. (0.5)**2 DQE = --------- = 0.25. (1.0)**2 0.25 COUNTING INTEGRATING SUPER-RESOLUTION OTHER The detector mode used during image recording. em_detector.type The detector type used for recording images. Usually film or CCD camera. em_detector.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_detector.id The value of attribute id in category em_detector must uniquely identify the detector used for imaging. 0 em_diffraction Microscopy parameters relevant only for crystallography Example 1 <PDBx:em_diffractionCategory> <PDBx:em_diffraction id="1"> <PDBx:camera_length>800</PDBx:camera_length> <PDBx:imaging_id>1</PDBx:imaging_id> </PDBx:em_diffraction> <PDBx:em_diffraction id="2"> <PDBx:camera_length>750</PDBx:camera_length> <PDBx:imaging_id>2</PDBx:imaging_id> </PDBx:em_diffraction> </PDBx: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 <PDBx:em_diffraction_shellCategory> <PDBx:em_diffraction_shell id="1"> <PDBx:fourier_space_coverage>93.0</PDBx:fourier_space_coverage> <PDBx:high_resolution>7.5</PDBx:high_resolution> <PDBx:low_resolution>45</PDBx:low_resolution> <PDBx:multiplicity>2.3</PDBx:multiplicity> <PDBx:num_structure_factors>327</PDBx:num_structure_factors> <PDBx:phase_residual>13.5</PDBx:phase_residual> </PDBx:em_diffraction_shell> </PDBx: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 <PDBx:em_diffraction_statsCategory> <PDBx:em_diffraction_stats id="1"> <PDBx:fourier_space_coverage>92</PDBx:fourier_space_coverage> <PDBx:high_resolution>7.2</PDBx:high_resolution> <PDBx:num_intensities_measured>1524</PDBx:num_intensities_measured> <PDBx:num_structure_factors>325</PDBx:num_structure_factors> <PDBx:overall_phase_error>18.6</PDBx:overall_phase_error> <PDBx:overall_phase_residual>9.5</PDBx:overall_phase_residual> <PDBx:phase_error_rejection_criteria>None</PDBx:phase_error_rejection_criteria> <PDBx:r_merge>19.5</PDBx:r_merge> <PDBx:r_sym>23.2</PDBx:r_sym> </PDBx:em_diffraction_stats> </PDBx: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 <PDBx:em_entity_assemblyCategory> <PDBx:em_entity_assembly id="1"> <PDBx:name>50S Ribosomal Subunit</PDBx:name> <PDBx:parent_id>0</PDBx:parent_id> <PDBx:type>RIBOSOME</PDBx:type> </PDBx:em_entity_assembly> </PDBx:em_entity_assemblyCategory> Example 2 -- based on PDB entry 3IY7 <PDBx:em_entity_assemblyCategory> <PDBx:em_entity_assembly id="1"> <PDBx:name>Fab fragment from MAb F interacting with feline panleukopenia virus (FPV)</PDBx:name> <PDBx:parent_id>0</PDBx:parent_id> <PDBx:type>COMPLEX</PDBx:type> </PDBx:em_entity_assembly> <PDBx:em_entity_assembly id="2"> <PDBx:name>feline panleukopenia virus</PDBx:name> <PDBx:parent_id>1</PDBx:parent_id> <PDBx:synonym>FPV</PDBx:synonym> <PDBx:type>VIRUS</PDBx:type> </PDBx:em_entity_assembly> <PDBx:em_entity_assembly id="3"> <PDBx:name>Fab fragment from Mab F</PDBx:name> <PDBx:parent_id>1</PDBx:parent_id> <PDBx:synonym>Fab</PDBx:synonym> <PDBx:type>COMPLEX</PDBx:type> </PDBx:em_entity_assembly> </PDBx:em_entity_assemblyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 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. em_entity_assembly.assembly_id This data item is a pointer to attribute id in category em_assembly in the ASSEMBLY category. 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.ebi_cell The cell from which the component was obtained. CHO HELA 3T3 em_entity_assembly.ebi_cellular_location The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane YES NO A flag to indicate whether the component is engineered. em_entity_assembly.ebi_expression_system The expression system used to produce the component. eschericia coli saccharomyces cerevisiae em_entity_assembly.ebi_expression_system_plasmid The plasmid used to produce the component. pBR322 pMB9 em_entity_assembly.ebi_organelle The organelle from which the component was obtained. golgi mitochondrion cytoskeleton em_entity_assembly.ebi_organism_common The common name of the species of the natural organism from which the component was obtained. em_entity_assembly.ebi_organism_scientific The species of the natural organism from which the component was obtained. em_entity_assembly.ebi_strain The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly.ebi_tissue The tissue of the natural organism from which the component was obtained. heart liver eye lens 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 em_entity_assembly.go_id The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). GO:0005876 GO:0015630 em_entity_assembly.ipr_id The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). 001304 002353 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 <PDBx:em_entity_assembly_molwtCategory> <PDBx:em_entity_assembly_molwt id="1"> <PDBx:entity_assembly_id>1</PDBx:entity_assembly_id> <PDBx:units>MEGADALTONS</PDBx:units> <PDBx:value>30.5</PDBx:value> </PDBx:em_entity_assembly_molwt> </PDBx:em_entity_assembly_molwtCategory> 1 1 0 1 0 1 0 1 0 1 1 em_entity_assembly_molwtCategory This property indicates that datablock has a category holder em_entity_assembly_molwtCategory. em_entity_assembly_molwtCategory This property indicates that em_entity_assembly_molwtCategory. has a category em_entity_assembly_molwt. em_entity_assembly_molwtItem Abstract datatype property for em_entity_assembly_molwt items. reference_to_em_entity_assembly_molwt cross-reference to em_entity_assembly_molwt. referenced_by_em_entity_assembly_molwt cross-reference from em_entity_assembly_molwt. em_entity_assembly_molwt.entity_assembly_id A reference to em_entity_assembly.id which uniquely identifies one sample or sample subcomponent of the imaged specimen. YES NO Identifies whether the given molecular weight was derived experimentally. em_entity_assembly_molwt.method The method used to determine the molecular weight. MEGADALTONS KILODALTONS/NANOMETER Molecular weight units. em_entity_assembly_molwt.value The molecular weight of the sample or sample subcomponent 0.53 em_entity_assembly_molwt.id PRIMARY KEY 0 em_entity_assembly_naturalsource Data items in this category record taxonomic details about the natural source for EM assemblies and assembly components. Example 1 <PDBx:em_entity_assembly_naturalsourceCategory> <PDBx:em_entity_assembly_naturalsource id="1"> <PDBx:cellular_location xsi:nil="true" /> <PDBx:entity_assembly_id>8333</PDBx:entity_assembly_id> <PDBx:ncbi_tax_id>Escherichia coli</PDBx:ncbi_tax_id> <PDBx:organ xsi:nil="true" /> <PDBx:organelle>cytoplasm</PDBx:organelle> <PDBx:organism>K12</PDBx:organism> <PDBx:strain xsi:nil="true" /> <PDBx:tissue xsi:nil="true" /> </PDBx:em_entity_assembly_naturalsource> </PDBx:em_entity_assembly_naturalsourceCategory> 0 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 0 1 0 1 1 em_entity_assembly_naturalsourceCategory This property indicates that datablock has a category holder em_entity_assembly_naturalsourceCategory. em_entity_assembly_naturalsourceCategory This property indicates that em_entity_assembly_naturalsourceCategory. has a category em_entity_assembly_naturalsource. em_entity_assembly_naturalsourceItem Abstract datatype property for em_entity_assembly_naturalsource items. reference_to_em_entity_assembly_naturalsource cross-reference to em_entity_assembly_naturalsource. referenced_by_em_entity_assembly_naturalsource cross-reference from em_entity_assembly_naturalsource. em_entity_assembly_naturalsource.cell The cell type from which the component was obtained. CHO HELA 3T3 em_entity_assembly_naturalsource.cellular_location The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane em_entity_assembly_naturalsource.details Additional details describing this natural source. em_entity_assembly_naturalsource.entity_assembly_id Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category. em_entity_assembly_naturalsource.ncbi_tax_id The NCBI taxonomy id for the natural organism source of the component. 10804 9606 em_entity_assembly_naturalsource.organ The organ of the organism from which the component was obtained. heart em_entity_assembly_naturalsource.organelle The organelle from which the component was obtained. Golgi Mitochondrion Cytoskeleton em_entity_assembly_naturalsource.organism The scientific name of the source organism for the component Homo sapiens Gallus gallus em_entity_assembly_naturalsource.strain The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly_naturalsource.tissue The tissue of the natural organism from which the component was obtained. Cartilage Liver Eye lens em_entity_assembly_naturalsource.id PRIMARY KEY 0 em_entity_assembly_recombinant Data items in this category record details about recombinant expression of the assembly or assembly component. Example 1 <PDBx:em_entity_assembly_recombinantCategory> <PDBx:em_entity_assembly_recombinant id="1"> <PDBx:entity_assembly_id>1</PDBx:entity_assembly_id> <PDBx:organism>Escherichia coli</PDBx:organism> <PDBx:plasmid>pET17c</PDBx:plasmid> </PDBx:em_entity_assembly_recombinant> </PDBx:em_entity_assembly_recombinantCategory> 0 1 1 1 1 1 1 1 0 1 0 1 1 em_entity_assembly_recombinantCategory This property indicates that datablock has a category holder em_entity_assembly_recombinantCategory. em_entity_assembly_recombinantCategory This property indicates that em_entity_assembly_recombinantCategory. has a category em_entity_assembly_recombinant. em_entity_assembly_recombinantItem Abstract datatype property for em_entity_assembly_recombinant items. reference_to_em_entity_assembly_recombinant cross-reference to em_entity_assembly_recombinant. referenced_by_em_entity_assembly_recombinant cross-reference from em_entity_assembly_recombinant. em_entity_assembly_recombinant.cell The cell of the host organism from which the expressed component was obtained, if relevant. Potato root em_entity_assembly_recombinant.entity_assembly_id Pointer to the expressed component described in the EM ENTITY ASSEMBLY category. em_entity_assembly_recombinant.ncbi_tax_id The NCBI taxonomy id of the expression host used to produce the component. em_entity_assembly_recombinant.organism Expression system host organism used to produce the component. escherichia coli saccharomyces cerevisiae em_entity_assembly_recombinant.plasmid The plasmid used to produce the component in the expression system. pBR322 pMB9 em_entity_assembly_recombinant.strain The strain of the host organism from which the expresed component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly_recombinant.id PRIMARY KEY 0 em_entity_assembly_synthetic Data items in this category record taxonomic details about the synthetic source for EM assemblies and assembly components. Example 1 <PDBx:em_entity_assembly_syntheticCategory> <PDBx:em_entity_assembly_synthetic entity_assembly_id="1" id="1"> <PDBx:cellular_location xsi:nil="true" /> <PDBx:ncbi_tax_id>8333</PDBx:ncbi_tax_id> <PDBx:organ xsi:nil="true" /> <PDBx:organelle xsi:nil="true" /> <PDBx:organism>Escherichia coli</PDBx:organism> <PDBx:strain>K12</PDBx:strain> <PDBx:tissue xsi:nil="true" /> </PDBx:em_entity_assembly_synthetic> </PDBx: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_euler_angle_assignment Category to describe the euler angle assignement Example 1 <PDBx:em_euler_angle_assignmentCategory> <PDBx:em_euler_angle_assignment id="1"> <PDBx:image_processing_id>1</PDBx:image_processing_id> <PDBx:order>FINAL</PDBx:order> <PDBx:type>COMMON LINE</PDBx:type> </PDBx:em_euler_angle_assignment> </PDBx:em_euler_angle_assignmentCategory> 0 1 1 1 1 1 0 1 0 1 0 1 1 1 1 em_euler_angle_assignmentCategory This property indicates that datablock has a category holder em_euler_angle_assignmentCategory. em_euler_angle_assignmentCategory This property indicates that em_euler_angle_assignmentCategory. has a category em_euler_angle_assignment. em_euler_angle_assignmentItem Abstract datatype property for em_euler_angle_assignment items. reference_to_em_euler_angle_assignment cross-reference to em_euler_angle_assignment. referenced_by_em_euler_angle_assignment cross-reference from em_euler_angle_assignment. em_euler_angle_assignment.details Any additional details about euler angle assignment em_euler_angle_assignment.image_processing_id Foreign key to the EM_IMAGE_PROCESSING category INITIAL FINAL Stage of the reconstruction in which the angle assignments were made. em_euler_angle_assignment.proj_matching_angular_sampling Angular sampling of projection matching 1.5 em_euler_angle_assignment.proj_matching_merit_function Overall figure of merit for projection matching Correlation coeficient (CC) em_euler_angle_assignment.proj_matching_num_projections Number of reference projections used for euler angle assignment PROJECTION MATCHING COMMON LINE ANGULAR RECONSTITUTION RANDOM ASSIGNMENT NOT APPLICABLE MAXIMUM LIKELIHOOD OTHER The procedure used to assigned euler angles. em_euler_angle_assignment.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 <PDBx:em_experimentCategory> <PDBx:em_experiment entry_id="1EG0"> <PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state> <PDBx:reconstruction_method>SINGLE PARTICLE</PDBx:reconstruction_method> <PDBx:specimen_type>VITREOUS ICE (CRYO EM)</PDBx:specimen_type> </PDBx:em_experiment> </PDBx:em_experimentCategory> 1 1 1 1 1 1 1 1 0 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.specimen_type The specimen type used in the EM experiment. VITREOUS ICE (CRYO EM) NEGATIVE STAIN FREEZE SUBSTITUTION em_experiment.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 em_fiducial_markers Description of fiducial markers. 1 1 1 1 1 1 1 em_fiducial_markersCategory This property indicates that datablock has a category holder em_fiducial_markersCategory. em_fiducial_markersCategory This property indicates that em_fiducial_markersCategory. has a category em_fiducial_markers. em_fiducial_markersItem Abstract datatype property for em_fiducial_markers items. reference_to_em_fiducial_markers cross-reference to em_fiducial_markers. referenced_by_em_fiducial_markers cross-reference from em_fiducial_markers. em_fiducial_markers.diameter Diameter of the fiducial markers 14 em_fiducial_markers.em_tomography_specimen_id Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category em_fiducial_markers.manufacturer Manufacturer source for the fiducial markers nanoprobes em_fiducial_markers.id PRIMARY KEY 0 em_figure_depositor_info Listing of image files (figures) associated with an EMDB entry Example 1 <PDBx:em_figure_depositor_infoCategory> <PDBx:em_figure_depositor_info id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experiment_id>1</PDBx:experiment_id> <PDBx:upload_file_name>groel-chimera-image.png</PDBx:upload_file_name> </PDBx:em_figure_depositor_info> </PDBx:em_figure_depositor_infoCategory> 0 1 0 1 1 1 1 em_figure_depositor_infoCategory This property indicates that datablock has a category holder em_figure_depositor_infoCategory. em_figure_depositor_infoCategory This property indicates that em_figure_depositor_infoCategory. has a category em_figure_depositor_info. em_figure_depositor_infoItem Abstract datatype property for em_figure_depositor_info items. reference_to_em_figure_depositor_info cross-reference to em_figure_depositor_info. referenced_by_em_figure_depositor_info cross-reference from em_figure_depositor_info. em_figure_depositor_info.details Details about the image file. em_figure_depositor_info.experiment_id This data item optionally associates an image (figure) with an experiment. em_figure_depositor_info.upload_file_name The name of the image file associated with the map entry em_figure_depositor_info.id This data item is the unique identifier for an image file. 0 em_final_classification Information about the final image classification Example 1 <PDBx:em_final_classificationCategory> <PDBx:em_final_classification id="1"> <PDBx:image_processing_id>1</PDBx:image_processing_id> </PDBx:em_final_classification> </PDBx:em_final_classificationCategory> 0 1 0 1 1 1 0 1 0 1 1 em_final_classificationCategory This property indicates that datablock has a category holder em_final_classificationCategory. em_final_classificationCategory This property indicates that em_final_classificationCategory. has a category em_final_classification. em_final_classificationItem Abstract datatype property for em_final_classification items. reference_to_em_final_classification cross-reference to em_final_classification. referenced_by_em_final_classification cross-reference from em_final_classification. em_final_classification.avg_num_images_per_class The average number of images per class in the final 2D/3D classification 75 em_final_classification.details Additional details about the final 2D/3D classification The final 2D classification had a highly asymmetric distribution owing to preferred orientations in the prepared specimen em_final_classification.image_processing_id Foreign key to the EM_IMAGE_PROCESSING category em_final_classification.num_classes The number of classes used in the final 2D/3D classification 2D 3D Space (2D/3D) for the classification. em_final_classification.id PRIMARY KEY 0 em_focused_ion_beam Description of sectioning by focused_ion_beam 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 em_focused_ion_beamCategory This property indicates that datablock has a category holder em_focused_ion_beamCategory. em_focused_ion_beamCategory This property indicates that em_focused_ion_beamCategory. has a category em_focused_ion_beam. em_focused_ion_beamItem Abstract datatype property for em_focused_ion_beam items. reference_to_em_focused_ion_beam cross-reference to em_focused_ion_beam. referenced_by_em_focused_ion_beam cross-reference from em_focused_ion_beam. em_focused_ion_beam.current Current of the ion beam, in nanoamperes (nA) em_focused_ion_beam.details Additional details about FIB milling em_focused_ion_beam.dose_rate ions per sq centimetre per second em_focused_ion_beam.duration Milling time in seconds em_focused_ion_beam.em_tomography_specimen_id Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category em_focused_ion_beam.final_thickness Final sample thickness em_focused_ion_beam.initial_thickness Initial sample thickness em_focused_ion_beam.instrument The instrument used for focused ion beam sectioning FEI Quanta FIB em_focused_ion_beam.ion The ion source used to ablate the specimen gallium ion gold ion iridium ion em_focused_ion_beam.temperature Temperature of the sample during milling, in kelvins 100 em_focused_ion_beam.voltage Voltage applied to the ion source, in kilovolts 30 em_focused_ion_beam.id PRIMARY KEY 0 em_fsc_curve Data items in the EMD_VALIDATION_FSC_CURVE category record details of the Fourier Shell Correlation (FSC) curve file. Example 1 <PDBx:em_fsc_curveCategory> <PDBx:em_fsc_curve id="1"> <PDBx:file>fsc_curve.txt</PDBx:file> </PDBx:em_fsc_curve> </PDBx:em_fsc_curveCategory> 0 1 0 1 1 em_fsc_curveCategory This property indicates that datablock has a category holder em_fsc_curveCategory. em_fsc_curveCategory This property indicates that em_fsc_curveCategory. has a category em_fsc_curve. em_fsc_curveItem Abstract datatype property for em_fsc_curve items. reference_to_em_fsc_curve cross-reference to em_fsc_curve. referenced_by_em_fsc_curve cross-reference from em_fsc_curve. em_fsc_curve.details Details about the FSC file. em_fsc_curve.file FSC file name. emd-5470-fsc.txt em_fsc_curve.id PRIMARY KEY 0 em_grid_pretreatment Data items describing glow discharge pretreatment for an EM grid Example 1 <PDBx:em_grid_pretreatmentCategory> <PDBx:em_grid_pretreatment id="1"> <PDBx:sample_support_id>1</PDBx:sample_support_id> <PDBx:time>12</PDBx:time> <PDBx:type>GLOW DISCHARGE</PDBx:type> </PDBx:em_grid_pretreatment> </PDBx:em_grid_pretreatmentCategory> 0 1 0 1 1 1 0 1 0 1 1 em_grid_pretreatmentCategory This property indicates that datablock has a category holder em_grid_pretreatmentCategory. em_grid_pretreatmentCategory This property indicates that em_grid_pretreatmentCategory. has a category em_grid_pretreatment. em_grid_pretreatmentItem Abstract datatype property for em_grid_pretreatment items. reference_to_em_grid_pretreatment cross-reference to em_grid_pretreatment. referenced_by_em_grid_pretreatment cross-reference from em_grid_pretreatment. em_grid_pretreatment.atmosphere The atmosphere used for glow discharge of the em grid. AIR AMYLAMINE em_grid_pretreatment.pressure Pressure of the glow discharge chamber, in pascals em_grid_pretreatment.sample_support_id Pointer to EM SAMPLE SUPPORT em_grid_pretreatment.time Time period for glow discharge of the em grid, in seconds 60 GLOW DISCHARGE PLASMA CLEANING Type of grid pretreatment em_grid_pretreatment.id PRIMARY KEY 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 0 1 0 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 YES NO Value should be YES if a the filament has two-fold symmetry perpendicular to the helical axis. em_helical_entity.entity_assembly_id The value of attribute entity_assembly_id in category em_helical_entity identifies a particular assembly component. This data item is a pointer to attribute id in category em_entity_assembly in the EM_ENTITY_ASSEMBLY category. em_helical_entity.hand Handedness of the helix: right handed or left handed Right Left 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_high_pressure_freezing Description of high pressure freezing 0 1 1 1 1 1 1 em_high_pressure_freezingCategory This property indicates that datablock has a category holder em_high_pressure_freezingCategory. em_high_pressure_freezingCategory This property indicates that em_high_pressure_freezingCategory. has a category em_high_pressure_freezing. em_high_pressure_freezingItem Abstract datatype property for em_high_pressure_freezing items. reference_to_em_high_pressure_freezing cross-reference to em_high_pressure_freezing. referenced_by_em_high_pressure_freezing cross-reference from em_high_pressure_freezing. em_high_pressure_freezing.details Additional details about high pressure freezing. High pressure freezing chamber was 250 um thick, 3.0 mm diameter, with central cavities 1.5 mm x 0.5 mm x 200 um deep. The chamber was pre-coated with 0.5% lecithin in chloroform. em_high_pressure_freezing.em_tomography_specimen_id Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category em_high_pressure_freezing.instrument The instrument used for high pressure freezing. Leica EM HP100 em_high_pressure_freezing.id PRIMARY KEY 0 em_image_processing Data items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure. Example 1 <PDBx:em_image_processingCategory> <PDBx:em_image_processing id="1" image_recording_id="1"> <PDBx:details>The selected images were high-pass filtered and normalized</PDBx:details> </PDBx:em_image_processing> </PDBx: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 <PDBx:em_image_recordingCategory> <PDBx:em_image_recording id="1" imaging_id="1"> <PDBx:avg_electron_dose_per_image>0.9</PDBx:avg_electron_dose_per_image> <PDBx:film_or_detector_model>GENERIC FILM</PDBx:film_or_detector_model> <PDBx:num_diffraction_images>48</PDBx:num_diffraction_images> </PDBx:em_image_recording> </PDBx: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 <PDBx:em_image_scansCategory> <PDBx:em_image_scans id="2"> <PDBx:details xsi:nil="true" /> <PDBx:entry_id>1DYL</PDBx:entry_id> <PDBx:number_digital_images>48</PDBx:number_digital_images> <PDBx:od_range xsi:nil="true" /> <PDBx:quant_bit_size xsi:nil="true" /> <PDBx:sampling_size xsi:nil="true" /> <PDBx:scanner_model xsi:nil="true" /> </PDBx:em_image_scans> </PDBx: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 grey 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 <PDBx:em_imagingCategory> <PDBx:em_imaging entry_id="1DYL" id="1"> <PDBx:accelerating_voltage>200</PDBx:accelerating_voltage> <PDBx:calibrated_magnification xsi:nil="true" /> <PDBx:date>1998-15-06</PDBx:date> <PDBx:details xsi:nil="true" /> <PDBx:detector_distance xsi:nil="true" /> <PDBx:electron_source>FEG</PDBx:electron_source> <PDBx:energy_filter xsi:nil="true" /> <PDBx:energy_window xsi:nil="true" /> <PDBx:illumination_mode>bright field</PDBx:illumination_mode> <PDBx:microscope_model>FEI/PHILIPS CM200 FEG</PDBx:microscope_model> <PDBx:mode>low dose</PDBx:mode> <PDBx:nominal_cs>2.0</PDBx:nominal_cs> <PDBx:nominal_defocus_max>7600</PDBx:nominal_defocus_max> <PDBx:nominal_defocus_min>975</PDBx:nominal_defocus_min> <PDBx:nominal_magnification>50000</PDBx:nominal_magnification> <PDBx:recording_temperature_maximum xsi:nil="true" /> <PDBx:recording_temperature_minimum xsi:nil="true" /> <PDBx:sample_support_id>1</PDBx:sample_support_id> <PDBx:specimen_holder_model>gatan 626-0300</PDBx:specimen_holder_model> <PDBx:specimen_holder_type>cryotransfer</PDBx:specimen_holder_type> <PDBx:temperature>95</PDBx:temperature> <PDBx:tilt_angle_max>0</PDBx:tilt_angle_max> <PDBx:tilt_angle_min>0</PDBx:tilt_angle_min> </PDBx:em_imaging> </PDBx:em_imagingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 1 em_imagingCategory This property indicates that datablock has a category holder em_imagingCategory. em_imagingCategory This property indicates that em_imagingCategory. has a category em_imaging. em_imagingItem Abstract datatype property for em_imaging items. reference_to_em_imaging cross-reference to em_imaging. referenced_by_em_imaging cross-reference from em_imaging. em_imaging.accelerating_voltage A value of accelerating voltage (in kV) used for imaging. 300 NONE BASIC ZEMLIN TABLEAU COMA FREE OTHER The type of procedure used to align the microscope electron beam. em_imaging.astigmatism astigmatism em_imaging.c2_aperture_diameter The open diameter of the c2 condenser lens, in microns. 100 em_imaging.calibrated_defocus_max The maximum calibrated defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 5000 em_imaging.calibrated_defocus_min The minimum calibrated defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 1200 em_imaging.calibrated_magnification The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. 61200 em_imaging.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. NITROGEN HELIUM Cryogen type used to maintain the specimen stage temperature during imaging in the microscope. em_imaging.date Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. 2001-05-08 em_imaging.details Any additional imaging details. Preliminary grid screening was performed manually. em_imaging.detector_distance The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. em_imaging.detector_id The value of attribute detector_id in category em_imaging must uniquely identify the type of detector used in the experiment. em_imaging.electron_beam_tilt_params electron beam tilt params em_imaging.electron_dose The electron dose received by the specimen (electrons per square angstrom). 0.9 em_imaging.electron_source The source of electrons. The electron gun. em_imaging.energy_filter The type of energy filter spectrometer apparatus. FEI em_imaging.energy_window The energy filter range in electron volts (eV)set by spectrometer. 0 - 15 FLOOD BEAM SPOT SCAN OTHER The mode of illumination. em_imaging.microscope_id This data item is a pointer to attribute id in category em_microscope in the EM_MICROSCOPE category. FEI MORGAGNI FEI POLARA 300 FEI TALOS ARCTICA FEI TECNAI 10 FEI TECNAI 12 FEI TECNAI 20 FEI TECNAI F20 FEI TECNAI F30 FEI TECNAI ARCTICA FEI TECNAI SPHERA FEI TECNAI SPIRIT FEI TITAN FEI TITAN KRIOS FEI/PHILIPS CM10 FEI/PHILIPS CM12 FEI/PHILIPS CM120T FEI/PHILIPS CM200FEG FEI/PHILIPS CM200FEG/SOPHIE FEI/PHILIPS CM200FEG/ST FEI/PHILIPS CM200FEG/UT FEI/PHILIPS CM200T FEI/PHILIPS CM300FEG/HE FEI/PHILIPS CM300FEG/ST FEI/PHILIPS CM300FEG/T FEI/PHILIPS EM400 FEI/PHILIPS EM420 HITACHI EF2000 HITACHI EF3000 HITACHI H7600 HITACHI HF2000 HITACHI HF3000 HITACHI H3000 UHVEM HITACHI H-9500SD JEOL 100B JEOL 100CX JEOL 1000EES JEOL 1010 JEOL 1200 JEOL 1200EX JEOL 1200EXII JEOL 1230 JEOL 1400 JEOL 1400/HR + YPS FEG JEOL 2000EX JEOL 2000EXII JEOL 2010 JEOL 2010F JEOL 2010HT JEOL 2010HC JEOL 2010UHR JEOL 2011 JEOL 2100 JEOL 2100F JEOL 2200FS JEOL 2200FSC JEOL 3000SFF JEOL 3100FEF JEOL 3100FFC JEOL 3200FS JEOL 3200FSC JEOL KYOTO-3000SFF JEOL 4000 JEOL 4000EX JEOL CRYO ARM 200 JEOL CRYO ARM 300 SIEMENS SULEIKA TFS GLACIOS TFS KRIOS TFS TALOS TFS TALOS F200C TFS TALOS L120C TFS TUNDRA ZEISS LEO912 ZEISS LIBRA120PLUS The name of the model of microscope. 4D-STEM BRIGHT FIELD DARK FIELD DIFFRACTION OTHER The mode of imaging. em_imaging.nominal_cs The spherical aberration coefficient (Cs) in millimeters, of the objective lens. 2.0 em_imaging.nominal_defocus_max The maximum defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 5000 em_imaging.nominal_defocus_min The minimum defocus value of the objective lens (in nanometers) used to obtain the recorded images. Negative values refer to overfocus. 1200 em_imaging.nominal_magnification The magnification indicated by the microscope readout. 60000 em_imaging.recording_temperature_maximum The specimen temperature maximum (kelvin) for the duration of imaging. 70 em_imaging.recording_temperature_minimum The specimen temperature minimum (kelvin) for the duration of imaging. em_imaging.residual_tilt Residual tilt of the electron beam (in miliradians) em_imaging.sample_support_id This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. em_imaging.scans_id The value of attribute scans_id in category em_imaging must uniquely identify the image_scans used in the experiment. FEI TITAN KRIOS AUTOGRID HOLDER FISCHIONE 2550 FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER GATAN HELIUM GATAN LIQUID NITROGEN GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER HOME BUILD JEOL JEOL CRYOSPECPORTER JEOL 3200FSC CRYOHOLDER PHILIPS ROTATION HOLDER SIDE ENTRY, EUCENTRIC OTHER The name of the model of specimen holder used during imaging. em_imaging.specimen_holder_type The type of specimen holder used during imaging. cryo em_imaging.specimen_id Foreign key to the EM_SPECIMEN category em_imaging.temperature The mean specimen stage temperature (in kelvin) during imaging in the microscope. 70 em_imaging.tilt_angle_max The maximum angle at which the specimen was tilted to obtain recorded images. 70 em_imaging.tilt_angle_min The minimum angle at which the specimen was tilted to obtain recorded images. -70 em_imaging.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_imaging.id PRIMARY KEY 0 em_imaging_optics Description of a few specialist optics apparatus Example 1 <PDBx:em_imaging_opticsCategory> <PDBx:em_imaging_optics id="1" imaging_id="1"> <PDBx:chr_aberration_corrector>CEOS manufactured Cc corrector</PDBx:chr_aberration_corrector> <PDBx:energyfilter_lower>0</PDBx:energyfilter_lower> <PDBx:energyfilter_name>FEI</PDBx:energyfilter_name> <PDBx:energyfilter_upper>15</PDBx:energyfilter_upper> </PDBx:em_imaging_optics> </PDBx:em_imaging_opticsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_imaging_opticsCategory This property indicates that datablock has a category holder em_imaging_opticsCategory. em_imaging_opticsCategory This property indicates that em_imaging_opticsCategory. has a category em_imaging_optics. em_imaging_opticsItem Abstract datatype property for em_imaging_optics items. reference_to_em_imaging_optics cross-reference to em_imaging_optics. referenced_by_em_imaging_optics cross-reference from em_imaging_optics. em_imaging_optics.chr_aberration_corrector Chromatic aberration corrector information CEOS manufactured Cc corrector em_imaging_optics.details Details on the use of the phase plate Phase plate evolution varied between different microscopes used to collect data but positions were shifted once phase evolution progressed past 120 degrees. em_imaging_optics.energyfilter_lower The energy filter range lower value in electron volts (eV) set by spectrometer. 0 em_imaging_optics.energyfilter_name The type of energy filter spectrometer GIF 200 em_imaging_optics.energyfilter_slit_width The energy filter range slit width in electron volts (eV). 35 em_imaging_optics.energyfilter_upper The energy filter range upper value in electron volts (eV) set by spectrometer. 15 em_imaging_optics.phase_plate Phase plate information ZERNIKE PHASE PLATE em_imaging_optics.sph_aberration_corrector Spherical aberration corrector information Microscope was modified with a Cs corrector with two hexapole elements. em_imaging_optics.id PRIMARY KEY em_imaging_optics.imaging_id Foreign key to the EM IMAGING category 0 em_interpret_figure Listing of all layer line files associated with the EM entry Example 1 <PDBx:em_interpret_figureCategory> <PDBx:em_interpret_figure id="1"> <PDBx:details xsi:nil="true" /> <PDBx:file>emd-1234.png</PDBx:file> </PDBx:em_interpret_figure> </PDBx:em_interpret_figureCategory> 0 1 1 1 1 em_interpret_figureCategory This property indicates that datablock has a category holder em_interpret_figureCategory. em_interpret_figureCategory This property indicates that em_interpret_figureCategory. has a category em_interpret_figure. em_interpret_figureItem Abstract datatype property for em_interpret_figure items. reference_to_em_interpret_figure cross-reference to em_interpret_figure. referenced_by_em_interpret_figure cross-reference from em_interpret_figure. em_interpret_figure.details Details about the image file. em_interpret_figure.file The name of the image file associated with the map entry em_interpret_figure.id PRIMARY KEY 0 em_layer_lines Listing of all layer line files associated with the EM entry Example 1 <PDBx:em_layer_linesCategory> <PDBx:em_layer_lines experiment_id="1" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:file>emd-1234-sf.cif</PDBx:file> </PDBx:em_layer_lines> </PDBx:em_layer_linesCategory> 0 1 1 1 1 1 em_layer_linesCategory This property indicates that datablock has a category holder em_layer_linesCategory. em_layer_linesCategory This property indicates that em_layer_linesCategory. has a category em_layer_lines. em_layer_linesItem Abstract datatype property for em_layer_lines items. reference_to_em_layer_lines cross-reference to em_layer_lines. referenced_by_em_layer_lines cross-reference from em_layer_lines. em_layer_lines.details Details about the layer line file. em_layer_lines.file The name of the layer line file associated with the map entry em_layer_lines.experiment_id This data item is a pointer to the EM EXPERIMENT category. em_layer_lines.id PRIMARY KEY 0 em_layer_lines_depositor_info Listing of layer line files associated with the EM entry Example 1 <PDBx:em_layer_lines_depositor_infoCategory> <PDBx:em_layer_lines_depositor_info id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experiment_id>1</PDBx:experiment_id> <PDBx:upload_file_name>emd-1234-ll.cif</PDBx:upload_file_name> </PDBx:em_layer_lines_depositor_info> </PDBx:em_layer_lines_depositor_infoCategory> 0 1 0 1 1 1 1 em_layer_lines_depositor_infoCategory This property indicates that datablock has a category holder em_layer_lines_depositor_infoCategory. em_layer_lines_depositor_infoCategory This property indicates that em_layer_lines_depositor_infoCategory. has a category em_layer_lines_depositor_info. em_layer_lines_depositor_infoItem Abstract datatype property for em_layer_lines_depositor_info items. reference_to_em_layer_lines_depositor_info cross-reference to em_layer_lines_depositor_info. referenced_by_em_layer_lines_depositor_info cross-reference from em_layer_lines_depositor_info. em_layer_lines_depositor_info.details Details about the layer line file. em_layer_lines_depositor_info.experiment_id This data item is a pointer to the EMD_STRUCT category. em_layer_lines_depositor_info.upload_file_name The name of the layer line file associated with the map entry em_layer_lines_depositor_info.id This data item is the unique identifier for the layer line file. 0 em_map Data items in the EMD_MAP category record parameters of the CCP4 binary-format map file header (see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf), parameters derived from the map header, pixel size, contour level, and annotation details from the depositor. The map is a three-dimensional array of data-values of the same data-type. Important parameters are data-type and array size in three dimensions (i.e. the number of columns, rows and sections). Columns are the fastest changing, followed by rows and sections. Example 1 - based on map entry EMD-5001 <PDBx:em_mapCategory> <PDBx:em_map entry_id="1ABC" id="1"> <PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details> <PDBx:axis_order_fast>X</PDBx:axis_order_fast> <PDBx:axis_order_medium>Y</PDBx:axis_order_medium> <PDBx:axis_order_slow>Z</PDBx:axis_order_slow> <PDBx:cell_a>212.0</PDBx:cell_a> <PDBx:cell_alpha>90.0</PDBx:cell_alpha> <PDBx:cell_b>212.0</PDBx:cell_b> <PDBx:cell_beta>90.0</PDBx:cell_beta> <PDBx:cell_c>212.0</PDBx:cell_c> <PDBx:cell_gamma>90.0</PDBx:cell_gamma> <PDBx:data_type>Image stored as Reals</PDBx:data_type> <PDBx:dimensions_col>200</PDBx:dimensions_col> <PDBx:dimensions_row>200</PDBx:dimensions_row> <PDBx:dimensions_sec>200</PDBx:dimensions_sec> <PDBx:format>CCP4</PDBx:format> <PDBx:origin_col>-100</PDBx:origin_col> <PDBx:origin_row>-100</PDBx:origin_row> <PDBx:origin_sec>-100</PDBx:origin_sec> <PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x> <PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y> <PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z> <PDBx:size_kb>32002</PDBx:size_kb> <PDBx:spacing_x>200</PDBx:spacing_x> <PDBx:spacing_y>200</PDBx:spacing_y> <PDBx:spacing_z>200</PDBx:spacing_z> <PDBx:statistics_average>0.0668982</PDBx:statistics_average> <PDBx:statistics_maximum>2.42436</PDBx:statistics_maximum> <PDBx:statistics_minimum>-0.965912</PDBx:statistics_minimum> <PDBx:statistics_std>0.23771</PDBx:statistics_std> <PDBx:symmetry_space_group>1</PDBx:symmetry_space_group> </PDBx:em_map> </PDBx:em_mapCategory> 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 em_mapCategory This property indicates that datablock has a category holder em_mapCategory. em_mapCategory This property indicates that em_mapCategory. has a category em_map. em_mapItem Abstract datatype property for em_map items. reference_to_em_map cross-reference to em_map. referenced_by_em_map cross-reference from em_map. em_map.annotation_details map annotation details X Y Z The map axis that corresponds to Columns. (CCP4 HEADER WORD 17 MAPC 1=x, 2=y, 3=z) X Y Z The map axis that corresponds to Rows. (CCP4 map header word 18 MAPR 1=x, 2=y, 3=z) X Y Z The map axis that corresponds to Sections. (CCP4 map header word 19 MAPS 1=x, 2=y, 3=z) em_map.cell_a Map unit cell length parameter a. (CCP4 map header word 11) em_map.cell_alpha Value of map unit cell angle parameter alpha in degrees. (CCP4 map header word 14) em_map.cell_b Map unit cell length parameter b. (CCP4 map header word 12) em_map.cell_beta Value of map unit cell angle parameter beta in degrees. (CCP4 map header word 15) em_map.cell_c Map unit cell length parameter c. (CCP4 map header word 13) em_map.cell_gamma Value of map unit cell angle parameter gamma in degrees. (CCP4 map header word 16) em_map.contour_level recommended contour level for viewing the map author emdb software source of the recommended contour level author Image stored as signed byte Image stored as signed integer (2 bytes) Image stored as floating point number (4 bytes) The map data_type describes the data structure of the map voxels. (CCP4 map header word 4 MODE) EMDB currently holds MODE=0,1,and 2 maps; the majority are MODE=2. MAPS with MODES other than 2 and 0 may not work in CCP4 programs. MODE = 0: 8 bits, density stored as a signed byte (-128 to 127, ISO/IEC 10967) MODE = 1: 16 bits, density stored as a signed integer (-32768 to 32767, ISO/IEC 10967) MODE = 2: 32 bits, density stored as a floating point number (IEEE 754) em_map.dimensions_col The number of columns in the map. (CCP4 map header word 1 NC) em_map.dimensions_row The number of rows in the map. (CCP4 map header word 2 NR) em_map.dimensions_sec The number of sections in the map. (CCP4 map header word 3 NS) big little map file endian type em_map.file Map file name. emd_5470.map.gz CCP4 map format em_map.label text stored in the label field of the CCP4 map header (WORDS 57-256) em_map.limit_col The final column position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived = .origin_col + .dimensions_col -1) em_map.limit_row The final row position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived = .origin_row + .dimensions_row -1) em_map.limit_sec The final section position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived -- .origin_sec + .dimensions_sec -1) em_map.origin_col The position of the first column of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 5 NCSTART) em_map.origin_row The position of the first row of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 6 NRSTART) em_map.origin_sec The position of the first section of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 7 NSSTART) em_map.original_file Depositiors original map file name. emd_5470.map.gz em_map.partition Identifies the archive file partition number of any map file em_map.pixel_spacing_x The length in angstroms of one voxel along the X axis. em_map.pixel_spacing_y The length in angstroms of one voxel along the Y axis. em_map.pixel_spacing_z The length in angstroms of one voxel along the Z axis. em_map.size_kb map storage size in Kilobytes (before compression) em_map.spacing_x The number of intervals per cell repeat in X. (CCP4 map header word 8 NX) em_map.spacing_y The number of intervals per cell repeat in Y. (CCP4 map header word 9 NY) em_map.spacing_z The number of intervals per cell repeat in Z. (CCP4 map header word 10 NZ) em_map.statistics_average Mean (average) density value of the map. em_map.statistics_maximum Maximum density value of the map. em_map.statistics_minimum Minimum density value of the map. em_map.statistics_std The standard deviation of the map density values. em_map.symmetry_space_group The space group number for the map. The value is 1 unless the sample is crystalline. (CCP4 map header word 23 ISPG) primary map half map additional map mask raw map FSC half map mask FSC map-model mask alignment mask focused refinement mask 3D classification map focus refinement map segmentation Map type em_map.entry_id This data item is a pointer to the ENTRY category. em_map.id PRIMARY KEY 0 em_map_depositor_info Data items in the EM_MAP_DEPOSITOR INFO category record map parameters that are provided by the depositor Example 1 - based on map entry EMD-5001 <PDBx:em_map_depositor_infoCategory> <PDBx:em_map_depositor_info entry_id="D_10005049" id="1"> <PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details> <PDBx:contour_level>5.0</PDBx:contour_level> <PDBx:experiment_id xsi:nil="true" /> <PDBx:map_type>primary</PDBx:map_type> <PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x> <PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y> <PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z> <PDBx:upload_file_name>GroelD7.mrc.gz</PDBx:upload_file_name> <PDBx:upload_format>CCP4/MRC</PDBx:upload_format> </PDBx:em_map_depositor_info> </PDBx:em_map_depositor_infoCategory> 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 em_map_depositor_infoCategory This property indicates that datablock has a category holder em_map_depositor_infoCategory. em_map_depositor_infoCategory This property indicates that em_map_depositor_infoCategory. has a category em_map_depositor_info. em_map_depositor_infoItem Abstract datatype property for em_map_depositor_info items. reference_to_em_map_depositor_info cross-reference to em_map_depositor_info. referenced_by_em_map_depositor_info cross-reference from em_map_depositor_info. em_map_depositor_info.annotation_details map annotation details em_map_depositor_info.contour_level recommended contour level for viewing the map em_map_depositor_info.experiment_id This data item optionally associates a map with a data item in the EM_EXPERIMENT category. primary additional Primary map or additional map classification. em_map_depositor_info.pixel_spacing_x The length in angstroms of one voxel along the X axis. em_map_depositor_info.pixel_spacing_y The length in angstroms of one voxel along the Y axis. em_map_depositor_info.pixel_spacing_z The length in angstroms of one voxel along the Z axis. em_map_depositor_info.upload_file_name The name of a file containing the map. CCP4/MRC SPIDER map format em_map_depositor_info.entry_id This data item is a pointer to the ENTRY category. em_map_depositor_info.id Unique identifier for each map listed. 0 em_mask_depositor_info Data items in the EM_MASK_DEPOSITOR_INFO category record mask parameters that are provided by the depositor Example 1 - based on map entry EMD-5001 <PDBx:em_mask_depositor_infoCategory> <PDBx:em_mask_depositor_info id="1"> <PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details> <PDBx:contour_level>5.0</PDBx:contour_level> <PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x> <PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y> <PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z> <PDBx:upload_file_name>GroelD7.mrc.gz</PDBx:upload_file_name> <PDBx:upload_format>CCP4/MRC</PDBx:upload_format> </PDBx:em_mask_depositor_info> </PDBx:em_mask_depositor_infoCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 em_mask_depositor_infoCategory This property indicates that datablock has a category holder em_mask_depositor_infoCategory. em_mask_depositor_infoCategory This property indicates that em_mask_depositor_infoCategory. has a category em_mask_depositor_info. em_mask_depositor_infoItem Abstract datatype property for em_mask_depositor_info items. reference_to_em_mask_depositor_info cross-reference to em_mask_depositor_info. referenced_by_em_mask_depositor_info cross-reference from em_mask_depositor_info. em_mask_depositor_info.annotation_details map annotation details em_mask_depositor_info.contour_level recommended contour level for viewing the map em_mask_depositor_info.pixel_spacing_x The length in angstroms of one voxel along the X axis. em_mask_depositor_info.pixel_spacing_y The length in angstroms of one voxel along the Y axis. em_mask_depositor_info.pixel_spacing_z The length in angstroms of one voxel along the Z axis. em_mask_depositor_info.upload_file_name The name of a file containing the map. CCP4/MRC SPIDER map format em_mask_depositor_info.id Unique identifier for each map listed. 0 em_obsolete List of EMD entries made obsolete by this entry. 1 1 0 1 1 1 1 em_obsoleteCategory This property indicates that datablock has a category holder em_obsoleteCategory. em_obsoleteCategory This property indicates that em_obsoleteCategory. has a category em_obsolete. em_obsoleteItem Abstract datatype property for em_obsolete items. reference_to_em_obsolete cross-reference to em_obsolete. referenced_by_em_obsolete cross-reference from em_obsolete. em_obsolete.date Dated when the entry made obsolete the other entry em_obsolete.details Description of the reason(s) for entry obsoletion em_obsolete.entry Entry made obsolete em_obsolete.id PRIMARY KEY 0 em_particle_selection Data items in this category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_particle_selectionCategory> <PDBx:em_particle_selection id="1" image_processing_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_particles_selected>5267</PDBx:num_particles_selected> </PDBx:em_particle_selection> </PDBx:em_particle_selectionCategory> 0 1 0 1 0 1 0 1 1 1 em_particle_selectionCategory This property indicates that datablock has a category holder em_particle_selectionCategory. em_particle_selectionCategory This property indicates that em_particle_selectionCategory. has a category em_particle_selection. em_particle_selectionItem Abstract datatype property for em_particle_selection items. reference_to_em_particle_selection cross-reference to em_particle_selection. referenced_by_em_particle_selection cross-reference from em_particle_selection. em_particle_selection.details Additional detail such as description of filters used, if selection was manual or automated, and/or template details. negative monitor contrast facilitated particle picking em_particle_selection.method The method used for selecting particles particles picked interactively from monitor em_particle_selection.num_particles_selected The number of particles selected from the projection set of images. 840 em_particle_selection.reference_model Description of reference model used for particle selection em_particle_selection.id PRIMARY KEY em_particle_selection.image_processing_id The value of attribute image_processing_id in category em_particle_selection points to the EM_IMAGE_PROCESSING category. 0 em_sample_preparation Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to and upon loading onto grid support. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_preparationCategory> <PDBx:em_sample_preparation entry_id="1DYL" id="1"> <PDBx:_2d_crystal_grow_id xsi:nil="true" /> <PDBx:buffer_id>1</PDBx:buffer_id> <PDBx:ph>7.6</PDBx:ph> <PDBx:sample_concentration>5</PDBx:sample_concentration> <PDBx:support_id>1</PDBx:support_id> </PDBx:em_sample_preparation> </PDBx:em_sample_preparationCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_sample_preparationCategory This property indicates that datablock has a category holder em_sample_preparationCategory. em_sample_preparationCategory This property indicates that em_sample_preparationCategory. has a category em_sample_preparation. em_sample_preparationItem Abstract datatype property for em_sample_preparation items. reference_to_em_sample_preparation cross-reference to em_sample_preparation. referenced_by_em_sample_preparation cross-reference from em_sample_preparation. em_sample_preparation._2d_crystal_grow_id This data item is a pointer to attribute id in category em_2d_crystal_grow in the 2D_CRYSTAL_GROW category. em_sample_preparation.buffer_id This data item is a pointer to attribute id in category em_buffer in the BUFFER category. em_sample_preparation.details Details of the specimen preparation 1 Detergent-solubilized particles eluted from the cation-exchange column were directly adsorbed for 1 min to parlodion carbon-coated copper grids rendered hydrophilic by glow discharge at low pressure in air. Grids were washed with 4 drops of double-distilled water and stained with 2 drops of 0.75% uranyl formate. 2 Selectively stained by injection of horseradish peroxidase, embedded in Spurr's resin and cut into 2-3 um thick sections. 3 S. cerevisiae PDC was purified to near homogeneity from baker's yeast by modification of a published procedure. Highly purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3 followed by FPLC on a Superdex 200 column. The weight-average molecular weight of the PDC was determined by light scattering measurement to be ~8 x 106. On the basis of the known molecular weight of the complex and its component enzymes and the experimentally determined polypeptide chain ratios of E2/BP/E3, we estimated that the subunit composition of the S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers, and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC preparation to increase the molar ratio of E1/E2 core to 60:1. 4 embedded in vitreous ice. em_sample_preparation.entity_assembly_id This data item is a pointer to attribute id in category entity_assembly in the em_entity_assembly category. em_sample_preparation.ph The pH value of the observed sample buffer. 5.5 em_sample_preparation.sample_concentration The value of the concentration (mg per milliliter) of the complex in the sample. 1.35 em_sample_preparation.support_id This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. em_sample_preparation.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_sample_preparation.id The value of attribute id in category em_sample_preparation must uniquely identify the sample preparation. 0 em_sample_support Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_supportCategory> <PDBx:em_sample_support id="1"> <PDBx:details>GLOW DISCHARGED 120 seconds</PDBx:details> <PDBx:film_material>HOLEY CARBON</PDBx:film_material> <PDBx:grid_material>COPPER</PDBx:grid_material> <PDBx:grid_mesh_size>400</PDBx:grid_mesh_size> </PDBx:em_sample_support> </PDBx:em_sample_supportCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_sample_supportCategory This property indicates that datablock has a category holder em_sample_supportCategory. em_sample_supportCategory This property indicates that em_sample_supportCategory. has a category em_sample_support. em_sample_supportItem Abstract datatype property for em_sample_support items. reference_to_em_sample_support cross-reference to em_sample_support. referenced_by_em_sample_support cross-reference from em_sample_support. em_sample_support.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_sample_support.details Any additional details concerning the sample support. The grid was coated with gold prior to use CARBON FORMVAR PLUS CARBON CELLULOSE ACETATE PLUS CARBON PARLODION PLUS CARBON HOLEY CARBON SILICON DIOXIDE The support material covering the em grid. COPPER COPPER/PALLADIUM COPPER/RHODIUM GOLD GRAPHENE OXIDE NICKEL NICKEL/TITANIUM PLATINUM SILICON NITRIDE TUNGSTEN TITANIUM MOLYBDENUM The name of the material from which the grid is made. em_sample_support.grid_mesh_size The value of the mesh size (divisions per inch) of the em grid. 400 em_sample_support.grid_type A description of the grid type. em_sample_support.method A description of the method used to produce the support film. 1%formvar in chloroform cast on distilled water em_sample_support.pretreatment A description of the grid plus support film pretreatment. glow-discharged for 30 sec in argon em_sample_support.id PRIMARY KEY em_sample_support.specimen_id This data item is a pointer to attribute id in category em_sample_preparation in the EM_SPECIMEN category. 0 em_shadowing Data items related to shadowing of an EM specimen Example 1 <PDBx:em_shadowingCategory> <PDBx:em_shadowing id="1" specimen_id="1"> <PDBx:angle>45</PDBx:angle> <PDBx:details>shadowing was used to create a platinum replica</PDBx:details> <PDBx:material>Platinum</PDBx:material> <PDBx:thickness>3</PDBx:thickness> </PDBx:em_shadowing> </PDBx:em_shadowingCategory> 1 1 0 1 1 1 1 1 1 1 em_shadowingCategory This property indicates that datablock has a category holder em_shadowingCategory. em_shadowingCategory This property indicates that em_shadowingCategory. has a category em_shadowing. em_shadowingItem Abstract datatype property for em_shadowing items. reference_to_em_shadowing cross-reference to em_shadowing. referenced_by_em_shadowing cross-reference from em_shadowing. em_shadowing.angle The shadowing angle (degrees) 20 em_shadowing.details Additional details about specimen shadowing rotary shadowing directional shadowing shadowing was used to create a carbon replica em_shadowing.material The chemical, compound or material used for shadowing Platinum em_shadowing.thickness Thickness of the deposited shadow coat, in angstroms. em_shadowing.id PRIMARY KEY em_shadowing.specimen_id Foreign key relationship to the EM SPECIMEN category 0 em_single_particle_entity Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type. Example <PDBx:em_single_particle_entityCategory> <PDBx:em_single_particle_entity id="1" image_processing_id="1"> <PDBx:point_symmetry>I</PDBx:point_symmetry> </PDBx:em_single_particle_entity> </PDBx:em_single_particle_entityCategory> 1 1 0 1 0 1 1 1 em_single_particle_entityCategory This property indicates that datablock has a category holder em_single_particle_entityCategory. em_single_particle_entityCategory This property indicates that em_single_particle_entityCategory. has a category em_single_particle_entity. em_single_particle_entityItem Abstract datatype property for em_single_particle_entity items. reference_to_em_single_particle_entity cross-reference to em_single_particle_entity. referenced_by_em_single_particle_entity cross-reference from em_single_particle_entity. em_single_particle_entity.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_single_particle_entity.point_symmetry Point symmetry symbol, either Cn, Dn, T, O, or I ASYMMETRIC CYCLIC DIHEDRAL TETRAHEDRAL OCTAHEDRAL ICOSAHEDRAL MIXED SYMMETRY The single particle symmetry type. em_single_particle_entity.id PRIMARY KEY em_single_particle_entity.image_processing_id pointer to attribute id in category em_image_processing. 0 em_software Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. Example 1 <PDBx:em_softwareCategory> <PDBx:em_software id="1"> <PDBx:category>IMAGE ACQUISITION</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>Leginon</PDBx:name> <PDBx:version>1.3</PDBx:version> </PDBx:em_software> <PDBx:em_software id="2"> <PDBx:category>PARTICLE SELECTION</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>X3D</PDBx:name> <PDBx:version xsi:nil="true" /> </PDBx:em_software> <PDBx:em_software id="3"> <PDBx:category>BACKGROUND MASKING</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>bsoft</PDBx:name> <PDBx:version>1.1</PDBx:version> </PDBx:em_software> <PDBx:em_software id="4"> <PDBx:category>RECONSTRUCTION</PDBx:category> <PDBx:details>em3dr2 -low 20</PDBx:details> <PDBx:name>EM2DR2</PDBx:name> <PDBx:version>3.2</PDBx:version> </PDBx:em_software> <PDBx:em_software id="5"> <PDBx:category>EULER ASSIGNMENT</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>erandom</PDBx:name> <PDBx:version xsi:nil="true" /> </PDBx:em_software> <PDBx:em_software id="6"> <PDBx:category>CTF CORRECTION</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>bctf</PDBx:name> <PDBx:version xsi:nil="true" /> </PDBx:em_software> <PDBx:em_software id="7"> <PDBx:category>MODEL FITTING</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>chimera</PDBx:name> <PDBx:version>1.6</PDBx:version> </PDBx:em_software> </PDBx:em_softwareCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 em_softwareCategory This property indicates that datablock has a category holder em_softwareCategory. em_softwareCategory This property indicates that em_softwareCategory. has a category em_software. em_softwareItem Abstract datatype property for em_software items. reference_to_em_software cross-reference to em_software. referenced_by_em_software cross-reference from em_software. IMAGE ACQUISITION PARTICLE SELECTION VOLUME SELECTION CLASSIFICATION MASKING RECONSTRUCTION INITIAL EULER ASSIGNMENT FINAL EULER ASSIGNMENT CTF CORRECTION LAYERLINE INDEXING DIFFRACTION INDEXING MODEL FITTING MODEL REFINEMENT SERIES ALIGNMENT MOLECULAR REPLACEMENT LATTICE DISTORTION CORRECTION SYMMETRY DETERMINATION CRYSTALLOGRAPHY MERGING EWALD SPHERE CORRECTION OTHER The purpose of the software. em_software.details Details about the software used. EMAN2 e2boxer.py was used to automatically select particle images. em_software.fitting_id pointer to attribute id in category em_3d_fitting in the EM_3D_FITTING category. em_software.image_processing_id pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. em_software.imaging_id pointer to attribute id in category em_imaging in the EM_IMAGING category. em_software.name The name of the software package used, e.g., RELION. Depositors are strongly encouraged to provide a value in this field. EMAN Imagic Spider Bsoft UCSF-Chimera em_software.version The version of the software. 9.03 2.1 em_software.id PRIMARY KEY 0 em_specimen Data items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy. Example 1 -- based on PDB 2FL8 <PDBx:em_specimenCategory> <PDBx:em_specimen experiment_id="1" id="1"> <PDBx:embedding_applied>NO</PDBx:embedding_applied> <PDBx:shadowing_applied>NO</PDBx:shadowing_applied> <PDBx:staining_applied>NO</PDBx:staining_applied> <PDBx:vitrification_applied>YES</PDBx:vitrification_applied> </PDBx:em_specimen> </PDBx:em_specimenCategory> 0 1 0 1 1 1 1 1 1 1 1 1 1 1 em_specimenCategory This property indicates that datablock has a category holder em_specimenCategory. em_specimenCategory This property indicates that em_specimenCategory. has a category em_specimen. em_specimenItem Abstract datatype property for em_specimen items. reference_to_em_specimen cross-reference to em_specimen. referenced_by_em_specimen cross-reference from em_specimen. em_specimen.concentration The concentration (in milligrams per milliliter, mg/ml) of the complex in the sample. 1.35 em_specimen.details A description of any additional details of the specimen preparation. This sample was monodisperse. Au was deposited at a 30 degree angle to 15 nm thickness. Colloidal gold particles were deposited by dipping into dilute solution. The specimen was frozen at high pressure using the bal-tec hpm 010 instrument. The embedded sample was sectioned at 100 K to 50 nm final thickness. YES NO 'YES' indicates that the specimen has been embedded. YES NO 'YES' indicates that the specimen has been shadowed. YES NO 'YES' indicates that the specimen has been stained. YES NO 'YES' indicates that the specimen was vitrified by cryopreservation. em_specimen.experiment_id Pointer to attribute id in category em_experiment. em_specimen.id PRIMARY KEY 0 em_staining Staining category Example 1 <PDBx:em_stainingCategory> <PDBx:em_staining id="1"> <PDBx:material>Uranyl Acetate</PDBx:material> <PDBx:specimen_id>1</PDBx:specimen_id> <PDBx:type>NEGATIVE</PDBx:type> </PDBx:em_staining> </PDBx:em_stainingCategory> 0 1 1 1 1 1 1 1 1 em_stainingCategory This property indicates that datablock has a category holder em_stainingCategory. em_stainingCategory This property indicates that em_stainingCategory. has a category em_staining. em_stainingItem Abstract datatype property for em_staining items. reference_to_em_staining cross-reference to em_staining. referenced_by_em_staining cross-reference from em_staining. em_staining.details Staining procedure used in the specimen preparation. Negatively stained EM specimens were prepared using a carbon-sandwich technique and uranyl-formate stain. em_staining.material The staining material. Uranyl Acetate em_staining.specimen_id Foreign key relationship to the EM SPECIMEN category NEGATIVE POSITIVE NONE type of staining em_staining.id PRIMARY KEY 0 em_start_model The startup model employed to begin refinement of the parameters for a 3DEM reconstruction Example 1 -- based on PDB 3IYD <PDBx:em_start_modelCategory> <PDBx:em_start_model id="1" image_processing_id="1"> <PDBx:details>a map created from PDB entry 3DXJ was gaussian blurred to 60 Angstroms</PDBx:details> <PDBx:pdb_id>3DXJ</PDBx:pdb_id> <PDBx:type>PDB ENTRY</PDBx:type> </PDBx:em_start_model> </PDBx:em_start_modelCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 em_start_modelCategory This property indicates that datablock has a category holder em_start_modelCategory. em_start_modelCategory This property indicates that em_start_modelCategory. has a category em_start_model. em_start_modelItem Abstract datatype property for em_start_model items. reference_to_em_start_model cross-reference to em_start_model. referenced_by_em_start_model cross-reference from em_start_model. em_start_model.details Any additional details about generating the startup model em_start_model.emdb_id EMDB id of the map used as the startup model EMD-12345 em_start_model.insilico_model Description of the "in silico" model used to generate the startup model em_start_model.orthogonal_tilt_angle1 Tilt angle for the 1st image set of the orthogonal tilt pairs -45 em_start_model.orthogonal_tilt_angle2 Tilt angle for the 2nd image set of the orthogonal tilt pairs 45 em_start_model.orthogonal_tilt_num_images number of images used to generate the orthogonal tilt startup model 40 em_start_model.other Description of other method/source used to generate the startup model em_start_model.pdb_id PDB id of the model coordinates used to generate the startup model em_start_model.random_conical_tilt_angle Angular difference between the conical tilt images used to generate the startup model 60 em_start_model.random_conical_tilt_num_images number of images used to generate the random conical tilt startup model 40 RANDOM CONICAL TILT ORTHOGONAL TILT EMDB MAP PDB ENTRY INSILICO MODEL NONE OTHER Type of startup model (map density) used to initiate the reconstruction em_start_model.id PRIMARY KEY em_start_model.image_processing_id Foreign key to the EM_IMAGE_PROCESSING category 0 em_structure_factors Listing of all structure factor files associated with the EM entry Example 1 <PDBx:em_structure_factorsCategory> <PDBx:em_structure_factors experiment_id="1" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:file>emd-1234-sf.cif</PDBx:file> </PDBx:em_structure_factors> </PDBx:em_structure_factorsCategory> 0 1 1 1 1 1 em_structure_factorsCategory This property indicates that datablock has a category holder em_structure_factorsCategory. em_structure_factorsCategory This property indicates that em_structure_factorsCategory. has a category em_structure_factors. em_structure_factorsItem Abstract datatype property for em_structure_factors items. reference_to_em_structure_factors cross-reference to em_structure_factors. referenced_by_em_structure_factors cross-reference from em_structure_factors. em_structure_factors.details Details about the structure factor file. em_structure_factors.file The name of the structure factor file associated with the map entry em_structure_factors.experiment_id This data item is a pointer to the EM EXPERIMENT category. em_structure_factors.id PRIMARY KEY 0 em_structure_factors_depositor_info Structure factor files associated with the EM entry Example 1 <PDBx:em_structure_factors_depositor_infoCategory> <PDBx:em_structure_factors_depositor_info id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experiment_id>1</PDBx:experiment_id> <PDBx:upload_file_name>emd-1234-sf.cif</PDBx:upload_file_name> </PDBx:em_structure_factors_depositor_info> </PDBx:em_structure_factors_depositor_infoCategory> 0 1 0 1 1 1 1 em_structure_factors_depositor_infoCategory This property indicates that datablock has a category holder em_structure_factors_depositor_infoCategory. em_structure_factors_depositor_infoCategory This property indicates that em_structure_factors_depositor_infoCategory. has a category em_structure_factors_depositor_info. em_structure_factors_depositor_infoItem Abstract datatype property for em_structure_factors_depositor_info items. reference_to_em_structure_factors_depositor_info cross-reference to em_structure_factors_depositor_info. referenced_by_em_structure_factors_depositor_info cross-reference from em_structure_factors_depositor_info. em_structure_factors_depositor_info.details Details about the structure factor file. em_structure_factors_depositor_info.experiment_id This data item is an optional pointer to the EM_EXPERIMENT category. em_structure_factors_depositor_info.upload_file_name The name of the structure factor file associated with the map entry em_structure_factors_depositor_info.id This data item is the unique identifier for the structure factor file. 0 em_supersede List of newer entries that replace this entry. 1 1 0 1 1 1 1 em_supersedeCategory This property indicates that datablock has a category holder em_supersedeCategory. em_supersedeCategory This property indicates that em_supersedeCategory. has a category em_supersede. em_supersedeItem Abstract datatype property for em_supersede items. reference_to_em_supersede cross-reference to em_supersede. referenced_by_em_supersede cross-reference from em_supersede. em_supersede.date Dated when the entry made supersede the other entry em_supersede.details Details em_supersede.entry Newer entry that replaces this entry em_supersede.id PRIMARY KEY 0 em_support_film Data items to describe films supporting the specimen Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_support_filmCategory> <PDBx:em_support_film id="1"> <PDBx:material>CARBON</PDBx:material> </PDBx:em_support_film> </PDBx:em_support_filmCategory> 0 1 1 1 0 1 0 1 1 em_support_filmCategory This property indicates that datablock has a category holder em_support_filmCategory. em_support_filmCategory This property indicates that em_support_filmCategory. has a category em_support_film. em_support_filmItem Abstract datatype property for em_support_film items. reference_to_em_support_film cross-reference to em_support_film. referenced_by_em_support_film cross-reference from em_support_film. CARBON FORMVAR CELLULOSE ACETATE PARLODION GOLD GRAPHENE GRAPHENE OXIDE SILICON DIOXIDE The support material covering the em grid. em_support_film.sample_support_id Pointer to EM SAMPLE SUPPORT em_support_film.thickness Thickness of the support film, in angstroms CONTINUOUS LACEY HOLEY HOLEY ARRAY The topology of the material from which the grid is made. em_support_film.id PRIMARY KEY 0 em_tomography Microscopy parameters only relevant for tomography Example 1 <PDBx:em_tomographyCategory> <PDBx:em_tomography id="1" imaging_id="1"> <PDBx:axis1_angle_increment>2</PDBx:axis1_angle_increment> <PDBx:axis1_max_angle>70.</PDBx:axis1_max_angle> <PDBx:axis1_min_angle>-70.</PDBx:axis1_min_angle> <PDBx:axis2_angle_increment>2</PDBx:axis2_angle_increment> <PDBx:axis2_max_angle>70.</PDBx:axis2_max_angle> <PDBx:axis2_min_angle>-70.</PDBx:axis2_min_angle> <PDBx:dual_tilt_axis_rotation>90.</PDBx:dual_tilt_axis_rotation> </PDBx:em_tomography> </PDBx:em_tomographyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_tomographyCategory This property indicates that datablock has a category holder em_tomographyCategory. em_tomographyCategory This property indicates that em_tomographyCategory. has a category em_tomography. em_tomographyItem Abstract datatype property for em_tomography items. reference_to_em_tomography cross-reference to em_tomography. referenced_by_em_tomography cross-reference from em_tomography. em_tomography.axis1_angle_increment The angle increment of specimen tilting to obtain the recorded images (axis 1). 2 em_tomography.axis1_max_angle The maximum angle at which the specimen was tilted to obtain recorded images (axis 1). 70 em_tomography.axis1_min_angle The minimum angle at which the specimen was tilted to obtain recorded images (axis 1). -70 em_tomography.axis2_angle_increment The angle increment of specimen tilting to obtain the recorded images (axis 2). 2 em_tomography.axis2_max_angle The maximum angle at which the specimen was tilted to obtain recorded images (axis 2). 70 em_tomography.axis2_min_angle The minimum angle at which the specimen was tilted to obtain recorded images (axis 2). -70 em_tomography.dual_tilt_axis_rotation Angular difference between axis1 and axis2 in degrees em_tomography.id PRIMARY KEY em_tomography.imaging_id Foreign key to the EM IMAGING category 0 em_tomography_specimen Description specimen preparation for imaging using tomography. 0 1 0 1 0 1 0 1 0 1 1 1 1 em_tomography_specimenCategory This property indicates that datablock has a category holder em_tomography_specimenCategory. em_tomography_specimenCategory This property indicates that em_tomography_specimenCategory. has a category em_tomography_specimen. em_tomography_specimenItem Abstract datatype property for em_tomography_specimen items. reference_to_em_tomography_specimen cross-reference to em_tomography_specimen. referenced_by_em_tomography_specimen cross-reference from em_tomography_specimen. em_tomography_specimen.cryo_protectant The type of cryo-protectant used during specimen preparation. 2% glycerol em_tomography_specimen.details Any additional details about specimen preparation. Axonemes were mixed with 15-nm colloidal gold suspension conjugated with BSA. Suspended axonemes plus colloidal gold were loaded onto grids and plunge-frozen in liquid ethane with a Leica EM GP automated plunge-freezing device. YES NO 'YES' indicates that fiducial markers were used in the specimen preparation YES NO 'YES' indicates that high pressure freezing was used in the specimen preparation NO SECTIONING ULTRAMICROTOMY FOCUSED ION BEAM The type of sectioning performed during specimen preparation. em_tomography_specimen.specimen_id Foreign key relationship to the EM SPECIMEN category em_tomography_specimen.id PRIMARY KEY 0 em_ultramicrotomy Description of sectioning by ultramicrotomy 0 1 1 1 1 1 1 1 1 1 1 em_ultramicrotomyCategory This property indicates that datablock has a category holder em_ultramicrotomyCategory. em_ultramicrotomyCategory This property indicates that em_ultramicrotomyCategory. has a category em_ultramicrotomy. em_ultramicrotomyItem Abstract datatype property for em_ultramicrotomy items. reference_to_em_ultramicrotomy cross-reference to em_ultramicrotomy. referenced_by_em_ultramicrotomy cross-reference from em_ultramicrotomy. em_ultramicrotomy.details Additional details about the ultramicrotomy sample preparation em_ultramicrotomy.em_tomography_specimen_id Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category em_ultramicrotomy.final_thickness Final thickness of the sectioned sample, in nanometers 60 em_ultramicrotomy.instrument Ultramicrotome instrument used for sectioning Leica EM UC7 em_ultramicrotomy.temperature Temperature of the sample during microtome sectioning, in kelvins 100 em_ultramicrotomy.id PRIMARY KEY 0 em_virus_entity Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_virus_entityCategory> <PDBx:em_virus_entity entity_assembly_id="1" id="1"> <PDBx:empty>NO</PDBx:empty> <PDBx:enveloped>YES</PDBx:enveloped> <PDBx:ictvdb_id>00.073.0.01.023</PDBx:ictvdb_id> <PDBx:virus_host_category>VERTERBRATES</PDBx:virus_host_category> <PDBx:virus_host_species>HOMO SAPIENS</PDBx:virus_host_species> <PDBx:virus_isolate>STRAIN</PDBx:virus_isolate> <PDBx:virus_type>VIRUS</PDBx:virus_type> </PDBx:em_virus_entity> </PDBx:em_virus_entityCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_virus_entityCategory This property indicates that datablock has a category holder em_virus_entityCategory. em_virus_entityCategory This property indicates that em_virus_entityCategory. has a category em_virus_entity. em_virus_entityItem Abstract datatype property for em_virus_entity items. reference_to_em_virus_entity cross-reference to em_virus_entity. referenced_by_em_virus_entity cross-reference from em_virus_entity. em_virus_entity.details Additional details about this virus entity YES NO Flag to indicate if the virus is empty or not. YES NO Flag to indicate if the virus is enveloped or not. em_virus_entity.ictvdb_id The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. NOTE: ICTV no longer maintains ids; maintained for legacy only. NL-54 em_virus_entity.virus_host_category The host category description for the virus. ALGAE ARCHAEA BACTERIA(EUBACTERIA) FUNGI INVERTEBRATES PLANTAE (HIGHER PLANTS) PROTOZOA VERTEBRATES em_virus_entity.virus_host_growth_cell The host cell from which the virus was isolated. HELA CHO em_virus_entity.virus_host_species The host species from which the virus was isolated. homo sapiens gallus gallus STRAIN SEROTYPE SEROCOMPLEX SUBSPECIES SPECIES OTHER The isolate from which the virus was obtained. VIRION SATELLITE PRION VIROID VIRUS-LIKE PARTICLE The type of virus. em_virus_entity.entity_assembly_id This data item is a pointer to attribute id in category em_virus_entity in the ENTITY_ASSEMBLY category. em_virus_entity.id PRIMARY KEY 0 em_virus_natural_host Data items in this category record details of a virus entity. 0 1 0 1 0 1 1 1 em_virus_natural_hostCategory This property indicates that datablock has a category holder em_virus_natural_hostCategory. em_virus_natural_hostCategory This property indicates that em_virus_natural_hostCategory. has a category em_virus_natural_host. em_virus_natural_hostItem Abstract datatype property for em_virus_natural_host items. reference_to_em_virus_natural_host cross-reference to em_virus_natural_host. referenced_by_em_virus_natural_host cross-reference from em_virus_natural_host. em_virus_natural_host.ncbi_tax_id The NCBI taxonomy id for the natural host organism of the virus 9606 9031 em_virus_natural_host.organism The host organism from which the virus was isolated. Homo sapiens Gallus gallus em_virus_natural_host.strain The strain of the host organism from which the virus was obtained, if relevant. DH5a BMH 71-18 em_virus_natural_host.entity_assembly_id Pointer to attribute id in category em_entity_assembly. em_virus_natural_host.id PRIMARY KEY 0 em_virus_shell Data items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number. Example 1 -- Bluetongue Virus <PDBx:em_virus_shellCategory> <PDBx:em_virus_shell entity_assembly_id="1" id="1"> <PDBx:diameter>348</PDBx:diameter> <PDBx:name>VP7 layer</PDBx:name> <PDBx:triangulation>13</PDBx:triangulation> </PDBx:em_virus_shell> <PDBx:em_virus_shell entity_assembly_id="1" id="2"> <PDBx:diameter>348</PDBx:diameter> <PDBx:name>VP3 layer</PDBx:name> <PDBx:triangulation>2</PDBx:triangulation> </PDBx:em_virus_shell> </PDBx:em_virus_shellCategory> 0 1 0 1 0 1 1 1 em_virus_shellCategory This property indicates that datablock has a category holder em_virus_shellCategory. em_virus_shellCategory This property indicates that em_virus_shellCategory. has a category em_virus_shell. em_virus_shellItem Abstract datatype property for em_virus_shell items. reference_to_em_virus_shell cross-reference to em_virus_shell. referenced_by_em_virus_shell cross-reference from em_virus_shell. em_virus_shell.diameter The value of the diameter (in angstroms) for this virus shell. 524.0 em_virus_shell.name The name for this virus shell. em_virus_shell.triangulation The triangulation number, T, describes the organization of subunits within an icosahedron. T is defined as T= h^2 + h*k + k^2, where h and k are positive integers that define the position of the five-fold vertex on the original hexagonal net. 27 em_virus_shell.entity_assembly_id The value of attribute entity_assembly_id in category em_virus_shell is a pointer to attribute id in category em_entity_assembly category. em_virus_shell.id PRIMARY KEY 0 em_virus_synthetic Data items in this category record details of a synthetic virus entity. 0 1 0 1 0 1 1 1 em_virus_syntheticCategory This property indicates that datablock has a category holder em_virus_syntheticCategory. em_virus_syntheticCategory This property indicates that em_virus_syntheticCategory. has a category em_virus_synthetic. em_virus_syntheticItem Abstract datatype property for em_virus_synthetic items. reference_to_em_virus_synthetic cross-reference to em_virus_synthetic. referenced_by_em_virus_synthetic cross-reference from em_virus_synthetic. em_virus_synthetic.ncbi_tax_id The NCBI taxonomy ID of the host species from which the virus was isolated 10804 9606 em_virus_synthetic.organism The host organism from which the virus was isolated. Homo sapiens Gallus gallus em_virus_synthetic.strain The strain of the host organism from which the virus was obtained, if relevant. DH5a BMH 71-18 em_virus_synthetic.entity_assembly_id Pointer to attribute id in category em_entity_assembly. em_virus_synthetic.id PRIMARY KEY 0 em_vitrification Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_vitrificationCategory> <PDBx:em_vitrification id="1"> <PDBx:cryogen_name>ETHANE</PDBx:cryogen_name> <PDBx:details> SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.</PDBx:details> <PDBx:entry_id>1DYL</PDBx:entry_id> <PDBx:humidity>90</PDBx:humidity> <PDBx:instrument xsi:nil="true" /> <PDBx:method>PLUNGE VITRIFICATION</PDBx:method> <PDBx:sample_preparation_id>1</PDBx:sample_preparation_id> <PDBx:temp>95</PDBx:temp> <PDBx:time_resolved_state xsi:nil="true" /> </PDBx:em_vitrification> </PDBx:em_vitrificationCategory> 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_vitrificationCategory This property indicates that datablock has a category holder em_vitrificationCategory. em_vitrificationCategory This property indicates that em_vitrificationCategory. has a category em_vitrification. em_vitrificationItem Abstract datatype property for em_vitrification items. reference_to_em_vitrification cross-reference to em_vitrification. referenced_by_em_vitrification cross-reference from em_vitrification. em_vitrification.chamber_temperature The temperature (in kelvin) of the sample just prior to vitrification. 298 em_vitrification.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. HELIUM NITROGEN PROPANE ETHANE ETHANE-PROPANE METHANE FREON 22 FREON 12 OTHER This is the name of the cryogen. em_vitrification.details Any additional details relating to vitrification. Vitrification carried out in argon atmosphere. em_vitrification.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_vitrification.humidity Relative humidity (%) of air surrounding the specimen just prior to vitrification. 90 CRYOSOL VITROJET EMS-002 RAPID IMMERSION FREEZER FEI VITROBOT MARK I FEI VITROBOT MARK II FEI VITROBOT MARK III FEI VITROBOT MARK IV GATAN CRYOPLUNGE 3 HOMEMADE PLUNGER LEICA PLUNGER LEICA EM GP LEICA EM CPC LEICA KF80 REICHERT-JUNG PLUNGER SPOTITON SPT LABTECH CHAMELEON ZEISS PLUNGE FREEZER CRYOBOX The type of instrument used in the vitrification process. em_vitrification.method The procedure for vitrification. plunge freezing em_vitrification.sample_preparation_id This data item is a pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category. em_vitrification.temp The vitrification temperature (in kelvin), e.g., temperature of the plunge instrument cryogen bath. 90 em_vitrification.time_resolved_state The length of time after an event effecting the sample that vitrification was induced and a description of the event. plunge 30 msec after spraying with effector em_vitrification.id PRIMARY KEY em_vitrification.specimen_id This data item is a pointer to attribute id in category em_specimen 0 em_volume_selection Volume selection in image processing Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_volume_selectionCategory> <PDBx:em_volume_selection id="1" image_processing_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_volumes_extracted>5267</PDBx:num_volumes_extracted> </PDBx:em_volume_selection> </PDBx:em_volume_selectionCategory> 0 1 0 1 1 1 1 1 0 1 1 1 em_volume_selectionCategory This property indicates that datablock has a category holder em_volume_selectionCategory. em_volume_selectionCategory This property indicates that em_volume_selectionCategory. has a category em_volume_selection. em_volume_selectionItem Abstract datatype property for em_volume_selection items. reference_to_em_volume_selection cross-reference to em_volume_selection. referenced_by_em_volume_selection cross-reference from em_volume_selection. em_volume_selection.details Any additional details used for selecting volumes. negative monitor contrast facilitated volume picking em_volume_selection.method The method used for selecting volumes. volumes picked interactively em_volume_selection.num_tomograms The number of tomograms used in the extraction/selection 20 em_volume_selection.num_volumes_extracted The number of volumes selected from the projection set of images. 840 em_volume_selection.reference_model Description of reference model used for volume selection em_volume_selection.id PRIMARY KEY em_volume_selection.image_processing_id The value of attribute image_processing_id in category em_volume_selection points to the EM_IMAGE_PROCESSING category. 0 entity Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entityCategory> <PDBx:entity id="1"> <PDBx:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</PDBx:details> <PDBx:formula_weight>10916</PDBx:formula_weight> <PDBx:type>polymer</PDBx:type> </PDBx:entity> <PDBx:entity id="2"> <PDBx:details xsi:nil="true" /> <PDBx:formula_weight>762</PDBx:formula_weight> <PDBx:type>non-polymer</PDBx:type> </PDBx:entity> <PDBx:entity id="3"> <PDBx:details xsi:nil="true" /> <PDBx:formula_weight>18</PDBx:formula_weight> <PDBx:type>water</PDBx:type> </PDBx:entity> </PDBx:entityCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entityCategory This property indicates that datablock has a category holder entityCategory. entityCategory This property indicates that entityCategory. has a category entity. entityItem Abstract datatype property for entity items. reference_to_entity cross-reference to entity. referenced_by_entity cross-reference from entity. entity.details A description of special aspects of the entity. entity.formula_weight Formula mass in daltons of the entity. entity.pdbx_description A description of the entity. Corresponds to the compound name in the PDB format. DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3') PROFLAVINE PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1)) entity.pdbx_ec Enzyme Commission (EC) number(s) 2.7.7.7 entity.pdbx_entities_per_biological_unit Number of entity molecules in the biological assembly. 1 2 3 entity.pdbx_formula_weight_exptl Experimentally determined formula mass in daltons of the entity MASS SPEC Method used to determine attribute pdbx_formula_weight_exptl in category entity. MASS SPEC entity.pdbx_fragment Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN entity.pdbx_modification Description(s) of any chemical or post-translational modifications entity.pdbx_mutation Details about any entity mutation(s). Y31H DEL(298-323) entity.pdbx_number_of_molecules A place holder for the number of molecules of the entity in the entry. 1 2 3 entity.pdbx_parent_entity_id An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source. 1 2 3 entity.pdbx_target_id The value of attribute target_id in category entity points to a TARGETDB target idenitifier from which this entity was generated. nat man syn The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. polymer non-polymer macrolide water branched Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. entity.id The value of attribute id in category entity must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. 0 entity_keywords Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_keywordsCategory> <PDBx:entity_keywords entity_id="2"> <PDBx:text>natural product, inhibitor, reduced peptide</PDBx:text> </PDBx:entity_keywords> </PDBx:entity_keywordsCategory> 0 1 0 1 0 1 0 1 0 1 1 entity_keywordsCategory This property indicates that datablock has a category holder entity_keywordsCategory. entity_keywordsCategory This property indicates that entity_keywordsCategory. has a category entity_keywords. entity_keywordsItem Abstract datatype property for entity_keywords items. reference_to_entity_keywords cross-reference to entity_keywords. referenced_by_entity_keywords cross-reference from entity_keywords. entity_keywords.pdbx_antibody_isotype PDB placeholder. entity_keywords.pdbx_ec Enzyme Commission (EC) number(s) 2.7.7.7 entity_keywords.pdbx_fragment Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN entity_keywords.pdbx_mutation Entity mutation description(s). Y31H DEL(298-323) entity_keywords.text Keywords describing this entity. polypeptide natural product polysaccharide entity_keywords.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_link Data items in the ENTITY_LINK category give details about the links between entities. 0 1 1 1 1 1 0 1 0 1 1 entity_linkCategory This property indicates that datablock has a category holder entity_linkCategory. entity_linkCategory This property indicates that entity_linkCategory. has a category entity_link. entity_linkItem Abstract datatype property for entity_link items. reference_to_entity_link cross-reference to entity_link. referenced_by_entity_link cross-reference from entity_link. entity_link.details A description of special aspects of a link between chemical components in the structure. entity_link.entity_id_1 The entity ID of the first of the two entities joined by the link. This data item is a pointer to attribute id in category entity in the ENTITY category. entity_link.entity_id_2 The entity ID of the second of the two entities joined by the link. This data item is a pointer to attribute id in category entity in the ENTITY category. entity_link.entity_seq_num_1 For a polymer entity, the sequence number in the first of the two entities containing the link. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. entity_link.entity_seq_num_2 For a polymer entity, the sequence number in the second of the two entities containing the link. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. entity_link.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 entity_name_com Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_name_comCategory> <PDBx:entity_name_com entity_id="1"> <PDBx:name>HIV-1 protease monomer</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="1"> <PDBx:name>HIV-1 PR monomer</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2"> <PDBx:name>acetyl-pepstatin</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2"> <PDBx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="3"> <PDBx:name>water</PDBx:name> </PDBx:entity_name_com> </PDBx:entity_name_comCategory> 0 1 0 1 1 entity_name_comCategory This property indicates that datablock has a category holder entity_name_comCategory. entity_name_comCategory This property indicates that entity_name_comCategory. has a category entity_name_com. entity_name_comItem Abstract datatype property for entity_name_com items. reference_to_entity_name_com cross-reference to entity_name_com. referenced_by_entity_name_com cross-reference from entity_name_com. entity_name_com.name A common name for the entity. HIV protease monomer hemoglobin alpha chain 2-fluoro-1,4-dichloro benzene arbutin UNIPROT AUTHOR Provides the provenance of the name in the attribute name in category entity_name_com field entity_name_com.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_name_sys Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_name_sysCategory> <PDBx:entity_name_sys entity_id="1"> <PDBx:name>EC 3.4.23.16</PDBx:name> </PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="2"> <PDBx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</PDBx:name> </PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="3"> <PDBx:name>water</PDBx:name> </PDBx:entity_name_sys> </PDBx:entity_name_sysCategory> 0 1 0 1 1 entity_name_sysCategory This property indicates that datablock has a category holder entity_name_sysCategory. entity_name_sysCategory This property indicates that entity_name_sysCategory. has a category entity_name_sys. entity_name_sysItem Abstract datatype property for entity_name_sys items. reference_to_entity_name_sys cross-reference to entity_name_sys. referenced_by_entity_name_sys cross-reference from entity_name_sys. entity_name_sys.name The systematic name for the entity. hydroquinone-beta-D-pyranoside EC 2.1.1.1 2-fluoro-1,4-dichlorobenzene entity_name_sys.system The system used to generate the systematic name of the entity. Chemical Abstracts conventions enzyme convention Sigma catalog entity_name_sys.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_poly Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_polyCategory> <PDBx:entity_poly entity_id="1"> <PDBx:nstd_chirality>no</PDBx:nstd_chirality> <PDBx:nstd_linkage>no</PDBx:nstd_linkage> <PDBx:nstd_monomer>no</PDBx:nstd_monomer> <PDBx:type>polypeptide(L)</PDBx:type> <PDBx:type_details xsi:nil="true" /> </PDBx:entity_poly> </PDBx:entity_polyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 entity_polyCategory This property indicates that datablock has a category holder entity_polyCategory. entity_polyCategory This property indicates that entity_polyCategory. has a category entity_poly. entity_polyItem Abstract datatype property for entity_poly items. reference_to_entity_poly cross-reference to entity_poly. referenced_by_entity_poly cross-reference from entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in attribute type in category entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by attribute type in category entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer that is not considered standard. entity_poly.number_of_monomers The number of monomers in the polymer. entity_poly.pdbx_C_terminal_seq_one_letter_code C-terminal cloning artifacts and/or HIS tag. HHHHHH entity_poly.pdbx_N_terminal_seq_one_letter_code N-terminal cloning artifacts and/or HIS tag. HHHHHH Y N A code to indicate that this sequence should be assigned a PDB sequence reference. Y Y N A flag to indicate that linking data is explicitly provided for this polymer in the PDBX_ENTITY_POLY_COMP_LINK_LIST category entity_poly.pdbx_seq_align_begin The sequence position in the database sequence at which the alignment with your sequence begins. 59 entity_poly.pdbx_seq_align_end The sequence position in the database sequence at which the alignment with your sequence ends. 685 entity_poly.pdbx_seq_db_id The identifier for this sequence in the sequence data base. P00730 EMBL GB PIR SWS UNP The name of the sequence data base containing a database entry for this sequence. Enter UNP for a Uniport entry Enter SWS for a Swiss-Prot entry Enter GB for a GenBank entry Enter EMBL for an European Molecular Biology Laboratory entry Enter PIR for a Protein Information Resource entry entity_poly.pdbx_seq_one_letter_code Sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymer, each residue is represented by the code of its individual type. A cyclic polymer is represented in linear sequence from the chosen start to end. A for Alanine or Adenosine-5'-monophosphate C for Cysteine or Cytidine-5'-monophosphate D for Aspartic acid E for Glutamic acid F for Phenylalanine G for Glycine or Guanosine-5'-monophosphate H for Histidine I for Isoleucine or Inosinic Acid L for Leucine K for Lysine M for Methionine N for Asparagine or Unknown ribonucleotide O for Pyrrolysine P for Proline Q for Glutamine R for Arginine S for Serine T for Threonine U for Selenocysteine or Uridine-5'-monophosphate V for Valine W for Tryptophan Y for Tyrosine (DA) for 2'-deoxyadenosine-5'-monophosphate (DC) for 2'-deoxycytidine-5'-monophosphate (DG) for 2'-deoxyguanosine-5'-monophosphate (DT) for Thymidine-5'-monophosphate (MSE) for Selenomethionine (SEP) for Phosphoserine (TPO) for Phosphothreonine (PTR) for Phosphotyrosine (PCA) for Pyroglutamic acid (UNK) for Unknown amino acid (ACE) for Acetylation cap (NH2) for Amidation cap (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD entity_poly.pdbx_seq_one_letter_code_can Canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in attribute pdbx_seq_one_letter_code in category entity_poly. Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in attribute mon_nstd_parent_comp_id in category chem_comp, or by letter 'X' if parent is not specified. Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. For modifications with several parent amino acids, all corresponding parent amino acid codes will be listed (ex. chromophores). MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD entity_poly.pdbx_seq_one_letter_code_sample For cases in which the sample and model sequence differ this item contains the sample chemical sequence expressed as string of one-letter amino acid codes. Modified may be include as 'X' or with their 3-letter codes in parentheses. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other entity_poly.pdbx_seq_three_letter_code Chemical sequence expressed as string of three-letter amino acid codes. alanine ALA arginine ARG asparagine ASN aspartic-acid ASP ambiguous asparagine/aspartic-acid ASX cysteine CYS glutamine GLN glutamic-acid GLU glycine GLY ambiguous glutamine/glutamic acid GLX histidine HIS isoleucine ILE leucine LEU lysine LYS methionine MET phenylalanine PHE proline PRO serine SER threonine THR tryptophan TRP tyrosine TYR valine VAL 1-methyladenosine 1MA 5-methycytosine 5MC 2(prime)-O-methycytodine OMC 1-methyguanosine 1MG N(2)-methyguanosine 2MG N(2)-dimethyguanosine M2G 7-methyguanosine 7MG 2(prime)-O-methyguanosine 0MG diydrouridine H2U ribosylthymidine 5MU pseudouridine PSU acetic acid ACE formic acid FOR water HOH other UNK depositor provided derived from coordinates Evidence for the assignment of the polymer sequence. entity_poly.pdbx_strand_id The PDB strand/chain id(s) corresponding to this polymer entity. A B A,B,C entity_poly.pdbx_target_identifier For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database. 356560 polypeptide(D) polypeptide(L) polydeoxyribonucleotide polyribonucleotide polydeoxyribonucleotide/polyribonucleotide hybrid cyclic-pseudo-peptide peptide nucleic acid other The type of the polymer. entity_poly.type_details A description of special aspects of the polymer type. monomer Ala 16 is a D-amino acid the oligomer contains alternating RNA and DNA units entity_poly.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_poly_seq Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_poly_seqCategory> <PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></PDBx:entity_poly_seq> </PDBx:entity_poly_seqCategory> 0 1 1 1 1 entity_poly_seqCategory This property indicates that datablock has a category holder entity_poly_seqCategory. entity_poly_seqCategory This property indicates that entity_poly_seqCategory. has a category entity_poly_seq. entity_poly_seqItem Abstract datatype property for entity_poly_seq items. reference_to_entity_poly_seq cross-reference to entity_poly_seq. referenced_by_entity_poly_seq cross-reference from entity_poly_seq. no n yes y A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. entity_poly_seq.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. entity_poly_seq.mon_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. entity_poly_seq.num The value of attribute num in category entity_poly_seq must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. 0 entity_src_gen Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_src_genCategory> <PDBx:entity_src_gen entity_id="1" pdbx_src_id="1"> <PDBx:gene_src_common_name>HIV-1</PDBx:gene_src_common_name> <PDBx:gene_src_strain>NY-5</PDBx:gene_src_strain> <PDBx:host_org_common_name>bacteria</PDBx:host_org_common_name> <PDBx:host_org_genus>Escherichia</PDBx:host_org_genus> <PDBx:host_org_species>coli</PDBx:host_org_species> <PDBx:plasmid_name>pB322</PDBx:plasmid_name> </PDBx:entity_src_gen> </PDBx:entity_src_genCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 entity_src_genCategory This property indicates that datablock has a category holder entity_src_genCategory. entity_src_genCategory This property indicates that entity_src_genCategory. has a category entity_src_gen. entity_src_genItem Abstract datatype property for entity_src_gen items. reference_to_entity_src_gen cross-reference to entity_src_gen. referenced_by_entity_src_gen cross-reference from entity_src_gen. entity_src_gen.expression_system_id A unique identifier for the expression system. This should be extracted from a local list of expression systems. entity_src_gen.gene_src_common_name The common name of the natural organism from which the gene was obtained. man yeast bacteria entity_src_gen.gene_src_details A description of special aspects of the natural organism from which the gene was obtained. entity_src_gen.gene_src_dev_stage A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active. entity_src_gen.gene_src_genus The genus of the natural organism from which the gene was obtained. Homo Saccharomyces Escherichia entity_src_gen.gene_src_species The species of the natural organism from which the gene was obtained. sapiens cerevisiae coli entity_src_gen.gene_src_strain The strain of the natural organism from which the gene was obtained, if relevant. DH5a BMH 71-18 entity_src_gen.gene_src_tissue The tissue of the natural organism from which the gene was obtained. heart liver eye lens entity_src_gen.gene_src_tissue_fraction The subcellular fraction of the tissue of the natural organism from which the gene was obtained. mitochondria nucleus membrane entity_src_gen.host_org_common_name The common name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item be derived from attribute host_org_common_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express yeast bacteria entity_src_gen.host_org_details A description of special aspects of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would derived from attribute host_org_details in category entity_src_gen_express entity_src_gen.host_org_genus The genus of the organism that served as host for the production of the entity. Saccharomyces Escherichia entity_src_gen.host_org_species The species of the organism that served as host for the production of the entity. cerevisiae coli entity_src_gen.host_org_strain The strain of the organism in which the entity was expressed. Where full details of the protein production are available it would be expected that this item be derived from attribute host_org_strain in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express DH5a BMH 71-18 sample model This data item identifies cases in which an alternative source modeled. entity_src_gen.pdbx_beg_seq_num The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. entity_src_gen.pdbx_description Information on the source which is not given elsewhere. entity_src_gen.pdbx_end_seq_num The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. entity_src_gen.pdbx_gene_src_atcc American Type Culture Collection tissue culture number. 6051 entity_src_gen.pdbx_gene_src_cell Cell type. ENDOTHELIAL entity_src_gen.pdbx_gene_src_cell_line The specific line of cells. HELA CELLS entity_src_gen.pdbx_gene_src_cellular_location Identifies the location inside (or outside) the cell. CYTOPLASM NUCLEUS entity_src_gen.pdbx_gene_src_culture_collection Culture collection identifier. 6051 entity_src_gen.pdbx_gene_src_fragment A domain or fragment of the molecule. CYTOPLASM NUCLEUS entity_src_gen.pdbx_gene_src_gene Identifies the gene. entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. entity_src_gen.pdbx_gene_src_organ Organized group of tissues that carries on a specialized function. KIDNEY LIVER PANCREAS entity_src_gen.pdbx_gene_src_organelle Organized structure within cell. MITOCHONDRIA entity_src_gen.pdbx_gene_src_plasmid The source plasmid. entity_src_gen.pdbx_gene_src_plasmid_name The source plasmid. entity_src_gen.pdbx_gene_src_scientific_name Scientific name of the organism. ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE entity_src_gen.pdbx_gene_src_variant Identifies the variant. DELTAH1DELTATRP entity_src_gen.pdbx_host_org_atcc Americal Tissue Culture Collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_culture_collection in category entity_src_gen_express entity_src_gen.pdbx_host_org_cell Cell type from which the gene is derived. Where entity.target_id is provided this should be derived from details of the target. ENDOTHELIAL entity_src_gen.pdbx_host_org_cell_line A specific line of cells used as the expression system. Where full details of the protein production are available it would be expected that this item would be derived from entity_src_gen_express.host_org_cell_line HELA entity_src_gen.pdbx_host_org_cellular_location Identifies the location inside (or outside) the cell which expressed the molecule. CYTOPLASM NUCLEUS entity_src_gen.pdbx_host_org_culture_collection Culture collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived somehwere, but exactly where is not clear. entity_src_gen.pdbx_host_org_gene Specific gene which expressed the molecule. HIV-1 POL GLNS7 U1A (2-98, Y31H, Q36R) entity_src_gen.pdbx_host_org_ncbi_taxonomy_id NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. entity_src_gen.pdbx_host_org_organ Specific organ which expressed the molecule. KIDNEY entity_src_gen.pdbx_host_org_organelle Specific organelle which expressed the molecule. MITOCHONDRIA entity_src_gen.pdbx_host_org_scientific_name The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_scientific_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express ESCHERICHIA COLI SACCHAROMYCES CEREVISIAE entity_src_gen.pdbx_host_org_strain The strain of the organism in which the entity was expressed. AR120 entity_src_gen.pdbx_host_org_tissue The specific tissue which expressed the molecule. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_tissue in category entity_src_gen_express heart liver eye lens entity_src_gen.pdbx_host_org_tissue_fraction The fraction of the tissue which expressed the molecule. mitochondria nucleus membrane entity_src_gen.pdbx_host_org_variant Variant of the organism used as the expression system. Where full details of the protein production are available it would be expected that this item be derived from entity_src_gen_express.host_org_variant or via attribute host_org_tax_id in category entity_src_gen_express TRP-LAC LAMBDA DE3 entity_src_gen.pdbx_host_org_vector Identifies the vector used. Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_name in category entity_src_gen_clone. PBIT36 PET15B PUC18 entity_src_gen.pdbx_host_org_vector_type Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_type in category entity_src_gen_express. COSMID PLASMID N-terminal tag C-terminal tag Biological sequence Linker This data item povides additional information about the sequence type. entity_src_gen.plasmid_details A description of special aspects of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute details in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. entity_src_gen.plasmid_name The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute name in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. pET3C pT123sab entity_src_gen.start_construct_id A pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct. entity_src_gen.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. entity_src_gen.pdbx_src_id This data item is an ordinal identifier for entity_src_gen data records. 0 entity_src_nat Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_src_natCategory> <PDBx:entity_src_nat entity_id="2" pdbx_src_id="1"> <PDBx:common_name>bacteria</PDBx:common_name> <PDBx:details> Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales.</PDBx:details> <PDBx:genus>Actinomycetes</PDBx:genus> </PDBx:entity_src_nat> </PDBx:entity_src_natCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 entity_src_natCategory This property indicates that datablock has a category holder entity_src_natCategory. entity_src_natCategory This property indicates that entity_src_natCategory. has a category entity_src_nat. entity_src_natItem Abstract datatype property for entity_src_nat items. reference_to_entity_src_nat cross-reference to entity_src_nat. referenced_by_entity_src_nat cross-reference from entity_src_nat. entity_src_nat.common_name The common name of the organism from which the entity was isolated. man yeast bacteria entity_src_nat.details A description of special aspects of the organism from which the entity was isolated. entity_src_nat.genus The genus of the organism from which the entity was isolated. Homo Saccharomyces Escherichia sample model This data item identifies cases in which an alternative source modeled. entity_src_nat.pdbx_atcc Americal Tissue Culture Collection number. 6051 entity_src_nat.pdbx_beg_seq_num The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. entity_src_nat.pdbx_cell A particular cell type. BHK-21 entity_src_nat.pdbx_cell_line The specific line of cells. HELA entity_src_nat.pdbx_cellular_location Identifies the location inside (or outside) the cell. entity_src_nat.pdbx_culture_collection Culture Collection identifier. 6051 entity_src_nat.pdbx_end_seq_num The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. entity_src_nat.pdbx_fragment A domain or fragment of the molecule. entity_src_nat.pdbx_ncbi_taxonomy_id NCBI Taxonomy identifier for the source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. entity_src_nat.pdbx_organ Organized group of tissues that carries on a specialized function. KIDNEY entity_src_nat.pdbx_organelle Organized structure within cell. MITOCHONDRIA entity_src_nat.pdbx_organism_scientific Scientific name of the organism of the natural source. BOS TAURUS SUS SCROFA ASPERGILLUS ORYZAE entity_src_nat.pdbx_plasmid_details Details about the plasmid. PLC28 DERIVATIVE entity_src_nat.pdbx_plasmid_name The plasmid containing the gene. pB322 entity_src_nat.pdbx_secretion Identifies the secretion from which the molecule was isolated. saliva urine venom entity_src_nat.pdbx_variant Identifies the variant. entity_src_nat.species The species of the organism from which the entity was isolated. sapiens cerevisiae coli entity_src_nat.strain The strain of the organism from which the entity was isolated. DH5a BMH 71-18 entity_src_nat.tissue The tissue of the organism from which the entity was isolated. heart liver eye lens entity_src_nat.tissue_fraction The subcellular fraction of the tissue of the organism from which the entity was isolated. mitochondria nucleus membrane entity_src_nat.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. entity_src_nat.pdbx_src_id This data item is an ordinal identifier for entity_src_nat data records. 0 entry There is only one item in the ENTRY category, attribute id in category entry. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entryCategory> <PDBx:entry id="5HVP"></PDBx:entry> </PDBx:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:entryCategory> <PDBx:entry id="TOZ"></PDBx:entry> </PDBx:entryCategory> 0 1 1 entryCategory This property indicates that datablock has a category holder entryCategory. entryCategory This property indicates that entryCategory. has a category entry. entryItem Abstract datatype property for entry items. reference_to_entry cross-reference to entry. referenced_by_entry cross-reference from entry. entry.pdbx_DOI Document Object Identifier (DOI) for this entry registered with http://crossref.org. entry.id The value of attribute id in category entry identifies the data block. Note that this item need not be a number; it can be any unique identifier. 0 entry_link Data items in the ENTRY_LINK category record the relationships between the current data block identified by attribute id in category entry and other data blocks within the current file which may be referenced in the current data block. Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:entry_linkCategory> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_COM"> <PDBx:details>experimental data common to ref./mod. structures</PDBx:details> </PDBx:entry_link> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_REF"> <PDBx:details>reference structure</PDBx:details> </PDBx:entry_link> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_MOD"> <PDBx:details>modulated structure</PDBx:details> </PDBx:entry_link> </PDBx:entry_linkCategory> 0 1 1 1 entry_linkCategory This property indicates that datablock has a category holder entry_linkCategory. entry_linkCategory This property indicates that entry_linkCategory. has a category entry_link. entry_linkItem Abstract datatype property for entry_link items. reference_to_entry_link cross-reference to entry_link. referenced_by_entry_link cross-reference from entry_link. entry_link.details A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. entry_link.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. entry_link.id The value of attribute id in category entry_link identifies a data block related to the current data block. 0 exptl Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <PDBx:exptlCategory> <PDBx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction"> <PDBx:absorpt_coefficient_mu>1.22</PDBx:absorpt_coefficient_mu> <PDBx:absorpt_correction_T_max>0.896</PDBx:absorpt_correction_T_max> <PDBx:absorpt_correction_T_min>0.802</PDBx:absorpt_correction_T_min> <PDBx:absorpt_correction_type>integration</PDBx:absorpt_correction_type> <PDBx:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</PDBx:absorpt_process_details> <PDBx:crystals_number>1</PDBx:crystals_number> <PDBx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</PDBx:details> <PDBx:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</PDBx:method_details> </PDBx:exptl> </PDBx:exptlCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 exptlCategory This property indicates that datablock has a category holder exptlCategory. exptlCategory This property indicates that exptlCategory. has a category exptl. exptlItem Abstract datatype property for exptl items. reference_to_exptl cross-reference to exptl. referenced_by_exptl cross-reference from exptl. exptl.absorpt_coefficient_mu The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. exptl.absorpt_correction_T_max The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. exptl.absorpt_correction_T_min The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. analytical cylinder empirical gaussian integration multi-scan none numerical psi-scan refdelf sphere The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. exptl.absorpt_process_details Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. Tompa analytical exptl.crystals_number The total number of crystals used in the measurement of intensities. exptl.details Any special information about the experimental work prior to the intensity measurement. See also attribute preparation in category exptl_crystal. exptl.method_details A description of special aspects of the experimental method. 29 structures minimized average structure exptl.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION INFRARED SPECTROSCOPY EPR FLUORESCENCE TRANSFER THEORETICAL MODEL The method used in the experiment. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION 0 exptl_crystal Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:F_000>202</PDBx:F_000> <PDBx:colour>pale yellow</PDBx:colour> <PDBx:density_Matthews>1.01</PDBx:density_Matthews> <PDBx:density_diffrn>1.113</PDBx:density_diffrn> <PDBx:density_meas>1.11</PDBx:density_meas> <PDBx:density_meas_temp>294.5</PDBx:density_meas_temp> <PDBx:density_method>neutral buoyancy</PDBx:density_method> <PDBx:density_percent_sol>0.15</PDBx:density_percent_sol> <PDBx:description>hexagonal rod, uncut</PDBx:description> <PDBx:preparation> hanging drop, crystal soaked in 10&#37; ethylene glycol for 10 h, then placed in nylon loop at data collection time</PDBx:preparation> <PDBx:size_max>0.30</PDBx:size_max> <PDBx:size_mid>0.20</PDBx:size_mid> <PDBx:size_min>0.05</PDBx:size_min> <PDBx:size_rad>0.025</PDBx:size_rad> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> Example 2 - using separate items to define upper and lower limits for a value. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:density_meas_gt>2.5</PDBx:density_meas_gt> <PDBx:density_meas_lt>5.0</PDBx:density_meas_lt> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> Example 3 - here the density was measured at some unspecified temperature below room temperature. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:density_meas_temp_lt>300</PDBx:density_meas_temp_lt> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 exptl_crystalCategory This property indicates that datablock has a category holder exptl_crystalCategory. exptl_crystalCategory This property indicates that exptl_crystalCategory. has a category exptl_crystal. exptl_crystalItem Abstract datatype property for exptl_crystal items. reference_to_exptl_crystal cross-reference to exptl_crystal. referenced_by_exptl_crystal cross-reference from exptl_crystal. exptl_crystal.F_000 The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 degree f~i~ = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell exptl_crystal.colour The colour of the crystal. dark green metallic dull clear The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. light dark whitish blackish grayish brownish reddish pinkish orangish yellowish greenish bluish The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. colourless white black gray brown red pink orange yellow green blue violet The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. exptl_crystal.density_Matthews The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. exptl_crystal.density_diffrn Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). exptl_crystal.density_meas Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). exptl_crystal.density_meas_esd The estimated standard deviation of attribute density_meas in category exptl_crystal. exptl_crystal.density_meas_gt The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which attribute density_meas in category exptl_crystal should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under attribute density_meas in category exptl_crystal. lower limit for the density (only the range within which the density lies was given in the original paper) 2.5 exptl_crystal.density_meas_lt The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which attribute density_meas in category exptl_crystal should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under attribute density_meas in category exptl_crystal. specimen floats in water 1.0 upper limit for the density (only the range within which the density lies was given in the original paper) 5.0 exptl_crystal.density_meas_temp Temperature in kelvins at which attribute density_meas in category exptl_crystal was determined. exptl_crystal.density_meas_temp_esd The estimated standard deviation of attribute density_meas_temp in category exptl_crystal. exptl_crystal.density_meas_temp_gt Temperature in kelvins above which attribute density_meas in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and attribute density_meas_temp_lt in category exptl_crystal should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under attribute density_meas_temp in category exptl_crystal. exptl_crystal.density_meas_temp_lt Temperature in kelvins below which attribute density_meas in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and attribute density_meas_temp_lt in category exptl_crystal should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under attribute density_meas_temp in category exptl_crystal. The density was measured at some unspecified temperature below room temperature. 300 exptl_crystal.density_method The method used to measure attribute density_meas in category exptl_crystal. exptl_crystal.density_percent_sol Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule exptl_crystal.description A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. exptl_crystal.pdbx_crystal_diffrn_lifetime The measured diffraction limit for this crystal. exptl_crystal.pdbx_crystal_diffrn_limit The measured diffraction limit for this crystal. exptl_crystal.pdbx_crystal_direction_1 The crystal size along the first measured direction in millimeters. exptl_crystal.pdbx_crystal_direction_2 The crystal size along the second measured direction in millimeters. exptl_crystal.pdbx_crystal_direction_3 The crystal size along the third measured direction in millimeters. Y N A code to indicate that a crystal image is available for this crystal. exptl_crystal.pdbx_crystal_image_format The image format for the file containing the image of crystal specified as an RFC2045/RFC2046 mime type. jpeg gif tiff exptl_crystal.pdbx_crystal_image_url The URL for an a file containing the image of crystal. exptl_crystal.pdbx_mosaic_block_size Isotropic and resolution-independent term representing the average size of mosaic domains in the crystal specified in Angstroms. Larger size indicates better ordered crystals. exptl_crystal.pdbx_mosaic_block_size_esd The uncertainty in the mosaic block size estimate for the crystal. exptl_crystal.pdbx_mosaic_method How parameters derived from the spot shape (such as mosaic block size and rotation, beam divergence, and crossfire) and their errors were estimated. See the related items section. This can be a written description or a citation to a specific software package that determined these parameters. Note, these parameters are considered derived terms from the data, as opposed to measured terms from the instrument (such as diffrn_radiation.div_x_source, a term similar to pdbx_crystal_alignment.crossfire_x). exptl_crystal.pdbx_mosaicity Isotropic approximation of the distribution of mis-orientation angles specified in degrees of all the mosaic domain blocks in the crystal, represented as a standard deviation. Here, a mosaic block is a set of contiguous unit cells assumed to be perfectly aligned. Lower mosaicity indicates better ordered crystals. See for example: Nave, C. (1998). Acta Cryst. D54, 848-853. Note that many software packages estimate the mosaic rotation distribution differently and may combine several physical properties of the experiment into a single mosaic term. This term will help fit the modeled spots to the observed spots without necessarily being directly related to the physics of the crystal itself. exptl_crystal.pdbx_mosaicity_esd The uncertainty in the mosaicity estimate for the crystal. Y N A code to indicate that an x-ray image is available for this crystal. exptl_crystal.pdbx_x-ray_image_type A description of the type of x-ray image for this crystal. exptl_crystal.preparation Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. mounted in an argon-filled quartz capillary exptl_crystal.size_max The maximum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.size_mid The medial dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.size_min The minimum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.size_rad The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.id The value of attribute id in category exptl_crystal must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. 0 exptl_crystal_face Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4 for the 100 face of crystal xstl1. <PDBx:exptl_crystal_faceCategory> <PDBx:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0"> <PDBx:diffr_chi>42.56</PDBx:diffr_chi> <PDBx:diffr_kappa>30.23</PDBx:diffr_kappa> <PDBx:diffr_phi>-125.56</PDBx:diffr_phi> <PDBx:diffr_psi>-0.34</PDBx:diffr_psi> <PDBx:perp_dist>0.025</PDBx:perp_dist> </PDBx:exptl_crystal_face> </PDBx:exptl_crystal_faceCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 1 exptl_crystal_faceCategory This property indicates that datablock has a category holder exptl_crystal_faceCategory. exptl_crystal_faceCategory This property indicates that exptl_crystal_faceCategory. has a category exptl_crystal_face. exptl_crystal_faceItem Abstract datatype property for exptl_crystal_face items. reference_to_exptl_crystal_face cross-reference to exptl_crystal_face. referenced_by_exptl_crystal_face cross-reference from exptl_crystal_face. exptl_crystal_face.diffr_chi The chi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.diffr_kappa The kappa diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.diffr_phi The phi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.diffr_psi The psi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.perp_dist The perpendicular distance in millimetres from the face to the centre of rotation of the crystal. exptl_crystal_face.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. exptl_crystal_face.index_h Miller index h of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.index_k Miller index k of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.index_l Miller index l of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. 0 exptl_crystal_grow Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:exptl_crystal_growCategory> <PDBx:exptl_crystal_grow crystal_id="1"> <PDBx:apparatus>Linbro plates</PDBx:apparatus> <PDBx:atmosphere>room air</PDBx:atmosphere> <PDBx:method>VAPOR DIFFUSION, HANGING DROP</PDBx:method> <PDBx:pH>4.7</PDBx:pH> <PDBx:temp>291</PDBx:temp> <PDBx:time>approximately 2 days</PDBx:time> </PDBx:exptl_crystal_grow> </PDBx:exptl_crystal_growCategory> 0 1 0 1 0 1 0 1 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 exptl_crystal_growCategory This property indicates that datablock has a category holder exptl_crystal_growCategory. exptl_crystal_growCategory This property indicates that exptl_crystal_growCategory. has a category exptl_crystal_grow. exptl_crystal_growItem Abstract datatype property for exptl_crystal_grow items. reference_to_exptl_crystal_grow cross-reference to exptl_crystal_grow. referenced_by_exptl_crystal_grow cross-reference from exptl_crystal_grow. exptl_crystal_grow.apparatus The physical apparatus in which the crystal was grown. Linbro plate sandwich box ACA plates exptl_crystal_grow.atmosphere The nature of the gas or gas mixture in which the crystal was grown. room air nitrogen argon exptl_crystal_grow.details A description of special aspects of the crystal growth. Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. exptl_crystal_grow.method The method used to grow the crystals. MICROBATCH VAPOR DIFFUSION, HANGING DROP exptl_crystal_grow.method_ref A literature reference that describes the method used to grow the crystals. McPherson et al., 1988 exptl_crystal_grow.pH The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in attribute details in category exptl_crystal_grow. 7.4 7.6 4.3 exptl_crystal_grow.pdbx_details Text description of crystal growth procedure. PEG 4000, potassium phosphate, magnesium chloride, cacodylate exptl_crystal_grow.pdbx_pH_range The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. 5.6 - 6.4 exptl_crystal_grow.pressure The ambient pressure in kilopascals at which the crystal was grown. exptl_crystal_grow.pressure_esd The standard uncertainty (estimated standard deviation) of attribute pressure in category exptl_crystal_grow. exptl_crystal_grow.seeding A description of the protocol used for seeding the crystal growth. macroseeding Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. exptl_crystal_grow.seeding_ref A literature reference that describes the protocol used to seed the crystal. Stura et al., 1989 exptl_crystal_grow.temp The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in attribute details in category exptl_crystal_grow. exptl_crystal_grow.temp_details A description of special aspects of temperature control during crystal growth. exptl_crystal_grow.temp_esd The standard uncertainty (estimated standard deviation) of attribute temp in category exptl_crystal_grow. exptl_crystal_grow.time The approximate time that the crystal took to grow to the size used for data collection. overnight 2-4 days 6 months exptl_crystal_grow.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. 0 exptl_crystal_grow_comp Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in attribute details in category exptl_crystal_grow_comp using the solutions described in EXPTL_CRYSTAL_GROW_COMP. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:exptl_crystal_grow_compCategory> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="1"> <PDBx:conc>6 mg/ml</PDBx:conc> <PDBx:details> The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</PDBx:details> <PDBx:name>HIV-1 protease</PDBx:name> <PDBx:sol_id>1</PDBx:sol_id> <PDBx:volume>0.002 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="2"> <PDBx:conc>4 M</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>NaCl</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.200 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="3"> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.047 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="4"> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details> in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured.</PDBx:details> <PDBx:name>Na Acetate</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.053 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="5"> <PDBx:conc>neat</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>water</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.700 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> </PDBx:exptl_crystal_grow_compCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 exptl_crystal_grow_compCategory This property indicates that datablock has a category holder exptl_crystal_grow_compCategory. exptl_crystal_grow_compCategory This property indicates that exptl_crystal_grow_compCategory. has a category exptl_crystal_grow_comp. exptl_crystal_grow_compItem Abstract datatype property for exptl_crystal_grow_comp items. reference_to_exptl_crystal_grow_comp cross-reference to exptl_crystal_grow_comp. referenced_by_exptl_crystal_grow_comp cross-reference from exptl_crystal_grow_comp. exptl_crystal_grow_comp.conc The concentration of the solution component. 200 \ml 0.1 ml exptl_crystal_grow_comp.details A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. in 3 mM NaAzide The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. exptl_crystal_grow_comp.name A common name for the component of the solution. protein in buffer acetic acid exptl_crystal_grow_comp.pdbx_bath The identification of the cystallization bath. exptl_crystal_grow_comp.pdbx_conc_final The concentration of this component in the final crystallization solution. This data item should include units of concentration. exptl_crystal_grow_comp.pdbx_salt The identification of the crystallization salt. exptl_crystal_grow_comp.pdbx_soak_salt The identification of the crystallization soaking salt. exptl_crystal_grow_comp.pdbx_soak_solv The identification of the crystallization soaking solvent exptl_crystal_grow_comp.pdbx_solv The identification of the crystallization solvent. exptl_crystal_grow_comp.sol_id An identifier for the solution to which the given solution component belongs. 1 well solution solution A exptl_crystal_grow_comp.volume The volume of the solution component. 200 \ml 0.1 ml exptl_crystal_grow_comp.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. exptl_crystal_grow_comp.id The value of attribute id in category exptl_crystal_grow_comp must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. 1 A protein in buffer 0 geom Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag. 0 1 1 geomCategory This property indicates that datablock has a category holder geomCategory. geomCategory This property indicates that geomCategory. has a category geom. geomItem Abstract datatype property for geom items. reference_to_geom cross-reference to geom. referenced_by_geom cross-reference from geom. geom.details A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes. geom.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 geom_angle Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:geom_angleCategory> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>111.6</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>110.9</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>122.2</PDBx:value> <PDBx:value_esd>0.3</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>127.0</PDBx:value> <PDBx:value_esd>0.3</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>101.3</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>111.3</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>107</PDBx:value> <PDBx:value_esd>1</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>116.7</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> </PDBx:geom_angleCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 geom_angleCategory This property indicates that datablock has a category holder geom_angleCategory. geom_angleCategory This property indicates that geom_angleCategory. has a category geom_angle. geom_angleItem Abstract datatype property for geom_angle items. reference_to_geom_angle cross-reference to geom_angle. referenced_by_geom_angle cross-reference from geom_angle. geom_angle.atom_site_auth_asym_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_asym_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_asym_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_atom_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_atom_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_atom_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_comp_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_comp_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_comp_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_seq_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_seq_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_seq_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_alt_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_alt_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_alt_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_asym_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_asym_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_asym_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_atom_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_atom_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_atom_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_comp_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_comp_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_comp_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_seq_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_seq_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_seq_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_angle.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site geom_angle.pdbx_atom_site_PDB_ins_code_1 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_angle.pdbx_atom_site_PDB_ins_code_2 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_angle.pdbx_atom_site_PDB_ins_code_3 Pointer to attribute pdbx_PDB_ins_code in category atom_site. no n yes y This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. geom_angle.value Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and attribute atom_site_id_3 in category geom_angle. geom_angle.value_esd The standard uncertainty (estimated standard deviation) of attribute value in category geom_angle. geom_angle.atom_site_id_1 The identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_id_2 The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_id_3 The identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_angle.site_symmetry_1 The symmetry code of the first of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_angle.site_symmetry_2 The symmetry code of the second of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_angle.site_symmetry_3 The symmetry code of the third of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 0 geom_bond Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:geom_bondCategory> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.342</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.439</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.512</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.199</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.465</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.537</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.00</PDBx:dist> <PDBx:dist_esd>0.03</PDBx:dist_esd> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.472</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> </PDBx:geom_bondCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 geom_bondCategory This property indicates that datablock has a category holder geom_bondCategory. geom_bondCategory This property indicates that geom_bondCategory. has a category geom_bond. geom_bondItem Abstract datatype property for geom_bond items. reference_to_geom_bond cross-reference to geom_bond. referenced_by_geom_bond cross-reference from geom_bond. geom_bond.atom_site_auth_asym_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_asym_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_atom_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_atom_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_comp_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_comp_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_seq_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_auth_seq_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_alt_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_alt_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_asym_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_asym_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_atom_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_atom_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_comp_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_comp_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_seq_id_1 An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_label_seq_id_2 An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_bond.dist The intramolecular bond distance in angstroms. geom_bond.dist_esd The standard uncertainty (estimated standard deviation) of attribute dist in category geom_bond. geom_bond.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site geom_bond.pdbx_atom_site_PDB_ins_code_1 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_bond.pdbx_atom_site_PDB_ins_code_2 Pointer to attribute pdbx_PDB_ins_code in category atom_site. no n yes y This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances. geom_bond.valence The bond valence calculated from attribute dist in category geom_bond. geom_bond.atom_site_id_1 The identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_bond.atom_site_id_2 The identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_bond.site_symmetry_1 The symmetry code of the first of the two atom sites that define the bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_bond.site_symmetry_2 The symmetry code of the second of the two atom sites that define the bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 0 geom_contact Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. <PDBx:geom_contactCategory> <PDBx:geom_contact atom_site_id_1="O(1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>2.735</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_contact> <PDBx:geom_contact atom_site_id_1="H(O1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.82</PDBx:dist> <PDBx:dist_esd xsi:nil="true" /> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_contact> </PDBx:geom_contactCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 geom_contactCategory This property indicates that datablock has a category holder geom_contactCategory. geom_contactCategory This property indicates that geom_contactCategory. has a category geom_contact. geom_contactItem Abstract datatype property for geom_contact items. reference_to_geom_contact cross-reference to geom_contact. referenced_by_geom_contact cross-reference from geom_contact. geom_contact.atom_site_auth_asym_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_asym_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_atom_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_atom_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_comp_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_comp_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_seq_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_auth_seq_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_alt_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_alt_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_asym_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_asym_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_atom_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_atom_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_comp_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_comp_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_seq_id_1 An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_label_seq_id_2 An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_contact.dist The interatomic contact distance in angstroms. geom_contact.dist_esd The standard uncertainty (estimated standard deviation) of attribute dist in category geom_contact. geom_contact.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site geom_contact.pdbx_atom_site_PDB_ins_code_1 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_contact.pdbx_atom_site_PDB_ins_code_2 Pointer to attribute pdbx_PDB_ins_code in category atom_site. no n yes y This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances. geom_contact.atom_site_id_1 The identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_contact.atom_site_id_2 The identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_contact.site_symmetry_1 The symmetry code of the first of the two atom sites that define the contact. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_contact.site_symmetry_2 The symmetry code of the second of the two atom sites that define the contact. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 0 geom_hbond Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. <PDBx:geom_hbondCategory> <PDBx:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6"> <PDBx:angle_DHA>169.6</PDBx:angle_DHA> <PDBx:dist_DA>2.801</PDBx:dist_DA> <PDBx:dist_DH>0.888</PDBx:dist_DH> <PDBx:dist_HA>1.921</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2"> <PDBx:angle_DHA>153.5</PDBx:angle_DHA> <PDBx:dist_DA>2.793</PDBx:dist_DA> <PDBx:dist_DH>0.917</PDBx:dist_DH> <PDBx:dist_HA>1.923</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1"> <PDBx:angle_DHA>179.7</PDBx:angle_DHA> <PDBx:dist_DA>2.842</PDBx:dist_DA> <PDBx:dist_DH>0.894</PDBx:dist_DH> <PDBx:dist_HA>1.886</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> </PDBx:geom_hbondCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 geom_hbondCategory This property indicates that datablock has a category holder geom_hbondCategory. geom_hbondCategory This property indicates that geom_hbondCategory. has a category geom_hbond. geom_hbondItem Abstract datatype property for geom_hbond items. reference_to_geom_hbond cross-reference to geom_hbond. referenced_by_geom_hbond cross-reference from geom_hbond. geom_hbond.angle_DHA The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond. geom_hbond.angle_DHA_esd The standard uncertainty (estimated standard deviation) of attribute angle_DHA in category geom_hbond. geom_hbond.atom_site_auth_asym_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_asym_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_asym_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_atom_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_atom_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_atom_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_comp_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_comp_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_comp_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_seq_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_seq_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_auth_seq_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_alt_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_alt_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_alt_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_asym_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_asym_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_asym_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_atom_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_atom_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_atom_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_comp_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_comp_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_comp_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_seq_id_A An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_seq_id_D An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_label_seq_id_H An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_hbond.dist_DA The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond. geom_hbond.dist_DA_esd The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DA in category geom_hbond. geom_hbond.dist_DH The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond. geom_hbond.dist_DH_esd The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DH in category geom_hbond. geom_hbond.dist_HA The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond. geom_hbond.dist_HA_esd The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_HA in category geom_hbond. no n yes y This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. geom_hbond.atom_site_id_A The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_id_D The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_hbond.atom_site_id_H The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_hbond.site_symmetry_A The symmetry code of the acceptor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_hbond.site_symmetry_D The symmetry code of the donor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_hbond.site_symmetry_H The symmetry code of the hydrogen-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 0 geom_torsion Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction attribute atom_site_id_2 in category geom_torsion to attribute atom_site_id_3 in category geom_torsion is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. <PDBx:geom_torsionCategory> <PDBx:geom_torsion atom_site_id_1="C(9)" atom_site_id_2="O(2)" atom_site_id_3="C(7)" atom_site_id_4="C(2)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>71.8</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(7)" atom_site_id_2="O(2)" atom_site_id_3="C(9)" atom_site_id_4="C(10)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>-168.0</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(10)" atom_site_id_2="O(3)" atom_site_id_3="C(8)" atom_site_id_4="C(6)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>-167.7</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(8)" atom_site_id_2="O(3)" atom_site_id_3="C(10)" atom_site_id_4="C(9)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>-69.7</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(3)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>-179.5</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(7)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>-0.6</PDBx:value> </PDBx:geom_torsion> </PDBx:geom_torsionCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 1 1 geom_torsionCategory This property indicates that datablock has a category holder geom_torsionCategory. geom_torsionCategory This property indicates that geom_torsionCategory. has a category geom_torsion. geom_torsionItem Abstract datatype property for geom_torsion items. reference_to_geom_torsion cross-reference to geom_torsion. referenced_by_geom_torsion cross-reference from geom_torsion. geom_torsion.atom_site_auth_asym_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_asym_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_asym_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_asym_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_atom_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_atom_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_atom_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_atom_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_comp_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_comp_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_comp_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_comp_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_seq_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_seq_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_seq_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_auth_seq_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_alt_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_alt_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_alt_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_alt_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_asym_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_asym_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_asym_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_asym_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_atom_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_atom_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_atom_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_atom_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_comp_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_comp_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_comp_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_comp_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_seq_id_1 An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_seq_id_2 An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_seq_id_3 An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_label_seq_id_4 An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_torsion.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site geom_torsion.pdbx_atom_site_PDB_ins_code_1 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_torsion.pdbx_atom_site_PDB_ins_code_2 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_torsion.pdbx_atom_site_PDB_ins_code_3 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_torsion.pdbx_atom_site_PDB_ins_code_4 Pointer to attribute pdbx_PDB_ins_code in category atom_site. no n yes y This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. geom_torsion.value The value of the torsion angle in degrees. geom_torsion.value_esd The standard uncertainty (estimated standard deviation) of attribute value in category geom_torsion. geom_torsion.atom_site_id_1 The identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_id_2 The identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_id_3 The identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_torsion.atom_site_id_4 The identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_torsion.site_symmetry_1 The symmetry code of the first of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_torsion.site_symmetry_2 The symmetry code of the second of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_torsion.site_symmetry_3 The symmetry code of the third of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_torsion.site_symmetry_4 The symmetry code of the fourth of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 0 journal Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only. Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. <PDBx:journalCategory> <PDBx:journal entry_id="TOZ"> <PDBx:coden_ASTM>ACSCEE</PDBx:coden_ASTM> <PDBx:coeditor_code>HL0007</PDBx:coeditor_code> <PDBx:date_accepted>1991-04-18</PDBx:date_accepted> <PDBx:date_from_coeditor>1991-04-18</PDBx:date_from_coeditor> <PDBx:date_printers_first>1991-08-07</PDBx:date_printers_first> <PDBx:date_proofs_out>1991-08-07</PDBx:date_proofs_out> <PDBx:date_recd_electronic>1991-04-15</PDBx:date_recd_electronic> <PDBx:issue>NOV91</PDBx:issue> <PDBx:name_full>Acta Crystallographica Section C</PDBx:name_full> <PDBx:page_first>2276</PDBx:page_first> <PDBx:page_last>2277</PDBx:page_last> <PDBx:techeditor_code>C910963</PDBx:techeditor_code> <PDBx:volume>47</PDBx:volume> <PDBx:year>1991</PDBx:year> </PDBx:journal> </PDBx:journalCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 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 journalCategory This property indicates that datablock has a category holder journalCategory. journalCategory This property indicates that journalCategory. has a category journal. journalItem Abstract datatype property for journal items. reference_to_journal cross-reference to journal. referenced_by_journal cross-reference from journal. journal.coden_ASTM Journal data items are defined by the journal staff. journal.coden_Cambridge Journal data items are defined by the journal staff. journal.coeditor_address Journal data items are defined by the journal staff. journal.coeditor_code Journal data items are defined by the journal staff. journal.coeditor_email Journal data items are defined by the journal staff. journal.coeditor_fax Journal data items are defined by the journal staff. journal.coeditor_name Journal data items are defined by the journal staff. journal.coeditor_notes Journal data items are defined by the journal staff. journal.coeditor_phone Journal data items are defined by the journal staff. journal.data_validation_number Journal data items are defined by the journal staff. journal.date_accepted Journal data items are defined by the journal staff. journal.date_from_coeditor Journal data items are defined by the journal staff. journal.date_printers_final Journal data items are defined by the journal staff. journal.date_printers_first Journal data items are defined by the journal staff. journal.date_proofs_in Journal data items are defined by the journal staff. journal.date_proofs_out Journal data items are defined by the journal staff. journal.date_recd_copyright Journal data items are defined by the journal staff. journal.date_recd_electronic Journal data items are defined by the journal staff. journal.date_recd_hard_copy Journal data items are defined by the journal staff. journal.date_to_coeditor Journal data items are defined by the journal staff. journal.issue Journal data items are defined by the journal staff. journal.language Journal data items are defined by the journal staff. journal.name_full Journal data items are defined by the journal staff. journal.page_first Journal data items are defined by the journal staff. journal.page_last Journal data items are defined by the journal staff. journal.paper_category Journal data items are defined by the journal staff. journal.suppl_publ_number Journal data items are defined by the journal staff. journal.suppl_publ_pages Journal data items are defined by the journal staff. journal.techeditor_address Journal data items are defined by the journal staff. journal.techeditor_code Journal data items are defined by the journal staff. journal.techeditor_email Journal data items are defined by the journal staff. journal.techeditor_fax Journal data items are defined by the journal staff. journal.techeditor_name Journal data items are defined by the journal staff. journal.techeditor_notes Journal data items are defined by the journal staff. journal.techeditor_phone Journal data items are defined by the journal staff. journal.volume Journal data items are defined by the journal staff. journal.year Journal data items are defined by the journal staff. journal.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 journal_index Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items. Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. <PDBx:journal_indexCategory> <PDBx:journal_index term="C16H19NO4" type="O"> <PDBx:subterm xsi:nil="true" /> </PDBx:journal_index> <PDBx:journal_index term="alkaloids" type="S"> <PDBx:subterm>(-)-norcocaine</PDBx:subterm> </PDBx:journal_index> <PDBx:journal_index term="(-)-norcocaine" type="S"> <PDBx:subterm xsi:nil="true" /> </PDBx:journal_index> <PDBx:journal_index term=" [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate" type="S"> <PDBx:subterm xsi:nil="true" /> </PDBx:journal_index> </PDBx:journal_indexCategory> 0 1 1 1 journal_indexCategory This property indicates that datablock has a category holder journal_indexCategory. journal_indexCategory This property indicates that journal_indexCategory. has a category journal_index. journal_indexItem Abstract datatype property for journal_index items. reference_to_journal_index cross-reference to journal_index. referenced_by_journal_index cross-reference from journal_index. journal_index.subterm Journal index data items are defined by the journal staff. journal_index.term Journal index data items are defined by the journal staff. journal_index.type Journal index data items are defined by the journal staff. 0 ndb_original_ndb_coordinates Placeholder category for PDB coordinate data. 1 ndb_original_ndb_coordinatesCategory This property indicates that datablock has a category holder ndb_original_ndb_coordinatesCategory. ndb_original_ndb_coordinatesCategory This property indicates that ndb_original_ndb_coordinatesCategory. has a category ndb_original_ndb_coordinates. ndb_original_ndb_coordinatesItem Abstract datatype property for ndb_original_ndb_coordinates items. reference_to_ndb_original_ndb_coordinates cross-reference to ndb_original_ndb_coordinates. referenced_by_ndb_original_ndb_coordinates cross-reference from ndb_original_ndb_coordinates. ndb_original_ndb_coordinates.coord_section Placeholder item to hold unparsed coordinate data. 0 ndb_struct_conf_na Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry. 0 1 1 1 ndb_struct_conf_naCategory This property indicates that datablock has a category holder ndb_struct_conf_naCategory. ndb_struct_conf_naCategory This property indicates that ndb_struct_conf_naCategory. has a category ndb_struct_conf_na. ndb_struct_conf_naItem Abstract datatype property for ndb_struct_conf_na items. reference_to_ndb_struct_conf_na cross-reference to ndb_struct_conf_na. referenced_by_ndb_struct_conf_na cross-reference from ndb_struct_conf_na. ndb_struct_conf_na.feature_count This data item counts the number of occurences of this feature in this entry. ndb_struct_conf_na.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. double helix a-form double helix b-form double helix z-form double helix other right-handed double helix triple helix quadruple helix parallel strands internal loop bulge loop tetraloop hairpin loop two-way junction three-way junction four-way junction mismatched base pair This data item identifies a secondary structure feature of this entry. 0 ndb_struct_feature_na Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry. 0 1 1 1 ndb_struct_feature_naCategory This property indicates that datablock has a category holder ndb_struct_feature_naCategory. ndb_struct_feature_naCategory This property indicates that ndb_struct_feature_naCategory. has a category ndb_struct_feature_na. ndb_struct_feature_naItem Abstract datatype property for ndb_struct_feature_na items. reference_to_ndb_struct_feature_na cross-reference to ndb_struct_feature_na. referenced_by_ndb_struct_feature_na cross-reference from ndb_struct_feature_na. ndb_struct_feature_na.feature_count This data item counts the number of occurences of this feature in this entry. ndb_struct_feature_na.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. pseudoknot intercalated base backbone turn intramolecular base triplet ribose zipper purine platform bent/kinked double helix This data item identifies a structural feature of this entry. 0 ndb_struct_na_base_pair Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions. <PDBx:ndb_struct_na_base_pairCategory> <PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="1" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="8" j_symmetry="7_555" model_number="1"> <PDBx:buckle>-5.523</PDBx:buckle> <PDBx:opening>-3.291</PDBx:opening> <PDBx:propeller>-6.752</PDBx:propeller> <PDBx:shear>-0.396</PDBx:shear> <PDBx:stagger>-0.018</PDBx:stagger> <PDBx:stretch>-0.156</PDBx:stretch> </PDBx:ndb_struct_na_base_pair> <PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="2" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="7" j_symmetry="7_555" model_number="1"> <PDBx:buckle>-4.727</PDBx:buckle> <PDBx:opening>2.311</PDBx:opening> <PDBx:propeller>-9.765</PDBx:propeller> <PDBx:shear>-0.094</PDBx:shear> <PDBx:stagger>-0.334</PDBx:stagger> <PDBx:stretch>-0.220</PDBx:stretch> </PDBx:ndb_struct_na_base_pair> <PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="3" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="6" j_symmetry="7_555" model_number="1"> <PDBx:buckle>-6.454</PDBx:buckle> <PDBx:opening>-1.181</PDBx:opening> <PDBx:propeller>-12.575</PDBx:propeller> <PDBx:shear>-0.285</PDBx:shear> <PDBx:stagger>0.008</PDBx:stagger> <PDBx:stretch>-0.239</PDBx:stretch> </PDBx:ndb_struct_na_base_pair> </PDBx:ndb_struct_na_base_pairCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 ndb_struct_na_base_pairCategory This property indicates that datablock has a category holder ndb_struct_na_base_pairCategory. ndb_struct_na_base_pairCategory This property indicates that ndb_struct_na_base_pairCategory. has a category ndb_struct_na_base_pair. ndb_struct_na_base_pairItem Abstract datatype property for ndb_struct_na_base_pair items. reference_to_ndb_struct_na_base_pair cross-reference to ndb_struct_na_base_pair. referenced_by_ndb_struct_na_base_pair cross-reference from ndb_struct_na_base_pair. ndb_struct_na_base_pair.buckle The value of the base pair buckle parameter. ndb_struct_na_base_pair.hbond_type_12 Base pair classification of Westhoff and Leontis. ndb_struct_na_base_pair.hbond_type_28 Base pair classification of Saenger cWW tWW cWH cHW tWH tHW cWS cSW tWS tSW cHH tHH cHS cSH tHS tSH cSS tSS Base pair classification of Leontis and Westhof. The Leontis-Westhof classification system annotates basepairs according to the interacting edge used by each base (Watson-Crick, Hoogsteen, or Sugar), and glycosidic bond orientation (cis, trans). For six of twelve classes, the correct Leontis-Westhof notation depends upon the order (i,j) of the identified nucleotides. Leontis NB and Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512. https://doi.org/10.1017/s1355838201002515 Replacement for category item attribute hbond_type_12 in category ndb_struct_na_base_pair. The older item encodes the 12 classes by a numerical index, without identifying the interacting edges used by each base in nucleotides i,j. ndb_struct_na_base_pair.i_PDB_ins_code Describes the PDB insertion code of the i-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_auth_asym_id Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_auth_seq_id Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_PDB_ins_code Describes the PDB insertion code of the j-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_auth_asym_id Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_auth_seq_id Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.opening The value of the base pair opening parameter. ndb_struct_na_base_pair.pair_name Text label for this base pair. ndb_struct_na_base_pair.pair_number Sequential number of pair in the pair sequence. ndb_struct_na_base_pair.propeller The value of the base pair propeller parameter. ndb_struct_na_base_pair.shear The value of the base pair shear parameter. ndb_struct_na_base_pair.stagger The value of the base pair stagger parameter. ndb_struct_na_base_pair.stretch The value of the base pair stretch parameter. ndb_struct_na_base_pair.i_label_asym_id Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_label_comp_id Describes the component id of the i-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_label_seq_id Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.i_symmetry Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the base pair. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair.j_label_asym_id Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_label_comp_id Describes the component id of the j-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_label_seq_id Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair.j_symmetry Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the base pair. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair.model_number Describes the model number of the base pair. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. 0 ndb_struct_na_base_pair_step Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions. <PDBx:ndb_struct_na_base_pair_stepCategory> <PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="1" i_label_seq_id_2="2" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="8" j_label_seq_id_2="7" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1"> <PDBx:rise>3.339</PDBx:rise> <PDBx:roll>9.755</PDBx:roll> <PDBx:shift>0.369</PDBx:shift> <PDBx:slide>-1.414</PDBx:slide> <PDBx:tilt>3.056</PDBx:tilt> <PDBx:twist>33.530</PDBx:twist> </PDBx:ndb_struct_na_base_pair_step> <PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="2" i_label_seq_id_2="3" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="7" j_label_seq_id_2="6" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1"> <PDBx:rise>3.371</PDBx:rise> <PDBx:roll>6.725</PDBx:roll> <PDBx:shift>0.176</PDBx:shift> <PDBx:slide>-1.672</PDBx:slide> <PDBx:tilt>-1.176</PDBx:tilt> <PDBx:twist>30.004</PDBx:twist> </PDBx:ndb_struct_na_base_pair_step> </PDBx:ndb_struct_na_base_pair_stepCategory> 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ndb_struct_na_base_pair_stepCategory This property indicates that datablock has a category holder ndb_struct_na_base_pair_stepCategory. ndb_struct_na_base_pair_stepCategory This property indicates that ndb_struct_na_base_pair_stepCategory. has a category ndb_struct_na_base_pair_step. ndb_struct_na_base_pair_stepItem Abstract datatype property for ndb_struct_na_base_pair_step items. reference_to_ndb_struct_na_base_pair_step cross-reference to ndb_struct_na_base_pair_step. referenced_by_ndb_struct_na_base_pair_step cross-reference from ndb_struct_na_base_pair_step. ndb_struct_na_base_pair_step.helical_rise The value of the base pair step helical rise parameter. ndb_struct_na_base_pair_step.helical_twist The value of the base pair step helical twist parameter. ndb_struct_na_base_pair_step.i_PDB_ins_code_1 Describes the PDB insertion code of the i-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_PDB_ins_code_2 Describes the PDB insertion code of the i-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_asym_id_1 Describes the author's asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_asym_id_2 Describes the author's asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_seq_id_1 Describes the author's sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_auth_seq_id_2 Describes the author's sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.inclination The value of the base pair step inclination parameter. ndb_struct_na_base_pair_step.j_PDB_ins_code_1 Describes the PDB insertion code of the j-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_PDB_ins_code_2 Describes the PDB insertion code of the j-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_asym_id_1 Describes the author's asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_asym_id_2 Describes the author's asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_seq_id_1 Describes the author's sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_auth_seq_id_2 Describes the author's sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.rise The value of the base pair step rise parameter. ndb_struct_na_base_pair_step.roll The value of the base pair step roll parameter. ndb_struct_na_base_pair_step.shift The value of the base pair step shift parameter. ndb_struct_na_base_pair_step.slide The value of the base pair step slide parameter. ndb_struct_na_base_pair_step.step_name The text name of this step. ndb_struct_na_base_pair_step.step_number The sequence number of this step in the step sequence. ndb_struct_na_base_pair_step.tilt The value of the base pair step tilt parameter. ndb_struct_na_base_pair_step.tip The value of the base pair step twist parameter. ndb_struct_na_base_pair_step.twist The value of the base pair step twist parameter. ndb_struct_na_base_pair_step.x_displacement The value of the base pair step X displacement parameter. ndb_struct_na_base_pair_step.y_displacement The value of the base pair step Y displacement parameter. ndb_struct_na_base_pair_step.i_label_asym_id_1 Describes the asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_asym_id_2 Describes the asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_comp_id_1 Describes the component id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_comp_id_2 Describes the component id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_seq_id_1 Describes the sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_label_seq_id_2 Describes the sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.i_symmetry_1 Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the first base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.i_symmetry_2 Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the second base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.j_label_asym_id_1 Describes the asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_asym_id_2 Describes the asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_comp_id_1 Describes the component id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_comp_id_2 Describes the component id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_seq_id_1 Describes the sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_label_seq_id_2 Describes the sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. ndb_struct_na_base_pair_step.j_symmetry_1 Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the first base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.j_symmetry_2 Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the second base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 ndb_struct_na_base_pair_step.model_number Describes the model number of the base pair step. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. 0 pdbx_SG_project Data items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center. Example 1 - <PDBx:pdbx_SG_projectCategory> <PDBx:pdbx_SG_project id="1"> <PDBx:full_name_of_center>Berkeley Structural Genomics Center</PDBx:full_name_of_center> <PDBx:initial_of_center>BSGC</PDBx:initial_of_center> <PDBx:project_name>PSI, Protein Structure Initiative</PDBx:project_name> </PDBx:pdbx_SG_project> </PDBx:pdbx_SG_projectCategory> 0 1 0 1 0 1 1 pdbx_SG_projectCategory This property indicates that datablock has a category holder pdbx_SG_projectCategory. pdbx_SG_projectCategory This property indicates that pdbx_SG_projectCategory. has a category pdbx_SG_project. pdbx_SG_projectItem Abstract datatype property for pdbx_SG_project items. reference_to_pdbx_SG_project cross-reference to pdbx_SG_project. referenced_by_pdbx_SG_project cross-reference from pdbx_SG_project. Accelerated Technologies Center for Gene to 3D Structure Bacterial targets at IGS-CNRS, France Berkeley Structural Genomics Center Montreal-Kingston Bacterial Structural Genomics Initiative Chaperone-Enabled Studies of Epigenetic Regulation Enzymes Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions Center for Eukaryotic Structural Genomics Structure, Dynamics and Activation Mechanisms of Chemokine Receptors Center for High-Throughput Structural Biology Center for Structural Biology of Infectious Diseases Center for Structural Genomics of Infectious Diseases Center for Structures of Membrane Proteins GPCR Network Atoms-to-Animals: The Immune Function Network Integrated Center for Structure and Function Innovation Israel Structural Proteomics Center Joint Center for Structural Genomics Midwest Center for Macromolecular Research Midwest Center for Structural Genomics Center for Membrane Proteins of Infectious Diseases Mitochondrial Protein Partnership Membrane Protein Structural Biology Consortium Membrane Protein Structures by Solution NMR Marseilles Structural Genomics Program @ AFMB Medical Structural Genomics of Pathogenic Protozoa Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors Enzyme Discovery for Natural Product Biosynthesis Nucleocytoplasmic Transport: a Target for Cellular Control New York Consortium on Membrane Protein Structure New York Structural Genomics Research Consortium New York SGX Research Center for Structural Genomics New York Structural GenomiX Research Consortium Northeast Structural Genomics Consortium Partnership for Nuclear Receptor Signaling Code Biology Ontario Centre for Structural Proteomics Oxford Protein Production Facility Program for the Characterization of Secreted Effector Proteins Protein Structure Factory RIKEN Structural Genomics/Proteomics Initiative Structure 2 Function Project South Africa Structural Targets Annotation Database Southeast Collaboratory for Structural Genomics Structural Genomics Consortium Structural Genomics Consortium for Research on Gene Expression Structural Genomics of Pathogenic Protozoa Consortium Structural Proteomics in Europe Structural Proteomics in Europe 2 Seattle Structural Genomics Center for Infectious Disease Scottish Structural Proteomics Facility Partnership for Stem Cell Biology TB Structural Genomics Consortium Partnership for T-Cell Biology Transcontinental EM Initiative for Membrane Protein Structure Structure-Function Studies of Tight Junction Membrane Proteins Transmembrane Protein Center Center for the X-ray Structure Determination of Human Transporters Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes Mycobacterium Tuberculosis Structural Proteomics Project Paris-Sud Yeast Structural Genomics The value identifies the full name of center. Midwest Center for Structural Genomics ATCG3D BIGS BSGC BSGI CEBS CELLMAT CESG CHSAM CHTSB CSBID CSGID CSMP GPCR IFN ISFI ISPC JCSG MCMR MCSG MPID MPP MPSBC MPSbyNMR MSGP MSGPP MTBI NatPro NHRs NPCXstals NYCOMPS NYSGRC NYSGXRC NESG OCSP OPPF PCSEP PSF RSGI S2F SASTAD SECSG SGC SGCGES SGPP SPINE SPINE-2 SSGCID SSPF STEMCELL TBSGC TCELL TEMIMPS TJMP TMPC TransportPDB UC4CDI XMTB YSG The value identifies the full name of center. JCSG PSI:Biology PSI, Protein Structure Initiative NIAID, National Institute of Allergy and Infectious Diseases NPPSFA, National Project on Protein Structural and Functional Analyses Enzyme Function Initiative The value identifies the Structural Genomics project. PSI, Protein Structure Initiative 1 2 3 4 5 6 7 8 9 10 A unique integer identifier for this center 1 2 3 0 pdbx_atlas Gives information about the organization of the NDB Structural Atlas. 1 1 1 1 pdbx_atlasCategory This property indicates that datablock has a category holder pdbx_atlasCategory. pdbx_atlasCategory This property indicates that pdbx_atlasCategory. has a category pdbx_atlas. pdbx_atlasItem Abstract datatype property for pdbx_atlas items. reference_to_pdbx_atlas cross-reference to pdbx_atlas. referenced_by_pdbx_atlas cross-reference from pdbx_atlas. pdbx_atlas.page_name Text of the Atlas index entry. pdbx_atlas.entry_id Entry ID. pdbx_atlas.page_id A unique identifier for a NDB ATLAS index page. 0 pdbx_atom_site_aniso_tls Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details about the TLS contribution to anisotropic displacement parameters. Example 1 <PDBx:pdbx_atom_site_aniso_tlsCategory> <PDBx:pdbx_atom_site_aniso_tls id="1" tls_group_id="1"> <PDBx:U_tls11>2541</PDBx:U_tls11> <PDBx:U_tls12>676</PDBx:U_tls12> <PDBx:U_tls13>-827</PDBx:U_tls13> <PDBx:U_tls22>2835</PDBx:U_tls22> <PDBx:U_tls23>341</PDBx:U_tls23> <PDBx:U_tls33>3175</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CB</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="2" tls_group_id="1"> <PDBx:U_tls11>3708</PDBx:U_tls11> <PDBx:U_tls12>633</PDBx:U_tls12> <PDBx:U_tls13>-724</PDBx:U_tls13> <PDBx:U_tls22>3876</PDBx:U_tls22> <PDBx:U_tls23>342</PDBx:U_tls23> <PDBx:U_tls33>4181</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>OG</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="3" tls_group_id="1"> <PDBx:U_tls11>7054</PDBx:U_tls11> <PDBx:U_tls12>619</PDBx:U_tls12> <PDBx:U_tls13>-966</PDBx:U_tls13> <PDBx:U_tls22>7457</PDBx:U_tls22> <PDBx:U_tls23>344</PDBx:U_tls23> <PDBx:U_tls33>7553</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>C</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="4" tls_group_id="1"> <PDBx:U_tls11>6837</PDBx:U_tls11> <PDBx:U_tls12>567</PDBx:U_tls12> <PDBx:U_tls13>-974</PDBx:U_tls13> <PDBx:U_tls22>7210</PDBx:U_tls22> <PDBx:U_tls23>341</PDBx:U_tls23> <PDBx:U_tls33>7184</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>O</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="5" tls_group_id="1"> <PDBx:U_tls11>5792</PDBx:U_tls11> <PDBx:U_tls12>538</PDBx:U_tls12> <PDBx:U_tls13>-778</PDBx:U_tls13> <PDBx:U_tls22>6180</PDBx:U_tls22> <PDBx:U_tls23>290</PDBx:U_tls23> <PDBx:U_tls33>6271</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>N</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="6" tls_group_id="1"> <PDBx:U_tls11>8440</PDBx:U_tls11> <PDBx:U_tls12>616</PDBx:U_tls12> <PDBx:U_tls13>-861</PDBx:U_tls13> <PDBx:U_tls22>8771</PDBx:U_tls22> <PDBx:U_tls23>331</PDBx:U_tls23> <PDBx:U_tls33>8935</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CA</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> </PDBx:pdbx_atom_site_aniso_tlsCategory> 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 pdbx_atom_site_aniso_tlsCategory This property indicates that datablock has a category holder pdbx_atom_site_aniso_tlsCategory. pdbx_atom_site_aniso_tlsCategory This property indicates that pdbx_atom_site_aniso_tlsCategory. has a category pdbx_atom_site_aniso_tls. pdbx_atom_site_aniso_tlsItem Abstract datatype property for pdbx_atom_site_aniso_tls items. reference_to_pdbx_atom_site_aniso_tls cross-reference to pdbx_atom_site_aniso_tls. referenced_by_pdbx_atom_site_aniso_tls cross-reference from pdbx_atom_site_aniso_tls. pdbx_atom_site_aniso_tls.PDB_ins_code This data item is a pointer to attribute pdbx_ins_code in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.U_tls11 The [1][1] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. pdbx_atom_site_aniso_tls.U_tls12 The [1][2] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. pdbx_atom_site_aniso_tls.U_tls13 The [1][3] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. pdbx_atom_site_aniso_tls.U_tls22 The [2][2] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. pdbx_atom_site_aniso_tls.U_tls23 The [2][3] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. pdbx_atom_site_aniso_tls.U_tls33 The [3][3] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. pdbx_atom_site_aniso_tls.auth_asym_id This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.auth_atom_id This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.auth_comp_id This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.auth_seq_id This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.label_alt_id This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITE category. pdbx_atom_site_aniso_tls.label_asym_id This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.label_atom_id This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.label_comp_id This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.label_seq_id This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. pdbx_atom_site_aniso_tls.id This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. pdbx_atom_site_aniso_tls.tls_group_id This data item identifies the TLS group membership for this atom. 0 pdbx_audit The PDBX_AUDIT holds current version information. 1 1 1 pdbx_auditCategory This property indicates that datablock has a category holder pdbx_auditCategory. pdbx_auditCategory This property indicates that pdbx_auditCategory. has a category pdbx_audit. pdbx_auditItem Abstract datatype property for pdbx_audit items. reference_to_pdbx_audit cross-reference to pdbx_audit. referenced_by_pdbx_audit cross-reference from pdbx_audit. pdbx_audit.current_version The value of attribute entry_id in category pdbx_audit identifies the data block. 1 pdbx_audit.entry_id The value of attribute entry_id in category pdbx_audit identifies the data block. BDL001 0 pdbx_audit_author Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:pdbx_audit_authorCategory> <PDBx:pdbx_audit_author ordinal="1"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Fitzgerald, Paula M.D.</PDBx:name> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="2"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>McKeever, Brian M.</PDBx:name> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="3"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Van Middlesworth, J.F.</PDBx:name> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="4"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Springer, James P.</PDBx:name> </PDBx:pdbx_audit_author> </PDBx:pdbx_audit_authorCategory> 0 1 1 1 1 pdbx_audit_authorCategory This property indicates that datablock has a category holder pdbx_audit_authorCategory. pdbx_audit_authorCategory This property indicates that pdbx_audit_authorCategory. has a category pdbx_audit_author. pdbx_audit_authorItem Abstract datatype property for pdbx_audit_author items. reference_to_pdbx_audit_author cross-reference to pdbx_audit_author. referenced_by_pdbx_audit_author cross-reference from pdbx_audit_author. pdbx_audit_author.address The address of an author of this data block. If there are multiple authors, attribute address in category pdbx_audit_author is looped with attribute name in category pdbx_audit_author. Department Institute Street City and postcode COUNTRY pdbx_audit_author.name The name of an author of this data block. If there are multiple authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A pdbx_audit_author.ordinal A unique sequential integer identifier for each author. 1 2 3 0 pdbx_audit_conform Data items in the PDBX_AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. Example 1 - Data file conforming to the current PDBx/mmCIF dictionary. <PDBx:pdbx_audit_conformCategory> <PDBx:pdbx_audit_conform dict_name="mmcif_pdbx.dic" dict_version="5.339"> <PDBx:dict_location>https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic</PDBx:dict_location> </PDBx:pdbx_audit_conform> </PDBx:pdbx_audit_conformCategory> 0 1 1 1 pdbx_audit_conformCategory This property indicates that datablock has a category holder pdbx_audit_conformCategory. pdbx_audit_conformCategory This property indicates that pdbx_audit_conformCategory. has a category pdbx_audit_conform. pdbx_audit_conformItem Abstract datatype property for pdbx_audit_conform items. reference_to_pdbx_audit_conform cross-reference to pdbx_audit_conform. referenced_by_pdbx_audit_conform cross-reference from pdbx_audit_conform. pdbx_audit_conform.dict_location A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. pdbx_audit_conform.dict_name The dictionary name defining data names used in this file. pdbx_audit_conform.dict_version The version number of the dictionary to which the current data block conforms. 0 pdbx_audit_conform_extension Data items in the PDBX_AUDIT_CONFORM_EXTENSION category describe extension dictionary versions against which the data names appearing the current data block are conformant. Example 1 - Conforming to EMD V 1.0 extension dictionary. <PDBx:pdbx_audit_conform_extensionCategory> <PDBx:pdbx_audit_conform_extension extension_dict_name="EMD" extension_dict_version="1.0"> <PDBx:extension_dict_location>http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v5_next.dic</PDBx:extension_dict_location> </PDBx:pdbx_audit_conform_extension> </PDBx:pdbx_audit_conform_extensionCategory> 0 1 1 1 pdbx_audit_conform_extensionCategory This property indicates that datablock has a category holder pdbx_audit_conform_extensionCategory. pdbx_audit_conform_extensionCategory This property indicates that pdbx_audit_conform_extensionCategory. has a category pdbx_audit_conform_extension. pdbx_audit_conform_extensionItem Abstract datatype property for pdbx_audit_conform_extension items. reference_to_pdbx_audit_conform_extension cross-reference to pdbx_audit_conform_extension. referenced_by_pdbx_audit_conform_extension cross-reference from pdbx_audit_conform_extension. pdbx_audit_conform_extension.extension_dict_location A file name or uniform resource locator (URL) for the file containing the extension dictionary. EMD An identifier for the extension dictionary to which the current data block conforms. pdbx_audit_conform_extension.extension_dict_version The version number of the extension dictionary to which the currrent data block conforms. 0 pdbx_audit_revision_category Data items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <PDBx:pdbx_audit_revision_categoryCategory> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <PDBx:category>audit_author</PDBx:category> </PDBx:pdbx_audit_revision_category> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="2" revision_ordinal="1"> <PDBx:category>citation</PDBx:category> </PDBx:pdbx_audit_revision_category> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="3" revision_ordinal="1"> <PDBx:category>citation_author</PDBx:category> </PDBx:pdbx_audit_revision_category> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="4" revision_ordinal="2"> <PDBx:category>citation</PDBx:category> </PDBx:pdbx_audit_revision_category> </PDBx:pdbx_audit_revision_categoryCategory> 1 1 1 1 1 pdbx_audit_revision_categoryCategory This property indicates that datablock has a category holder pdbx_audit_revision_categoryCategory. pdbx_audit_revision_categoryCategory This property indicates that pdbx_audit_revision_categoryCategory. has a category pdbx_audit_revision_category. pdbx_audit_revision_categoryItem Abstract datatype property for pdbx_audit_revision_category items. reference_to_pdbx_audit_revision_category cross-reference to pdbx_audit_revision_category. referenced_by_pdbx_audit_revision_category cross-reference from pdbx_audit_revision_category. pdbx_audit_revision_category.category The category updated in the pdbx_audit_revision_category record. audit_author citation Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_category.ordinal A unique identifier for the pdbx_audit_revision_category record. 1 pdbx_audit_revision_category.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_revision_details Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records. Example 1 <PDBx:pdbx_audit_revision_detailsCategory> <PDBx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <PDBx:provider>repository</PDBx:provider> <PDBx:type>Initial release</PDBx:type> </PDBx:pdbx_audit_revision_details> <PDBx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="2" revision_ordinal="7"> <PDBx:description>Remodeling of inhibitor</PDBx:description> <PDBx:provider>author</PDBx:provider> <PDBx:type>Coordinate replacement</PDBx:type> </PDBx:pdbx_audit_revision_details> </PDBx:pdbx_audit_revision_detailsCategory> 0 1 0 1 0 1 0 1 1 1 1 pdbx_audit_revision_detailsCategory This property indicates that datablock has a category holder pdbx_audit_revision_detailsCategory. pdbx_audit_revision_detailsCategory This property indicates that pdbx_audit_revision_detailsCategory. has a category pdbx_audit_revision_details. pdbx_audit_revision_detailsItem Abstract datatype property for pdbx_audit_revision_details items. reference_to_pdbx_audit_revision_details cross-reference to pdbx_audit_revision_details. referenced_by_pdbx_audit_revision_details cross-reference from pdbx_audit_revision_details. pdbx_audit_revision_details.description Additional details describing the revision. pdbx_audit_revision_details.details Further details describing the revision. repository author The provider of the revision. repository Initial release Coordinate replacement Obsolete Remediation A type classification of the revision Initial release Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_details.ordinal A unique identifier for the pdbx_audit_revision_details record. 1 pdbx_audit_revision_details.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_revision_group Data items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <PDBx:pdbx_audit_revision_groupCategory> <PDBx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="1" revision_ordinal="2"> <PDBx:group>citation</PDBx:group> </PDBx:pdbx_audit_revision_group> <PDBx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="2" revision_ordinal="3"> <PDBx:group>sample</PDBx:group> </PDBx:pdbx_audit_revision_group> </PDBx:pdbx_audit_revision_groupCategory> 1 1 1 1 1 pdbx_audit_revision_groupCategory This property indicates that datablock has a category holder pdbx_audit_revision_groupCategory. pdbx_audit_revision_groupCategory This property indicates that pdbx_audit_revision_groupCategory. has a category pdbx_audit_revision_group. pdbx_audit_revision_groupItem Abstract datatype property for pdbx_audit_revision_group items. reference_to_pdbx_audit_revision_group cross-reference to pdbx_audit_revision_group. referenced_by_pdbx_audit_revision_group cross-reference from pdbx_audit_revision_group. Advisory Atomic model Author supporting evidence Data collection Data processing Database references Derived calculations Experimental data Experimental preparation Initial release Non-polymer description Other Polymer sequence Refinement description Structure summary Source and taxonomy Version format compliance The collection of categories updated with this revision. citation Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_group.ordinal A unique identifier for the pdbx_audit_revision_group record. 1 pdbx_audit_revision_group.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_revision_history Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry. Example 1 <PDBx:pdbx_audit_revision_historyCategory> <PDBx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="1"> <PDBx:internal_deposition_id>D_123456789</PDBx:internal_deposition_id> <PDBx:internal_version>4</PDBx:internal_version> <PDBx:major_revision>1</PDBx:major_revision> <PDBx:minor_revision>0</PDBx:minor_revision> <PDBx:revision_date>2017-03-01</PDBx:revision_date> </PDBx:pdbx_audit_revision_history> <PDBx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="2"> <PDBx:internal_deposition_id>D_123456789</PDBx:internal_deposition_id> <PDBx:internal_version>6</PDBx:internal_version> <PDBx:major_revision>1</PDBx:major_revision> <PDBx:minor_revision>1</PDBx:minor_revision> <PDBx:revision_date>2017-03-08</PDBx:revision_date> </PDBx:pdbx_audit_revision_history> </PDBx:pdbx_audit_revision_historyCategory> 0 1 0 1 1 1 1 1 1 1 1 1 pdbx_audit_revision_historyCategory This property indicates that datablock has a category holder pdbx_audit_revision_historyCategory. pdbx_audit_revision_historyCategory This property indicates that pdbx_audit_revision_historyCategory. has a category pdbx_audit_revision_history. pdbx_audit_revision_historyItem Abstract datatype property for pdbx_audit_revision_history items. reference_to_pdbx_audit_revision_history cross-reference to pdbx_audit_revision_history. referenced_by_pdbx_audit_revision_history cross-reference from pdbx_audit_revision_history. pdbx_audit_revision_history.internal_deposition_id The deposition id that corresponds to this millestone file D_123456789 pdbx_audit_revision_history.internal_version An internal version number corresponding to millestone file 13 pdbx_audit_revision_history.major_revision The major version number of deposition release. 1 pdbx_audit_revision_history.minor_revision The minor version number of deposition release. 1 pdbx_audit_revision_history.revision_date The release date of the revision 2017-03-08 Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_history.ordinal A unique identifier for the pdbx_audit_revision_history record. 1 0 pdbx_audit_revision_item Data items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <PDBx:pdbx_audit_revision_itemCategory> <PDBx:pdbx_audit_revision_item data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <PDBx:item>_atom_site.type_symbol</PDBx:item> </PDBx:pdbx_audit_revision_item> </PDBx:pdbx_audit_revision_itemCategory> 1 1 1 1 1 pdbx_audit_revision_itemCategory This property indicates that datablock has a category holder pdbx_audit_revision_itemCategory. pdbx_audit_revision_itemCategory This property indicates that pdbx_audit_revision_itemCategory. has a category pdbx_audit_revision_item. pdbx_audit_revision_itemItem Abstract datatype property for pdbx_audit_revision_item items. reference_to_pdbx_audit_revision_item cross-reference to pdbx_audit_revision_item. referenced_by_pdbx_audit_revision_item cross-reference from pdbx_audit_revision_item. pdbx_audit_revision_item.item A high level explanation the author has provided for submitting a revision. _atom_site.type_symbol Structure model NMR restraints NMR shifts Structure factors Chemical component The type of file that the pdbx_audit_revision_history record refers to. Structure model pdbx_audit_revision_item.ordinal A unique identifier for the pdbx_audit_revision_item record. 1 pdbx_audit_revision_item.revision_ordinal A pointer to attribute ordinal in category pdbx_audit_revision_history 1 0 pdbx_audit_support Data items in the PDBX_AUDIT_SUPPORT category record details about funding support for the entry. Example 1 - <PDBx:pdbx_audit_supportCategory> <PDBx:pdbx_audit_support ordinal="1"> <PDBx:country>United States</PDBx:country> <PDBx:funding_organization>National Institutes of Health/National Institute of General Medical Sciences</PDBx:funding_organization> <PDBx:grant_number>1R01GM072999-01</PDBx:grant_number> </PDBx:pdbx_audit_support> </PDBx:pdbx_audit_supportCategory> 0 1 0 1 0 1 0 1 1 pdbx_audit_supportCategory This property indicates that datablock has a category holder pdbx_audit_supportCategory. pdbx_audit_supportCategory This property indicates that pdbx_audit_supportCategory. has a category pdbx_audit_support. pdbx_audit_supportItem Abstract datatype property for pdbx_audit_support items. reference_to_pdbx_audit_support cross-reference to pdbx_audit_support. referenced_by_pdbx_audit_support cross-reference from pdbx_audit_support. pdbx_audit_support.country The country/region providing the funding support for the entry. pdbx_audit_support.details Additional details regarding the funding of this entry pdbx_audit_support.funding_organization The name of the organization providing funding support for the entry. National Institutes of Health Wellcome Trust National Institutes of Health/National Institute of General Medical Sciences pdbx_audit_support.grant_number The grant number associated with this source of support. pdbx_audit_support.ordinal A unique sequential integer identifier for each source of support for this entry. 1 2 3 0 pdbx_bond_distance_limits This category provides a table of upper and lower distance limits used as criteria in determining covalent bonds. The table is organized by atom type pairs. Example 1 - Abbreviated bond distance limit table <PDBx:pdbx_bond_distance_limitsCategory> <PDBx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Ag"> <PDBx:lower_limit>1.85</PDBx:lower_limit> <PDBx:upper_limit>2.70</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Ag"> <PDBx:lower_limit>1.85</PDBx:lower_limit> <PDBx:upper_limit>2.70</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Ag"> <PDBx:lower_limit>2.00</PDBx:lower_limit> <PDBx:upper_limit>3.00</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="Al" atom_type_2="H"> <PDBx:lower_limit>1.35</PDBx:lower_limit> <PDBx:upper_limit>1.65</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="As" atom_type_2="H"> <PDBx:lower_limit>1.20</PDBx:lower_limit> <PDBx:upper_limit>1.60</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Au"> <PDBx:lower_limit>1.80</PDBx:lower_limit> <PDBx:upper_limit>2.80</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Au"> <PDBx:lower_limit>1.80</PDBx:lower_limit> <PDBx:upper_limit>2.80</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Au"> <PDBx:lower_limit>1.80</PDBx:lower_limit> <PDBx:upper_limit>3.00</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="B" atom_type_2="B"> <PDBx:lower_limit>1.45</PDBx:lower_limit> <PDBx:upper_limit>1.95</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="C" atom_type_2="B"> <PDBx:lower_limit>1.20</PDBx:lower_limit> <PDBx:upper_limit>1.85</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="F" atom_type_2="B"> <PDBx:lower_limit>1.20</PDBx:lower_limit> <PDBx:upper_limit>1.75</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> </PDBx:pdbx_bond_distance_limitsCategory> 1 1 1 1 1 1 pdbx_bond_distance_limitsCategory This property indicates that datablock has a category holder pdbx_bond_distance_limitsCategory. pdbx_bond_distance_limitsCategory This property indicates that pdbx_bond_distance_limitsCategory. has a category pdbx_bond_distance_limits. pdbx_bond_distance_limitsItem Abstract datatype property for pdbx_bond_distance_limits items. reference_to_pdbx_bond_distance_limits cross-reference to pdbx_bond_distance_limits. referenced_by_pdbx_bond_distance_limits cross-reference from pdbx_bond_distance_limits. pdbx_bond_distance_limits.lower_limit The lower bond distance limit. pdbx_bond_distance_limits.upper_limit The upper bond distance limit. pdbx_bond_distance_limits.atom_type_1 The first atom type defining the bond C N P pdbx_bond_distance_limits.atom_type_2 The first atom type defining the bond C N P 0 pdbx_branch_scheme The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities. Example 1 - <PDBx:pdbx_branch_schemeCategory> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="NAG" num="1"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>NAG</PDBx:auth_mon_id> <PDBx:auth_seq_num>1592</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>NAG</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>1</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="GAL" num="2"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>GAL</PDBx:auth_mon_id> <PDBx:auth_seq_num>1591</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>GAL</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>2</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="3"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>FUC</PDBx:auth_mon_id> <PDBx:auth_seq_num>1590</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>FUC</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>3</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="4"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>FUC</PDBx:auth_mon_id> <PDBx:auth_seq_num>1593</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>FUC</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>4</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> </PDBx:pdbx_branch_schemeCategory> 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 pdbx_branch_schemeCategory This property indicates that datablock has a category holder pdbx_branch_schemeCategory. pdbx_branch_schemeCategory This property indicates that pdbx_branch_schemeCategory. has a category pdbx_branch_scheme. pdbx_branch_schemeItem Abstract datatype property for pdbx_branch_scheme items. reference_to_pdbx_branch_scheme cross-reference to pdbx_branch_scheme. referenced_by_pdbx_branch_scheme cross-reference from pdbx_branch_scheme. pdbx_branch_scheme.auth_asym_id This data item is a pointer to attribute pdbx_auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.auth_mon_id This data item is a pointer to attribute pdbx_auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.auth_seq_num This data item is a pointer to attribute pdbx_auth_seq_id in category atom_site in the ATOM_SITE category. no n yes y A flag to indicate whether this monomer in the entity is heterogeneous in sequence. pdbx_branch_scheme.pdb_asym_id This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.pdb_ins_code This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.pdb_mon_id This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.pdb_seq_num This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. pdbx_branch_scheme.asym_id Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 pdbx_branch_scheme.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. pdbx_branch_scheme.mon_id This data item is a pointer to attribute label_comp_id in category atom_site in the PDBX_ENTITY_BRANCH_LIST category. pdbx_branch_scheme.num This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. 0 pdbx_buffer Data items in the PDBX_BUFFER category record details of the sample buffer. 0 1 0 1 1 pdbx_bufferCategory This property indicates that datablock has a category holder pdbx_bufferCategory. pdbx_bufferCategory This property indicates that pdbx_bufferCategory. has a category pdbx_buffer. pdbx_bufferItem Abstract datatype property for pdbx_buffer items. reference_to_pdbx_buffer cross-reference to pdbx_buffer. referenced_by_pdbx_buffer cross-reference from pdbx_buffer. pdbx_buffer.details Any additional details to do with buffer. aerated pdbx_buffer.name The name of each buffer. Acetic acid pdbx_buffer.id The value of attribute id in category pdbx_buffer must uniquely identify the sample buffer. 0 pdbx_buffer_components Constituents of buffer in sample Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:pdbx_buffer_componentsCategory> <PDBx:pdbx_buffer_components buffer_id="1" id="1"> <PDBx:conc>4 </PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>NaCl</PDBx:name> <PDBx:volume>0.200 </PDBx:volume> </PDBx:pdbx_buffer_components> <PDBx:pdbx_buffer_components buffer_id="1" id="2"> <PDBx:conc>100</PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:volume>0.047 </PDBx:volume> </PDBx:pdbx_buffer_components> <PDBx:pdbx_buffer_components buffer_id="1" id="3"> <PDBx:conc>neat</PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>water</PDBx:name> <PDBx:volume>0.700 </PDBx:volume> </PDBx:pdbx_buffer_components> </PDBx:pdbx_buffer_componentsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 pdbx_buffer_componentsCategory This property indicates that datablock has a category holder pdbx_buffer_componentsCategory. pdbx_buffer_componentsCategory This property indicates that pdbx_buffer_componentsCategory. has a category pdbx_buffer_components. pdbx_buffer_componentsItem Abstract datatype property for pdbx_buffer_components items. reference_to_pdbx_buffer_components cross-reference to pdbx_buffer_components. referenced_by_pdbx_buffer_components cross-reference from pdbx_buffer_components. pdbx_buffer_components.conc The millimolar concentration of buffer component. 200 % mM mg/mL M g/L The concentration units of the component. mg/mL for mg per milliliter mM for millimolar % for percent by volume pdbx_buffer_components.details Any additional details to do with buffer composition. pH adjusted with NaOH pdbx_buffer_components.isotopic_labeling The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H U-15N U-13C U-15N,13C U-2H other pdbx_buffer_components.name The name of each buffer component. Acetic acid pdbx_buffer_components.volume The volume of buffer component. 0.200 pdbx_buffer_components.buffer_id This data item is a pointer to attribute id in category pdbx_buffer in the BUFFER category. pdbx_buffer_components.id The value of attribute id in category pdbx_buffer_components must uniquely identify a component of the buffer. 0 pdbx_chain_remapping When producing a biological assembly model file, data items in the pdbx_chain_remapping provide a mapping from the entity in original model file to this data file. Example 1 - 6vjo <PDBx:pdbx_chain_remappingCategory> <PDBx:pdbx_chain_remapping entity_id="1" label_asym_id="A"> <PDBx:applied_operations>1</PDBx:applied_operations> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>A</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="2" label_asym_id="B"> <PDBx:applied_operations>1</PDBx:applied_operations> <PDBx:auth_asym_id>B</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>B</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="1" label_asym_id="A_2"> <PDBx:applied_operations>2</PDBx:applied_operations> <PDBx:auth_asym_id>A_2</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>A</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="2" label_asym_id="B_2"> <PDBx:applied_operations>2</PDBx:applied_operations> <PDBx:auth_asym_id>B_2</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>B</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="1" label_asym_id="A_3"> <PDBx:applied_operations>3</PDBx:applied_operations> <PDBx:auth_asym_id>A_3</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>A</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="2" label_asym_id="B_3"> <PDBx:applied_operations>3</PDBx:applied_operations> <PDBx:auth_asym_id>B_3</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>B</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="C"> <PDBx:applied_operations>1</PDBx:applied_operations> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>C</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="D"> <PDBx:applied_operations>1</PDBx:applied_operations> <PDBx:auth_asym_id>B</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>D</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="C_2"> <PDBx:applied_operations>2</PDBx:applied_operations> <PDBx:auth_asym_id>A_2</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>C</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="D_2"> <PDBx:applied_operations>2</PDBx:applied_operations> <PDBx:auth_asym_id>B_2</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>D</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="C_3"> <PDBx:applied_operations>3</PDBx:applied_operations> <PDBx:auth_asym_id>A_3</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>A</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>C</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> <PDBx:pdbx_chain_remapping entity_id="3" label_asym_id="D_3"> <PDBx:applied_operations>3</PDBx:applied_operations> <PDBx:auth_asym_id>B_3</PDBx:auth_asym_id> <PDBx:orig_auth_asym_id>B</PDBx:orig_auth_asym_id> <PDBx:orig_label_asym_id>D</PDBx:orig_label_asym_id> </PDBx:pdbx_chain_remapping> </PDBx:pdbx_chain_remappingCategory> 1 1 1 1 1 1 1 1 1 1 pdbx_chain_remappingCategory This property indicates that datablock has a category holder pdbx_chain_remappingCategory. pdbx_chain_remappingCategory This property indicates that pdbx_chain_remappingCategory. has a category pdbx_chain_remapping. pdbx_chain_remappingItem Abstract datatype property for pdbx_chain_remapping items. reference_to_pdbx_chain_remapping cross-reference to pdbx_chain_remapping. referenced_by_pdbx_chain_remapping cross-reference from pdbx_chain_remapping. pdbx_chain_remapping.applied_operations The set of operations identified pdbx_struct_oper_list.id that were applied to original atom_site coordinates to produce the coordinates in atom_site in this data block. pdbx_chain_remapping.auth_asym_id An alternative identifier for attribute label_asym_id in category atom_site. Frequently the chain id. pdbx_chain_remapping.orig_auth_asym_id An alternative identifier for attribute label_asym_id in category atom_site in the original model file. Frequently the author's chain id. pdbx_chain_remapping.orig_label_asym_id This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category in the original model file. pdbx_chain_remapping.entity_id Identifies an attribute id in category entity in this data block. pdbx_chain_remapping.label_asym_id This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. 0 pdbx_chem_comp_atom_edit Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide atom level editing instructions to be applied to imported chemical components. Example 1 - <PDBx:pdbx_chem_comp_atom_editCategory> <PDBx:pdbx_chem_comp_atom_edit ordinal="1"> <PDBx:atom_id>HN2</PDBx:atom_id> <PDBx:comp_id>LYS</PDBx:comp_id> <PDBx:edit_op>DELETE</PDBx:edit_op> </PDBx:pdbx_chem_comp_atom_edit> </PDBx:pdbx_chem_comp_atom_editCategory> 1 1 1 1 1 1 0 1 1 1 1 pdbx_chem_comp_atom_editCategory This property indicates that datablock has a category holder pdbx_chem_comp_atom_editCategory. pdbx_chem_comp_atom_editCategory This property indicates that pdbx_chem_comp_atom_editCategory. has a category pdbx_chem_comp_atom_edit. pdbx_chem_comp_atom_editItem Abstract datatype property for pdbx_chem_comp_atom_edit items. reference_to_pdbx_chem_comp_atom_edit cross-reference to pdbx_chem_comp_atom_edit. referenced_by_pdbx_chem_comp_atom_edit cross-reference from pdbx_chem_comp_atom_edit. pdbx_chem_comp_atom_edit.atom_id The identifier for the target atom in imported component to be edited. pdbx_chem_comp_atom_edit.comp_id This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP category. pdbx_chem_comp_atom_edit.edit_atom_id The identifier for the edited atom in the generated component. pdbx_chem_comp_atom_edit.edit_atom_value The value for the edited atomic property value in the generated component. RENAME DELETE ADD CHARGE PARTIAL_CHARGE MODEL_CARTN_X MODEL_CARTN_Y MODEL_CARTN_Z STEREO_CONFIG AROMATIC_FLAG The operation applied to the named imported component. pdbx_chem_comp_atom_edit.ordinal This data item uniquely identifies and orders each atom edit instruction. 0 pdbx_chem_comp_atom_feature Data items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide a selected list of atom level features for the chemical component. Example 1 - <PDBx:pdbx_chem_comp_atom_featureCategory> <PDBx:pdbx_chem_comp_atom_feature atom_id="N" comp_id="LYS" feature_type="NT"></PDBx:pdbx_chem_comp_atom_feature> <PDBx:pdbx_chem_comp_atom_feature atom_id="C" comp_id="LYS" feature_type="CT"></PDBx:pdbx_chem_comp_atom_feature> <PDBx:pdbx_chem_comp_atom_feature atom_id="CA" comp_id="LYS" feature_type="CPA"></PDBx:pdbx_chem_comp_atom_feature> </PDBx:pdbx_chem_comp_atom_featureCategory> 1 1 1 pdbx_chem_comp_atom_featureCategory This property indicates that datablock has a category holder pdbx_chem_comp_atom_featureCategory. pdbx_chem_comp_atom_featureCategory This property indicates that pdbx_chem_comp_atom_featureCategory. has a category pdbx_chem_comp_atom_feature. pdbx_chem_comp_atom_featureItem Abstract datatype property for pdbx_chem_comp_atom_feature items. reference_to_pdbx_chem_comp_atom_feature cross-reference to pdbx_chem_comp_atom_feature. referenced_by_pdbx_chem_comp_atom_feature cross-reference from pdbx_chem_comp_atom_feature. pdbx_chem_comp_atom_feature.atom_id The identifier for the target atom to which the feature is assigned. pdbx_chem_comp_atom_feature.comp_id This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP category. CT NT 5PT 3PT CPA CNA The feature assigned to this atom. 0 pdbx_chem_comp_atom_related PDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components. Example 1 - <PDBx:pdbx_chem_comp_atom_relatedCategory> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="1" related_comp_id="GLC"> <PDBx:atom_id>C1</PDBx:atom_id> <PDBx:related_atom_id>C1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="2" related_comp_id="GLC"> <PDBx:atom_id>C2</PDBx:atom_id> <PDBx:related_atom_id>C2</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="3" related_comp_id="GLC"> <PDBx:atom_id>C3</PDBx:atom_id> <PDBx:related_atom_id>C3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="4" related_comp_id="GLC"> <PDBx:atom_id>C4</PDBx:atom_id> <PDBx:related_atom_id>C4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="5" related_comp_id="GLC"> <PDBx:atom_id>C5</PDBx:atom_id> <PDBx:related_atom_id>C5</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="6" related_comp_id="GLC"> <PDBx:atom_id>C6</PDBx:atom_id> <PDBx:related_atom_id>C6</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="7" related_comp_id="GLC"> <PDBx:atom_id>N</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="8" related_comp_id="GLC"> <PDBx:atom_id>O1</PDBx:atom_id> <PDBx:related_atom_id>O1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="9" related_comp_id="GLC"> <PDBx:atom_id>O3</PDBx:atom_id> <PDBx:related_atom_id>O3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="10" related_comp_id="GLC"> <PDBx:atom_id>O4</PDBx:atom_id> <PDBx:related_atom_id>O4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="11" related_comp_id="GLC"> <PDBx:atom_id>O5</PDBx:atom_id> <PDBx:related_atom_id>O5</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="12" related_comp_id="GLC"> <PDBx:atom_id>O6</PDBx:atom_id> <PDBx:related_atom_id>O6</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="13" related_comp_id="GLC"> <PDBx:atom_id>S1</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="14" related_comp_id="GLC"> <PDBx:atom_id>O1S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="15" related_comp_id="GLC"> <PDBx:atom_id>O2S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="16" related_comp_id="GLC"> <PDBx:atom_id>O3S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="17" related_comp_id="GLC"> <PDBx:atom_id>S2</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="18" related_comp_id="GLC"> <PDBx:atom_id>O4S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="19" related_comp_id="GLC"> <PDBx:atom_id>O5S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="20" related_comp_id="GLC"> <PDBx:atom_id>O6S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="21" related_comp_id="GLC"> <PDBx:atom_id>H1</PDBx:atom_id> <PDBx:related_atom_id>H1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="22" related_comp_id="GLC"> <PDBx:atom_id>H2</PDBx:atom_id> <PDBx:related_atom_id>H2</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="23" related_comp_id="GLC"> <PDBx:atom_id>H3</PDBx:atom_id> <PDBx:related_atom_id>H3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="24" related_comp_id="GLC"> <PDBx:atom_id>H4</PDBx:atom_id> <PDBx:related_atom_id>H4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="25" related_comp_id="GLC"> <PDBx:atom_id>H5</PDBx:atom_id> <PDBx:related_atom_id>H5</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="26" related_comp_id="GLC"> <PDBx:atom_id>H61</PDBx:atom_id> <PDBx:related_atom_id>H61</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="27" related_comp_id="GLC"> <PDBx:atom_id>H62</PDBx:atom_id> <PDBx:related_atom_id>H62</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="28" related_comp_id="GLC"> <PDBx:atom_id>HN</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="29" related_comp_id="GLC"> <PDBx:atom_id>HO1</PDBx:atom_id> <PDBx:related_atom_id>HO1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="30" related_comp_id="GLC"> <PDBx:atom_id>HO3</PDBx:atom_id> <PDBx:related_atom_id>HO3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="31" related_comp_id="GLC"> <PDBx:atom_id>HO4</PDBx:atom_id> <PDBx:related_atom_id>HO4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="32" related_comp_id="GLC"> <PDBx:atom_id>HOS3</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="33" related_comp_id="GLC"> <PDBx:atom_id>HOS6</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> </PDBx:pdbx_chem_comp_atom_relatedCategory> 1 1 0 1 1 1 1 1 1 pdbx_chem_comp_atom_relatedCategory This property indicates that datablock has a category holder pdbx_chem_comp_atom_relatedCategory. pdbx_chem_comp_atom_relatedCategory This property indicates that pdbx_chem_comp_atom_relatedCategory. has a category pdbx_chem_comp_atom_related. pdbx_chem_comp_atom_relatedItem Abstract datatype property for pdbx_chem_comp_atom_related items. reference_to_pdbx_chem_comp_atom_related cross-reference to pdbx_chem_comp_atom_related. referenced_by_pdbx_chem_comp_atom_related cross-reference from pdbx_chem_comp_atom_related. pdbx_chem_comp_atom_related.atom_id The atom identifier/name for the atom mapping pdbx_chem_comp_atom_related.related_atom_id The atom identifier/name for the atom mapping in the related chemical component Carbohydrate core Precursor Describes the type of relationship pdbx_chem_comp_atom_related.comp_id The chemical component for which this relationship applies. pdbx_chem_comp_atom_related.ordinal An ordinal index for this category 1 2 pdbx_chem_comp_atom_related.related_comp_id The related chemical component for which this chemical component is based. 0 pdbx_chem_comp_audit Data items in the PDBX_CHEM_COMP_AUDIT category records the status and tracking information for this component. Example 1 - <PDBx:pdbx_chem_comp_auditCategory> <PDBx:pdbx_chem_comp_audit action_type="Create componenet" comp_id="ATP" date="2007-12-01"> <PDBx:annotator>JY</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_audit> <PDBx:pdbx_chem_comp_audit action_type="Modify leaving atom flag" comp_id="ATP" date="2008-10-03"> <PDBx:annotator>CS</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_audit> <PDBx:pdbx_chem_comp_audit action_type="Modify synonyms" comp_id="ATP" date="2009-07-03"> <PDBx:annotator>MZ</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_audit> </PDBx:pdbx_chem_comp_auditCategory> 0 1 0 1 0 1 1 1 1 pdbx_chem_comp_auditCategory This property indicates that datablock has a category holder pdbx_chem_comp_auditCategory. pdbx_chem_comp_auditCategory This property indicates that pdbx_chem_comp_auditCategory. has a category pdbx_chem_comp_audit. pdbx_chem_comp_auditItem Abstract datatype property for pdbx_chem_comp_audit items. reference_to_pdbx_chem_comp_audit cross-reference to pdbx_chem_comp_audit. referenced_by_pdbx_chem_comp_audit cross-reference from pdbx_chem_comp_audit. pdbx_chem_comp_audit.annotator The initials of the annotator creating of modifying the component. JO SJ KB pdbx_chem_comp_audit.details Additional details decribing this change. Added C14 as a leaving atom. pdbx_chem_comp_audit.processing_site An identifier for the wwPDB site creating or modifying the component. RCSB PDBE PDBJ BMRB PDBC Create component Modify name Modify formula Modify synonyms Modify linking type Modify internal type Modify parent residue Modify processing site Modify subcomponent list Modify one letter code Modify model coordinates code Modify formal charge Modify atom id Modify charge Modify aromatic_flag Modify leaving atom flag Modify component atom id Modify component comp_id Modify value order Modify descriptor Modify identifier Modify coordinates Modify backbone Modify PCM Other modification Obsolete component Initial release The action associated with this audit record. pdbx_chem_comp_audit.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. pdbx_chem_comp_audit.date The date associated with this audit record. 0 pdbx_chem_comp_bond_edit Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide bond level editing instructions to be applied to imported chemical components. Example 1 - <PDBx:pdbx_chem_comp_bond_editCategory> <PDBx:pdbx_chem_comp_bond_edit atom_id_1="OXT" atom_id_2="HXT" comp_id="LYS" edit_op="DELETE"> <PDBx:ordinal>1</PDBx:ordinal> </PDBx:pdbx_chem_comp_bond_edit> </PDBx:pdbx_chem_comp_bond_editCategory> 0 1 1 1 1 1 1 1 pdbx_chem_comp_bond_editCategory This property indicates that datablock has a category holder pdbx_chem_comp_bond_editCategory. pdbx_chem_comp_bond_editCategory This property indicates that pdbx_chem_comp_bond_editCategory. has a category pdbx_chem_comp_bond_edit. pdbx_chem_comp_bond_editItem Abstract datatype property for pdbx_chem_comp_bond_edit items. reference_to_pdbx_chem_comp_bond_edit cross-reference to pdbx_chem_comp_bond_edit. referenced_by_pdbx_chem_comp_bond_edit cross-reference from pdbx_chem_comp_bond_edit. pdbx_chem_comp_bond_edit.edit_bond_value The value for the edited bond property value in the generated component. pdbx_chem_comp_bond_edit.ordinal This data item uniquely identifies and orders each bond edit instruction. pdbx_chem_comp_bond_edit.atom_id_1 The identifier for the first atom in the target bond in imported component. pdbx_chem_comp_bond_edit.atom_id_2 The identifier for the second atom in the target bond in imported component. pdbx_chem_comp_bond_edit.comp_id This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP category. DELETE ADD VALUE_ORDER VALUE_DIST STEREO_CONFIG AROMATIC_FLAG The operation or assignment applied to the named imported component. 0 pdbx_chem_comp_depositor_info Data items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional details provided by depositors about deposited chemical components. Example 1 - <PDBx:pdbx_chem_comp_depositor_infoCategory> <PDBx:pdbx_chem_comp_depositor_info ordinal="1"> <PDBx:alt_comp_id xsi:nil="true" /> <PDBx:comp_id>GNC</PDBx:comp_id> <PDBx:descriptor>CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O</PDBx:descriptor> <PDBx:descriptor_type>SMILES</PDBx:descriptor_type> <PDBx:formula>C8 H15 N O6</PDBx:formula> <PDBx:name>N-acetyl-beta-D-glucosamine</PDBx:name> </PDBx:pdbx_chem_comp_depositor_info> </PDBx:pdbx_chem_comp_depositor_infoCategory> 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_chem_comp_depositor_infoCategory This property indicates that datablock has a category holder pdbx_chem_comp_depositor_infoCategory. pdbx_chem_comp_depositor_infoCategory This property indicates that pdbx_chem_comp_depositor_infoCategory. has a category pdbx_chem_comp_depositor_info. pdbx_chem_comp_depositor_infoItem Abstract datatype property for pdbx_chem_comp_depositor_info items. reference_to_pdbx_chem_comp_depositor_info cross-reference to pdbx_chem_comp_depositor_info. referenced_by_pdbx_chem_comp_depositor_info cross-reference from pdbx_chem_comp_depositor_info. pdbx_chem_comp_depositor_info.alt_comp_id The alternate chemical component identifier matching the deposited chemical component. pdbx_chem_comp_depositor_info.comp_id The chemical component identifier used by the depositor to represent this component. pdbx_chem_comp_depositor_info.descriptor This data item contains the descriptor value for this component. SMILES InChI InChIKey This data item contains the descriptor type. pdbx_chem_comp_depositor_info.details This data item contains additional details about this component. pdbx_chem_comp_depositor_info.formula The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S Y N A flag to indicate if the chemical component is defined in the chemical component dictionary. pdbx_chem_comp_depositor_info.name The chemical name of the component. alanine valine adenine cytosine peptide_like heterogen none_of_abv carbohydrate lipid D-peptide linking L-peptide linking DNA linking RNA linking L-RNA linking L-DNA linking saccharide non-polymer peptide linking peptide-like other This data item contains the chemical component type. pdbx_chem_comp_depositor_info.upload_file_name The filename of an uploaded description of a component component. pdbx_chem_comp_depositor_info.upload_file_type The type of an uploaded description of a component component. pdbx_chem_comp_depositor_info.ordinal Ordinal index for this category. 0 pdbx_chem_comp_descriptor Data items in the CHEM_COMP_DESCRIPTOR category provide string descriptors of component chemical structure. Example 1 - <PDBx:pdbx_chem_comp_descriptorCategory> <PDBx:pdbx_chem_comp_descriptor comp_id="ATP" program="OPENEYE" program_version="1.5.0" type="SMILES"> <PDBx:descriptor>c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N</PDBx:descriptor> </PDBx:pdbx_chem_comp_descriptor> </PDBx:pdbx_chem_comp_descriptorCategory> 1 1 0 1 1 1 1 1 pdbx_chem_comp_descriptorCategory This property indicates that datablock has a category holder pdbx_chem_comp_descriptorCategory. pdbx_chem_comp_descriptorCategory This property indicates that pdbx_chem_comp_descriptorCategory. has a category pdbx_chem_comp_descriptor. pdbx_chem_comp_descriptorItem Abstract datatype property for pdbx_chem_comp_descriptor items. reference_to_pdbx_chem_comp_descriptor cross-reference to pdbx_chem_comp_descriptor. referenced_by_pdbx_chem_comp_descriptor cross-reference from pdbx_chem_comp_descriptor. pdbx_chem_comp_descriptor.descriptor This data item contains the descriptor value for this component. pdbx_chem_comp_descriptor.ordinal Ordinal index for this category. pdbx_chem_comp_descriptor.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. pdbx_chem_comp_descriptor.program This data item contains the name of the program or library used to compute the descriptor. OpenEye OECHEM library OPENEYE CACTVS program library CACTVS Daylight program library DAYLIGHT Other program or library OTHER pdbx_chem_comp_descriptor.program_version This data item contains the version of the program or library used to compute the descriptor. SMILES_CANNONICAL SMILES_CANONICAL SMILES InChI InChI_MAIN InChI_MAIN_FORMULA InChI_MAIN_CONNECT InChI_MAIN_HATOM InChI_CHARGE InChI_STEREO InChI_ISOTOPE InChI_FIXEDH InChI_RECONNECT InChIKey This data item contains the descriptor type. 0 pdbx_chem_comp_feature Additional features associated with the chemical component. Example 1 - <PDBx:pdbx_chem_comp_featureCategory> <PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="ENZYME INHIBITED" value="ASPARTIC PROTEINASE"></PDBx:pdbx_chem_comp_feature> <PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="FUNCTION" value="Transistion-state analogue inhibitor"></PDBx:pdbx_chem_comp_feature> <PDBx:pdbx_chem_comp_feature comp_id="00X" source="IUCR" type="STRUCTURE IMAGE URL" value="http://journals.iucr.org/00X.jpg"></PDBx:pdbx_chem_comp_feature> </PDBx:pdbx_chem_comp_featureCategory> 0 1 1 1 1 1 pdbx_chem_comp_featureCategory This property indicates that datablock has a category holder pdbx_chem_comp_featureCategory. pdbx_chem_comp_featureCategory This property indicates that pdbx_chem_comp_featureCategory. has a category pdbx_chem_comp_feature. pdbx_chem_comp_featureItem Abstract datatype property for pdbx_chem_comp_feature items. reference_to_pdbx_chem_comp_feature cross-reference to pdbx_chem_comp_feature. referenced_by_pdbx_chem_comp_feature cross-reference from pdbx_chem_comp_feature. pdbx_chem_comp_feature.support The supporting evidence for this feature. Biological assay Data obtained from PNAS August 17, 1999 vol. 96 no. 17 9586-9590 pdbx_chem_comp_feature.comp_id The component identifier for this feature. ABC ATP pdbx_chem_comp_feature.source The information source for the component feature. PDB CHEBI DRUGBANK PUBCHEM CARBOHYDRATE ANOMER CARBOHYDRATE ISOMER CARBOHYDRATE RING CARBOHYDRATE PRIMARY CARBONYL GROUP The component feature type. CARBOHYDRATE ANOMER CARBOHYDRATE ISOMER CARBOHYDRATE RING pdbx_chem_comp_feature.value The component feature value. 0 pdbx_chem_comp_identifier Data items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components. Example 1 - <PDBx:pdbx_chem_comp_identifierCategory> <PDBx:pdbx_chem_comp_identifier comp_id="ATP" program="ACDLabs" program_version="10.04" type="SYSTEMATIC NAME"> <PDBx:identifier>adenosine 5&apos;-(tetrahydrogen triphosphate)</PDBx:identifier> </PDBx:pdbx_chem_comp_identifier> </PDBx:pdbx_chem_comp_identifierCategory> 1 1 0 1 1 1 1 1 pdbx_chem_comp_identifierCategory This property indicates that datablock has a category holder pdbx_chem_comp_identifierCategory. pdbx_chem_comp_identifierCategory This property indicates that pdbx_chem_comp_identifierCategory. has a category pdbx_chem_comp_identifier. pdbx_chem_comp_identifierItem Abstract datatype property for pdbx_chem_comp_identifier items. reference_to_pdbx_chem_comp_identifier cross-reference to pdbx_chem_comp_identifier. referenced_by_pdbx_chem_comp_identifier cross-reference from pdbx_chem_comp_identifier. pdbx_chem_comp_identifier.identifier This data item contains the identifier value for this component. pdbx_chem_comp_identifier.ordinal Ordinal index for this category. pdbx_chem_comp_identifier.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. pdbx_chem_comp_identifier.program This data item contains the name of the program or library used to compute the identifier. OpenEye OECHEM program OPENEYE Daylight program library DAYLIGHT Advanced Chemistry Development Naming Program ACD Belstein AutoNom Naming Program AUTONOM Compound identifier PUBCHEM_CID Substance identifier PUBCHEM_SID Other program or library OTHER Non-programmatic identifier NONE pdbx_chem_comp_identifier.program_version This data item contains the version of the program or library used to compute the identifier. COMMON NAME SYSTEMATIC NAME CAS REGISTRY NUMBER PUBCHEM Identifier MDL Identifier SYNONYM CONDENSED IUPAC CARB SYMBOL IUPAC CARB SYMBOL SNFG CARB SYMBOL CONDENSED IUPAC CARBOHYDRATE SYMBOL IUPAC CARBOHYDRATE SYMBOL SNFG CARBOHYDRATE SYMBOL This data item contains the identifier type. 0 pdbx_chem_comp_import Data items in the PDBX_CHEM_COMP_IMPORT category identify existing chemical components to be imported into the current component definition. Components in this list can be edited by instructions in categories pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit. Example 1 - <PDBx:pdbx_chem_comp_importCategory> <PDBx:pdbx_chem_comp_import comp_id="ATP"></PDBx:pdbx_chem_comp_import> </PDBx:pdbx_chem_comp_importCategory> 1 pdbx_chem_comp_importCategory This property indicates that datablock has a category holder pdbx_chem_comp_importCategory. pdbx_chem_comp_importCategory This property indicates that pdbx_chem_comp_importCategory. has a category pdbx_chem_comp_import. pdbx_chem_comp_importItem Abstract datatype property for pdbx_chem_comp_import items. reference_to_pdbx_chem_comp_import cross-reference to pdbx_chem_comp_import. referenced_by_pdbx_chem_comp_import cross-reference from pdbx_chem_comp_import. pdbx_chem_comp_import.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 pdbx_chem_comp_instance_depositor_info Data items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records depositor provided information about the chemical context of component instances. Example - <PDBx:pdbx_chem_comp_instance_depositor_infoCategory> <PDBx:pdbx_chem_comp_instance_depositor_info ordinal="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_asym_id>W</PDBx:auth_asym_id> <PDBx:auth_seq_id>102</PDBx:auth_seq_id> <PDBx:author_provided_flag>Y</PDBx:author_provided_flag> <PDBx:comp_id>X78</PDBx:comp_id> <PDBx:in_polymer_flag>N</PDBx:in_polymer_flag> <PDBx:label_alt_id xsi:nil="true" /> </PDBx:pdbx_chem_comp_instance_depositor_info> </PDBx:pdbx_chem_comp_instance_depositor_infoCategory> 0 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 1 pdbx_chem_comp_instance_depositor_infoCategory This property indicates that datablock has a category holder pdbx_chem_comp_instance_depositor_infoCategory. pdbx_chem_comp_instance_depositor_infoCategory This property indicates that pdbx_chem_comp_instance_depositor_infoCategory. has a category pdbx_chem_comp_instance_depositor_info. pdbx_chem_comp_instance_depositor_infoItem Abstract datatype property for pdbx_chem_comp_instance_depositor_info items. reference_to_pdbx_chem_comp_instance_depositor_info cross-reference to pdbx_chem_comp_instance_depositor_info. referenced_by_pdbx_chem_comp_instance_depositor_info cross-reference from pdbx_chem_comp_instance_depositor_info. pdbx_chem_comp_instance_depositor_info.PDB_ins_code Optional element of the chemical component instance identifier. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. pdbx_chem_comp_instance_depositor_info.auth_asym_id An element of the chemical component instance identifier. This data item corresponds to attribute auth_asym_id in category atom_site in the ATOM_SITE category. pdbx_chem_comp_instance_depositor_info.auth_seq_id An element of the chemical component instance identifier. This data item corresponds to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Y N A flag to indicate if details about this chemical component instance have been provided by the depositor. pdbx_chem_comp_instance_depositor_info.comp_id An element of the chemical component instance identifier. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. pdbx_chem_comp_instance_depositor_info.formula The observed formula for the chemical component in the deposited coordinates. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S Y N A flag to indicate if the chemical component instance is a part of a polymer molecule. pdbx_chem_comp_instance_depositor_info.label_alt_id An element of the chemical component instance identifier. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. pdbx_chem_comp_instance_depositor_info.ordinal The value of pdbx_chem_comp_instance_depositor_info.ordinal must uniquely identify a record in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO list. 0 pdbx_chem_comp_model Data items in the PDBX_CHEM_COMP_MODEL category give details about each of the chemical component model instances. Example 1 - <PDBx:pdbx_chem_comp_modelCategory> <PDBx:pdbx_chem_comp_model id="M_ZZV_00001"> <PDBx:comp_id>ZZV</PDBx:comp_id> </PDBx:pdbx_chem_comp_model> </PDBx:pdbx_chem_comp_modelCategory> 1 1 1 pdbx_chem_comp_modelCategory This property indicates that datablock has a category holder pdbx_chem_comp_modelCategory. pdbx_chem_comp_modelCategory This property indicates that pdbx_chem_comp_modelCategory. has a category pdbx_chem_comp_model. pdbx_chem_comp_modelItem Abstract datatype property for pdbx_chem_comp_model items. reference_to_pdbx_chem_comp_model cross-reference to pdbx_chem_comp_model. referenced_by_pdbx_chem_comp_model cross-reference from pdbx_chem_comp_model. pdbx_chem_comp_model.comp_id An identifier for chemical component definition. ABC pdbx_chem_comp_model.id The value of attribute id in category pdbx_chem_comp_model must uniquely identify each model instance the PDBX_CHEM_COMP_MODEL list. M_ABC_00001 0 pdbx_chem_comp_model_atom Data items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates for the chemical component model instance. Example 1 - <PDBx:pdbx_chem_comp_model_atomCategory> <PDBx:pdbx_chem_comp_model_atom atom_id="CAA" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>2.180</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.561</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.402</PDBx:model_Cartn_z> <PDBx:ordinal_id>1</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAB" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>5.709</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.659</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.211</PDBx:model_Cartn_z> <PDBx:ordinal_id>2</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAC" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>1.912</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.185</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>12.303</PDBx:model_Cartn_z> <PDBx:ordinal_id>3</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAD" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.002</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>7.560</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>6.491</PDBx:model_Cartn_z> <PDBx:ordinal_id>4</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAE" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.992</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>9.134</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.117</PDBx:model_Cartn_z> <PDBx:ordinal_id>5</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAF" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>2.970</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>10.013</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>13.854</PDBx:model_Cartn_z> <PDBx:ordinal_id>6</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="FAG" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-3.392</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.249</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>6.995</PDBx:model_Cartn_z> <PDBx:ordinal_id>7</PDBx:ordinal_id> <PDBx:type_symbol>F</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAH" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.361</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>5.472</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>12.379</PDBx:model_Cartn_z> <PDBx:ordinal_id>8</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAI" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.277</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.182</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>13.595</PDBx:model_Cartn_z> <PDBx:ordinal_id>9</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAJ" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-2.132</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.408</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.958</PDBx:model_Cartn_z> <PDBx:ordinal_id>10</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAK" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-1.112</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.651</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>6.807</PDBx:model_Cartn_z> <PDBx:ordinal_id>11</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAL" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-0.902</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.579</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>9.557</PDBx:model_Cartn_z> <PDBx:ordinal_id>12</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAM" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>0.139</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.801</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>7.421</PDBx:model_Cartn_z> <PDBx:ordinal_id>13</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAN" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.004</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.101</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>11.237</PDBx:model_Cartn_z> <PDBx:ordinal_id>14</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> </PDBx:pdbx_chem_comp_model_atomCategory> 0 1 0 1 0 1 0 1 1 1 1 1 1 1 pdbx_chem_comp_model_atomCategory This property indicates that datablock has a category holder pdbx_chem_comp_model_atomCategory. pdbx_chem_comp_model_atomCategory This property indicates that pdbx_chem_comp_model_atomCategory. has a category pdbx_chem_comp_model_atom. pdbx_chem_comp_model_atomItem Abstract datatype property for pdbx_chem_comp_model_atom items. reference_to_pdbx_chem_comp_model_atom cross-reference to pdbx_chem_comp_model_atom. referenced_by_pdbx_chem_comp_model_atom cross-reference from pdbx_chem_comp_model_atom. pdbx_chem_comp_model_atom.charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 pdbx_chem_comp_model_atom.model_Cartn_x The x component of the coordinates for this atom in this component model specified as orthogonal angstroms. pdbx_chem_comp_model_atom.model_Cartn_y The y component of the coordinates for this atom in this component model specified as orthogonal angstroms. pdbx_chem_comp_model_atom.model_Cartn_z The z component of the coordinates for this atom in this component model specified as orthogonal angstroms. pdbx_chem_comp_model_atom.ordinal_id The value of attribute ordinal_id in category pdbx_chem_comp_model_atom is an ordinal identifer for each atom in the PDBX_CHEM_COMP_MODEL_ATOM list. pdbx_chem_comp_model_atom.type_symbol The code used to identify the atom species representing this atom type. Normally this code is the element symbol. C N O pdbx_chem_comp_model_atom.atom_id The value of attribute atom_id in category pdbx_chem_comp_model_atom uniquely identifies each atom in the PDBX_CHEM_COMP_MODEL_ATOM list. pdbx_chem_comp_model_atom.model_id This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. 0 pdbx_chem_comp_model_audit Data items in the PDBX_CHEM_COMP_MODEL_AUDIT category records the status and tracking information for this component model instance. Example 1 - <PDBx:pdbx_chem_comp_model_auditCategory> <PDBx:pdbx_chem_comp_model_audit action_type="Create component model" date="2014-11-30" model_id="M_ZZV_00001"> <PDBx:annotator>JDW</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_model_audit> </PDBx:pdbx_chem_comp_model_auditCategory> 0 1 0 1 0 1 1 1 1 pdbx_chem_comp_model_auditCategory This property indicates that datablock has a category holder pdbx_chem_comp_model_auditCategory. pdbx_chem_comp_model_auditCategory This property indicates that pdbx_chem_comp_model_auditCategory. has a category pdbx_chem_comp_model_audit. pdbx_chem_comp_model_auditItem Abstract datatype property for pdbx_chem_comp_model_audit items. reference_to_pdbx_chem_comp_model_audit cross-reference to pdbx_chem_comp_model_audit. referenced_by_pdbx_chem_comp_model_audit cross-reference from pdbx_chem_comp_model_audit. pdbx_chem_comp_model_audit.annotator The initials of the annotator creating of modifying the component. JO SJ KB pdbx_chem_comp_model_audit.details Additional details decribing this change. Added C14 as a leaving atom. pdbx_chem_comp_model_audit.processing_site An identifier for the wwPDB site creating or modifying the component. RCSB PDBE PDBJ BMRB PDBC Create component Modify formal charge Modify atom id Modify charge Modify component atom id Modify component comp_id Modify value order Modify descriptor Modify identifier Modify coordinates Other modification Obsolete model Initial release The action associated with this audit record. pdbx_chem_comp_model_audit.date The date associated with this audit record. pdbx_chem_comp_model_audit.model_id This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. 0 pdbx_chem_comp_model_bond Data items in the PDBX_CHEM_COMP_MODEL_BOND category record details about the bonds between atoms in a chemical component model instance. Example 1 - <PDBx:pdbx_chem_comp_model_bondCategory> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="NBA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>1</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>2</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAAA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>3</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAAB" model_id="M_ZZV_00001"> <PDBx:ordinal_id>4</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="SBC" model_id="M_ZZV_00001"> <PDBx:ordinal_id>5</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HAB" model_id="M_ZZV_00001"> <PDBx:ordinal_id>6</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HABA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>7</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HABB" model_id="M_ZZV_00001"> <PDBx:ordinal_id>8</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAC" atom_id_2="CAR" model_id="M_ZZV_00001"> <PDBx:ordinal_id>9</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAD" atom_id_2="SBC" model_id="M_ZZV_00001"> <PDBx:ordinal_id>10</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAE" atom_id_2="SBC" model_id="M_ZZV_00001"> <PDBx:ordinal_id>11</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAF" atom_id_2="CAU" model_id="M_ZZV_00001"> <PDBx:ordinal_id>12</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAF" atom_id_2="HOAF" model_id="M_ZZV_00001"> <PDBx:ordinal_id>13</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="FAG" atom_id_2="CAS" model_id="M_ZZV_00001"> <PDBx:ordinal_id>14</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="CAI" model_id="M_ZZV_00001"> <PDBx:ordinal_id>15</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="CAN" model_id="M_ZZV_00001"> <PDBx:ordinal_id>16</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="HAH" model_id="M_ZZV_00001"> <PDBx:ordinal_id>17</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAI" atom_id_2="NAQ" model_id="M_ZZV_00001"> <PDBx:ordinal_id>18</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAI" atom_id_2="HAI" model_id="M_ZZV_00001"> <PDBx:ordinal_id>19</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> </PDBx:pdbx_chem_comp_model_bondCategory> 1 1 0 1 1 1 1 pdbx_chem_comp_model_bondCategory This property indicates that datablock has a category holder pdbx_chem_comp_model_bondCategory. pdbx_chem_comp_model_bondCategory This property indicates that pdbx_chem_comp_model_bondCategory. has a category pdbx_chem_comp_model_bond. pdbx_chem_comp_model_bondItem Abstract datatype property for pdbx_chem_comp_model_bond items. reference_to_pdbx_chem_comp_model_bond cross-reference to pdbx_chem_comp_model_bond. referenced_by_pdbx_chem_comp_model_bond cross-reference from pdbx_chem_comp_model_bond. pdbx_chem_comp_model_bond.ordinal_id The value of attribute ordinal_id in category pdbx_chem_comp_model_bond is an ordinal identifer for each atom in the PDBX_CHEM_COMP_MODEL_BOND list. SING DOUB TRIP QUAD AROM POLY DELO PI The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. pdbx_chem_comp_model_bond.atom_id_1 The ID of the first of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category pdbx_chem_comp_model_atom in the PDBX_CHEM_COMP_MODEL_ATOM category. pdbx_chem_comp_model_bond.atom_id_2 The ID of the second of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category pdbx_chem_comp_model_atom in the PDBX_CHEM_COMP_MODEL_ATOM category. pdbx_chem_comp_model_bond.model_id This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. 0 pdbx_chem_comp_model_descriptor Data items in the CHEM_COMP_MODEL_DESCRIPTOR category provide string descriptors for component model structures. Example 1 - <PDBx:pdbx_chem_comp_model_descriptorCategory> <PDBx:pdbx_chem_comp_model_descriptor model_id="M_ZZV_00001" type="SMILES"> <PDBx:descriptor>CN(c1c2cccnc2c(c3c1CN(C3=O)Cc4ccc(cc4)F)O)S(=O)(=O)C</PDBx:descriptor> </PDBx:pdbx_chem_comp_model_descriptor> <PDBx:pdbx_chem_comp_model_descriptor model_id="M_ZZV_00001" type="SMILES_CANNONICAL"> <PDBx:descriptor>CN(c1c2cccnc2c(c3c1CN(C3=O)Cc4ccc(cc4)F)O)S(=O)(=O)C</PDBx:descriptor> </PDBx:pdbx_chem_comp_model_descriptor> </PDBx:pdbx_chem_comp_model_descriptorCategory> 1 1 1 1 pdbx_chem_comp_model_descriptorCategory This property indicates that datablock has a category holder pdbx_chem_comp_model_descriptorCategory. pdbx_chem_comp_model_descriptorCategory This property indicates that pdbx_chem_comp_model_descriptorCategory. has a category pdbx_chem_comp_model_descriptor. pdbx_chem_comp_model_descriptorItem Abstract datatype property for pdbx_chem_comp_model_descriptor items. reference_to_pdbx_chem_comp_model_descriptor cross-reference to pdbx_chem_comp_model_descriptor. referenced_by_pdbx_chem_comp_model_descriptor cross-reference from pdbx_chem_comp_model_descriptor. pdbx_chem_comp_model_descriptor.descriptor This data item contains the descriptor value for this component. pdbx_chem_comp_model_descriptor.model_id This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. SMILES_CANONICAL SMILES InChI InChIKey This data item contains the descriptor type. 0 pdbx_chem_comp_model_feature Additional features associated with the chemical component. Example 1 - <PDBx:pdbx_chem_comp_model_featureCategory> <PDBx:pdbx_chem_comp_model_feature feature_name="experiment_temperature" model_id="M_ZZV_00001"> <PDBx:feature_value>218.0</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="publication_doi" model_id="M_ZZV_00001"> <PDBx:feature_value>10.1016/j.bmcl.2008.01.018</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="r_factor" model_id="M_ZZV_00001"> <PDBx:feature_value>6.92</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="all_atoms_have_sites" model_id="M_ZZV_00001"> <PDBx:feature_value>Y</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="has_disorder" model_id="M_ZZV_00001"> <PDBx:feature_value>Y</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> </PDBx:pdbx_chem_comp_model_featureCategory> 1 1 1 1 pdbx_chem_comp_model_featureCategory This property indicates that datablock has a category holder pdbx_chem_comp_model_featureCategory. pdbx_chem_comp_model_featureCategory This property indicates that pdbx_chem_comp_model_featureCategory. has a category pdbx_chem_comp_model_feature. pdbx_chem_comp_model_featureItem Abstract datatype property for pdbx_chem_comp_model_feature items. reference_to_pdbx_chem_comp_model_feature cross-reference to pdbx_chem_comp_model_feature. referenced_by_pdbx_chem_comp_model_feature cross-reference from pdbx_chem_comp_model_feature. pdbx_chem_comp_model_feature.feature_value The component feature value. pdbx_chem_comp_model_feature.feature_name The component model feature type. experiment_temperature publication_doi r_factor all_atoms_have_sites has_disorder pdbx_chem_comp_model_feature.model_id The component model identifier for this feature. M_ABC_00001 M_ATP_00001 0 pdbx_chem_comp_model_reference Additional features associated with the chemical component. Example 1 - <PDBx:pdbx_chem_comp_model_referenceCategory> <PDBx:pdbx_chem_comp_model_reference db_code="PIWVIB" db_name="CSD" model_id="M_ZZV_00001"></PDBx:pdbx_chem_comp_model_reference> </PDBx:pdbx_chem_comp_model_referenceCategory> 1 1 1 pdbx_chem_comp_model_referenceCategory This property indicates that datablock has a category holder pdbx_chem_comp_model_referenceCategory. pdbx_chem_comp_model_referenceCategory This property indicates that pdbx_chem_comp_model_referenceCategory. has a category pdbx_chem_comp_model_reference. pdbx_chem_comp_model_referenceItem Abstract datatype property for pdbx_chem_comp_model_reference items. reference_to_pdbx_chem_comp_model_reference cross-reference to pdbx_chem_comp_model_reference. referenced_by_pdbx_chem_comp_model_reference cross-reference from pdbx_chem_comp_model_reference. pdbx_chem_comp_model_reference.db_code The component feature value. pdbx_chem_comp_model_reference.db_name The component model feature type. CSD pdbx_chem_comp_model_reference.model_id The component model identifier for this feature. M_ABC_00001 M_ATP_00001 0 pdbx_chem_comp_nonstandard Data items in the PDBX_CHEM_COMP_NONSTANDARD category describes common nucleotide modifications and nonstandard features. 1 1 pdbx_chem_comp_nonstandardCategory This property indicates that datablock has a category holder pdbx_chem_comp_nonstandardCategory. pdbx_chem_comp_nonstandardCategory This property indicates that pdbx_chem_comp_nonstandardCategory. has a category pdbx_chem_comp_nonstandard. pdbx_chem_comp_nonstandardItem Abstract datatype property for pdbx_chem_comp_nonstandard items. reference_to_pdbx_chem_comp_nonstandard cross-reference to pdbx_chem_comp_nonstandard. referenced_by_pdbx_chem_comp_nonstandard cross-reference from pdbx_chem_comp_nonstandard. pdbx_chem_comp_nonstandard.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. base modification sugar modification phosphate modification This data item describes modification type. 0 pdbx_chem_comp_pcm Data items in the PDBX_CHEM_COMP_PCM category provide information about the protein modifications that are described by the chemical component. An example of the category for the phosphoserine (SEP) chemical component. <PDBx:pdbx_chem_comp_pcmCategory> <PDBx:pdbx_chem_comp_pcm pcm_id="1"> <PDBx:category>Named protein modification</PDBx:category> <PDBx:comp_id>SEP</PDBx:comp_id> <PDBx:comp_id_linking_atom xsi:nil="true" /> <PDBx:modified_residue_id>SER</PDBx:modified_residue_id> <PDBx:modified_residue_id_linking_atom xsi:nil="true" /> <PDBx:polypeptide_position>Any position</PDBx:polypeptide_position> <PDBx:position>Amino-acid side chain</PDBx:position> <PDBx:type>Phosphorylation</PDBx:type> <PDBx:uniprot_specific_ptm_accession>PTM-0253</PDBx:uniprot_specific_ptm_accession> </PDBx:pdbx_chem_comp_pcm> </PDBx:pdbx_chem_comp_pcmCategory> An example of the category for the Alpha-L-fucopyranose (FUC) chemical component. <PDBx:pdbx_chem_comp_pcmCategory> <PDBx:pdbx_chem_comp_pcm pcm_id="1"> <PDBx:category>Carbohydrate</PDBx:category> <PDBx:comp_id>FUC</PDBx:comp_id> <PDBx:comp_id_linking_atom>C1</PDBx:comp_id_linking_atom> <PDBx:modified_residue_id>SER</PDBx:modified_residue_id> <PDBx:modified_residue_id_linking_atom>OG</PDBx:modified_residue_id_linking_atom> <PDBx:polypeptide_position>Any position</PDBx:polypeptide_position> <PDBx:position>Amino-acid side chain</PDBx:position> <PDBx:type>None</PDBx:type> </PDBx:pdbx_chem_comp_pcm> <PDBx:pdbx_chem_comp_pcm pcm_id="2"> <PDBx:category>Carbohydrate</PDBx:category> <PDBx:comp_id>FUC</PDBx:comp_id> <PDBx:comp_id_linking_atom>C1</PDBx:comp_id_linking_atom> <PDBx:modified_residue_id>THR</PDBx:modified_residue_id> <PDBx:modified_residue_id_linking_atom>OG1</PDBx:modified_residue_id_linking_atom> <PDBx:polypeptide_position>Any position</PDBx:polypeptide_position> <PDBx:position>Amino-acid side chain</PDBx:position> <PDBx:type>None</PDBx:type> </PDBx:pdbx_chem_comp_pcm> </PDBx:pdbx_chem_comp_pcmCategory> 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 1 pdbx_chem_comp_pcmCategory This property indicates that datablock has a category holder pdbx_chem_comp_pcmCategory. pdbx_chem_comp_pcmCategory This property indicates that pdbx_chem_comp_pcmCategory. has a category pdbx_chem_comp_pcm. pdbx_chem_comp_pcmItem Abstract datatype property for pdbx_chem_comp_pcm items. reference_to_pdbx_chem_comp_pcm cross-reference to pdbx_chem_comp_pcm. referenced_by_pdbx_chem_comp_pcm cross-reference from pdbx_chem_comp_pcm. ADP-ribose Amino acid Biotin Carbohydrate Chromophore/chromophore-like Covalent chemical modification Crosslinker Flavin Heme/heme-like Lipid/lipid-like Named protein modification Non-standard residue Nucleotide monophosphate Terminal acetylation Terminal amidation The category of protein modification. Named protein modification pdbx_chem_comp_pcm.comp_id Chemical component identifier for the CCD that contains the modification group. SEP pdbx_chem_comp_pcm.comp_id_linking_atom The atom on the modification group that covalently links the modification to the residue that is being modified. This is only added when the protein modification is linked and so the amino acid group and the modification group are described by separate CCDs. C1 pdbx_chem_comp_pcm.first_instance_model_db_code The PDB Entry ID for the first model that contains the protein modification. 4PEP pdbx_chem_comp_pcm.modified_residue_id Chemical component identifier for the amino acid residue that is being modified. SER pdbx_chem_comp_pcm.modified_residue_id_linking_atom The atom on the polypeptide residue group that covalently links the modification to the residue that is being modified. This is only added when the protein modification is linked and so the amino acid group and the modification group are described by separate CCDs. OG C-terminal N-terminal Any position The position of the modification on the polypeptide. Any position Amino-acid side chain Amino-acid backbone Amino-acid side chain and backbone The position of the modification on the amino acid. Amino acid side chain 12-Hydroxyfarnesylation 12-Oxomyristoylation 12R-Hydroxymyristoylation 14-Hydroxy-10,13-dioxo-7-heptadecenoic acid (3-Aminopropyl)(5'-adenosyl)phosphono amidation 2-Aminoadipylation 2-Aminoethylphosphorylation 2-Cholinephosphorylation 2-Hydroxyisobutyrylation 2-Oxo-5,5-dimethylhexanoylation 2-Oxobutanoic acid 2,3-Dicarboxypropylation 3-Oxoalanine 3-Phenyllactic acid (3R)-3-Hydroxybutyrylation 4-Phosphopantetheine ADP-ribosylation ADP-riboxanation AMPylation Acetamidation Acetamidomethylation Acetylation Alanylation Allysine Amination Arachidoylation Archaeol Arginylation Arsenylation Asparaginylation Aspartylation Bacillithiolation Benzoylation Benzylation Beta-amino acid Beta-hydroxybutyrylation Beta-lysylation Beta-mercaptoethanol Biotinylation Bromination Butyrylation Carbamoylation Carboxyethylation Carboxylation Carboxymethylation cGMPylation Chlorination Cholesterylation Citrullination Crotonylation Cyanation Cysteinylation C-Mannosylation Deamidation Decanoylation Decarboxylation Dehydroamino acid Dehydrocoelenterazination Dehydrogenation Dehydroxylation Deoxidation Deoxyhypusine Diacylglycerol Dihydroxyacetonation Dimethylamination Diphosphorylation Diphthamide Dipyrromethane methylation Dopaminylation D-alanylation D-arginylation D-asparaginylation D-aspartylation D-cysteinylation D-glutaminylation D-glutamylation D-histidinylation D-isoleucylation D-lactate D-leucylation D-lysylation D-methionylation D-phenylalanylation D-prolylation D-serylation D-threoninylation D-tryptophanylation D-tyrosination D-valylation Ethylation Ethylsulfanylation Farnesylation Fluorination Formylation GMPylation Geranylgeranylation Glutaminylation Glutamylation Glutarylation Glutathionylation Glycerophosphorylation Glycerylphosphorylethanolamination Glycylation Heptanoylation Hexanoylation Histaminylation Histidinylation Hydrogenation Hydroperoxylation Hydroxyamination Hydroxyethylation Hydroxylation Hydroxymethylation Hydroxysulfanylation Hypusine Iodination Isoleucylation Lactoylation Laurylation Leucylation Lipoylation L-lactate Lysylation Malonylation Methionylation Methoxylation Methylamination Methylation Methylsulfanylation Methylsulfation Myristoylation N-pyruvic acid 2-iminylation N-methylcarbamoylation Nitration Nitrosylation None Noradrenylation Norleucine Norvaline N-Glycosylation Octanoylation Oleoylation Ornithine Oxidation O-Glycosylation Palmitoleoylation Palmitoylation Pentadecanoylation Pentanoylation Phenylalanylation Phosphatidylethanolamine amidation Phosphoenolpyruvate Phosphorylation Prolylation Propionylation Pyridoxal phosphate Pyrrolidone carboxylic acid Pyruvic acid Retinoylation Selanylation Selenomethionine Serotonylation Serylation Stearoylation Stereoisomerisation Succinamide ring Succination Succinylation Sulfanylmethylation Sulfation Sulfhydration S-Glycosylation Tert-butylation Tert-butyloxycarbonylation Threoninylation Thyroxine Triiodothyronine Triphosphorylation Tryptophanylation Tyrosination UMPylation Valylation The type of protein modification. Phosphorylation pdbx_chem_comp_pcm.uniprot_generic_ptm_accession The UniProt PTM accession code that describes the group of PTMs of which this protein modification is a member. PTM-0252 pdbx_chem_comp_pcm.uniprot_specific_ptm_accession The UniProt PTM accession code that is an exact match for the protein modification. PTM-0253 pdbx_chem_comp_pcm.pcm_id An ordinal index for this category. 1 0 pdbx_chem_comp_related PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components. Example 1 - <PDBx:pdbx_chem_comp_relatedCategory> <PDBx:pdbx_chem_comp_related comp_id="SGN" related_comp_id="GLC" relationship_type="Carbohydrate core"> </PDBx:pdbx_chem_comp_related> </PDBx:pdbx_chem_comp_relatedCategory> 0 1 1 1 1 pdbx_chem_comp_relatedCategory This property indicates that datablock has a category holder pdbx_chem_comp_relatedCategory. pdbx_chem_comp_relatedCategory This property indicates that pdbx_chem_comp_relatedCategory. has a category pdbx_chem_comp_related. pdbx_chem_comp_relatedItem Abstract datatype property for pdbx_chem_comp_related items. reference_to_pdbx_chem_comp_related cross-reference to pdbx_chem_comp_related. referenced_by_pdbx_chem_comp_related cross-reference from pdbx_chem_comp_related. pdbx_chem_comp_related.details Describes the type of relationship pdbx_chem_comp_related.comp_id The chemical component for which this relationship applies. pdbx_chem_comp_related.related_comp_id The related chemical component for which this chemical component is based. Carbohydrate core Precursor Describes the type of relationship 0 pdbx_chem_comp_subcomponent_entity_list Data items in the pdbx_chem_comp_subcomponent_entity_list category list the constituent chemical entities and entity features in this chemical component. Example 1 - <PDBx:pdbx_chem_comp_subcomponent_entity_listCategory> <PDBx:pdbx_chem_comp_subcomponent_entity_list id="1"> <PDBx:class>polymer</PDBx:class> <PDBx:parent_comp_id>CE8</PDBx:parent_comp_id> <PDBx:type>saccharide</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_entity_list> </PDBx:pdbx_chem_comp_subcomponent_entity_listCategory> 1 1 1 1 1 1 1 pdbx_chem_comp_subcomponent_entity_listCategory This property indicates that datablock has a category holder pdbx_chem_comp_subcomponent_entity_listCategory. pdbx_chem_comp_subcomponent_entity_listCategory This property indicates that pdbx_chem_comp_subcomponent_entity_listCategory. has a category pdbx_chem_comp_subcomponent_entity_list. pdbx_chem_comp_subcomponent_entity_listItem Abstract datatype property for pdbx_chem_comp_subcomponent_entity_list items. reference_to_pdbx_chem_comp_subcomponent_entity_list cross-reference to pdbx_chem_comp_subcomponent_entity_list. referenced_by_pdbx_chem_comp_subcomponent_entity_list cross-reference from pdbx_chem_comp_subcomponent_entity_list. polymer non-polymer macrolide water Defines the predominant linking type of the entity. pdbx_chem_comp_subcomponent_entity_list.parent_comp_id The parent component identifier corresponding to this entity. D-peptide linking L-peptide linking D-peptide NH3 amino terminus L-peptide NH3 amino terminus D-peptide COOH carboxy terminus L-peptide COOH carboxy terminus DNA linking RNA linking L-RNA linking L-DNA linking DNA OH 5 prime terminus RNA OH 5 prime terminus DNA OH 3 prime terminus RNA OH 3 prime terminus D-saccharide 1,4 and 1,4 linking L-saccharide 1,4 and 1,4 linking D-saccharide 1,4 and 1,6 linking L-saccharide 1,4 and 1,6 linking L-saccharide D-saccharide saccharide non-polymer peptide linking peptide-like L-gamma-peptide, C-delta linking D-gamma-peptide, C-delta linking L-beta-peptide, C-gamma linking D-beta-peptide, C-gamma linking other Defines the type of the entity. pdbx_chem_comp_subcomponent_entity_list.id Ordinal index for the entities listed in this category. 0 pdbx_chem_comp_subcomponent_struct_conn Data items in the pdbx_chem_comp_subcomponent_struct_conn list the chemical interactions among the subcomponents in the chemical component. Example 1 - <PDBx:pdbx_chem_comp_subcomponent_struct_connCategory> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="1"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>1</PDBx:seq_id_1> <PDBx:seq_id_2>2</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="2"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>2</PDBx:seq_id_1> <PDBx:seq_id_2>3</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="3"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>3</PDBx:seq_id_1> <PDBx:seq_id_2>4</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="4"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>4</PDBx:seq_id_1> <PDBx:seq_id_2>5</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="5"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>5</PDBx:seq_id_1> <PDBx:seq_id_2>6</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="6"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>6</PDBx:seq_id_1> <PDBx:seq_id_2>7</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="7"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>7</PDBx:seq_id_1> <PDBx:seq_id_2>8</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> </PDBx:pdbx_chem_comp_subcomponent_struct_connCategory> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 pdbx_chem_comp_subcomponent_struct_connCategory This property indicates that datablock has a category holder pdbx_chem_comp_subcomponent_struct_connCategory. pdbx_chem_comp_subcomponent_struct_connCategory This property indicates that pdbx_chem_comp_subcomponent_struct_connCategory. has a category pdbx_chem_comp_subcomponent_struct_conn. pdbx_chem_comp_subcomponent_struct_connItem Abstract datatype property for pdbx_chem_comp_subcomponent_struct_conn items. reference_to_pdbx_chem_comp_subcomponent_struct_conn cross-reference to pdbx_chem_comp_subcomponent_struct_conn. referenced_by_pdbx_chem_comp_subcomponent_struct_conn cross-reference from pdbx_chem_comp_subcomponent_struct_conn. pdbx_chem_comp_subcomponent_struct_conn.atom_id_1 The atom identifier for the first atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.atom_id_2 The atom identifier for the second atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.comp_id_1 The component identifier for the first atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.comp_id_2 The component identifier for the second atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.entity_id_1 The entity identifier for the first atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.entity_id_2 The entity identifier for the second atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.seq_id_1 The positional index for the first atom in the interaction. pdbx_chem_comp_subcomponent_struct_conn.seq_id_2 The positional index for the first atom in the interaction. covale disulf hydrog metalc mismat saltbr covale_base covale_sugar covale_phosphate The chemical or structural type of the interaction. pdbx_chem_comp_subcomponent_struct_conn.id Ordinal index for the interactions listed in this category. 0 pdbx_chem_comp_synonyms PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences. Example 1 - <PDBx:pdbx_chem_comp_synonymsCategory> <PDBx:pdbx_chem_comp_synonyms comp_id="ROC" ordinal="1"> <PDBx:name>Fortovase</PDBx:name> <PDBx:provenance>DRUGBANK</PDBx:provenance> </PDBx:pdbx_chem_comp_synonyms> <PDBx:pdbx_chem_comp_synonyms comp_id="ROC" ordinal="2"> <PDBx:name>SAQUINAVIR</PDBx:name> <PDBx:provenance>DRUGBANK</PDBx:provenance> </PDBx:pdbx_chem_comp_synonyms> <PDBx:pdbx_chem_comp_synonyms comp_id="ROC" ordinal="3"> <PDBx:name>RO 31-8959</PDBx:name> </PDBx:pdbx_chem_comp_synonyms> </PDBx:pdbx_chem_comp_synonymsCategory> 1 1 0 1 0 1 1 1 pdbx_chem_comp_synonymsCategory This property indicates that datablock has a category holder pdbx_chem_comp_synonymsCategory. pdbx_chem_comp_synonymsCategory This property indicates that pdbx_chem_comp_synonymsCategory. has a category pdbx_chem_comp_synonyms. pdbx_chem_comp_synonymsItem Abstract datatype property for pdbx_chem_comp_synonyms items. reference_to_pdbx_chem_comp_synonyms cross-reference to pdbx_chem_comp_synonyms. referenced_by_pdbx_chem_comp_synonyms cross-reference from pdbx_chem_comp_synonyms. pdbx_chem_comp_synonyms.name The synonym of this particular chemical component. AUTHOR DRUGBANK CHEBI CHEMBL PDB PUBCHEM The provenance of this synonym. pdbx_chem_comp_synonyms.type The type of this synonym. Preferred Trade name pdbx_chem_comp_synonyms.comp_id The chemical component for which this synonym applies. pdbx_chem_comp_synonyms.ordinal An ordinal index for this category 0 pdbx_chem_comp_upload_depositor_info Data items in the PDBX_CHEM_COMP_UPLOAD_DEPOSITOR_INFO category record details of the uploaded files related to depositor provided chemical assignments. Example 1 - <PDBx:pdbx_chem_comp_upload_depositor_infoCategory> <PDBx:pdbx_chem_comp_upload_depositor_info ordinal="1"> <PDBx:comp_id>GNC</PDBx:comp_id> <PDBx:upload_file_name>GNC.gif</PDBx:upload_file_name> <PDBx:upload_file_type>GIF</PDBx:upload_file_type> </PDBx:pdbx_chem_comp_upload_depositor_info> </PDBx:pdbx_chem_comp_upload_depositor_infoCategory> 1 1 1 1 1 1 1 pdbx_chem_comp_upload_depositor_infoCategory This property indicates that datablock has a category holder pdbx_chem_comp_upload_depositor_infoCategory. pdbx_chem_comp_upload_depositor_infoCategory This property indicates that pdbx_chem_comp_upload_depositor_infoCategory. has a category pdbx_chem_comp_upload_depositor_info. pdbx_chem_comp_upload_depositor_infoItem Abstract datatype property for pdbx_chem_comp_upload_depositor_info items. reference_to_pdbx_chem_comp_upload_depositor_info cross-reference to pdbx_chem_comp_upload_depositor_info. referenced_by_pdbx_chem_comp_upload_depositor_info cross-reference from pdbx_chem_comp_upload_depositor_info. pdbx_chem_comp_upload_depositor_info.comp_id The chemical component identifier used by the depositor to represent this component. pdbx_chem_comp_upload_depositor_info.upload_file_name The name of the uploaded file containing information about this component. CIF PDBX GIF JPG JPEG PNG SDF SVG TIF TIFF other The type of the uploaded file containing information about this component. pdbx_chem_comp_upload_depositor_info.ordinal Ordinal index for this category. 0 pdbx_columninfo <PDBx:pdbx_columninfoCategory> <PDBx:pdbx_columninfo columnname="id" tablename="summary"> <PDBx:WWW_Report_Criteria>1</PDBx:WWW_Report_Criteria> <PDBx:WWW_Selection_Criteria>1</PDBx:WWW_Selection_Criteria> <PDBx:column_serial_no>1</PDBx:column_serial_no> <PDBx:description>id code</PDBx:description> <PDBx:example>id1, id2</PDBx:example> <PDBx:table_serial_no>1</PDBx:table_serial_no> <PDBx:type>1</PDBx:type> </PDBx:pdbx_columninfo> </PDBx:pdbx_columninfoCategory> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 pdbx_columninfoCategory This property indicates that datablock has a category holder pdbx_columninfoCategory. pdbx_columninfoCategory This property indicates that pdbx_columninfoCategory. has a category pdbx_columninfo. pdbx_columninfoItem Abstract datatype property for pdbx_columninfo items. reference_to_pdbx_columninfo cross-reference to pdbx_columninfo. referenced_by_pdbx_columninfo cross-reference from pdbx_columninfo. pdbx_columninfo.WWW_Report_Criteria SQL column visibility in WWW reports queries. 0=no, 1=yes pdbx_columninfo.WWW_Selection_Criteria SQL column visibility in WWW selection querires. 0=no, 1=yes pdbx_columninfo.column_serial_no SQL column serial number. 1,2,3,4,... pdbx_columninfo.description SQL column description. Table of solvent coordinates pdbx_columninfo.example SQL column example. Table of solvent coordinates pdbx_columninfo.table_serial_no SQL table serial number. 1,2,3,4,... pdbx_columninfo.type SQL column type. 1:integer, 2:float, 3:string-single-left, 4:string-single-right, 5:string-multi-left, 6:string-multi-right, 7:angle, 8:boolean, 9:single character, 10:author or atom name column, 11: Date pdbx_columninfo.columnname SQL column name. id pdbx_columninfo.tablename SQL table name. structure_summary 0 pdbx_connect Local data items describing ligand and monomer chemical features. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_connectCategory This property indicates that datablock has a category holder pdbx_connectCategory. pdbx_connectCategory This property indicates that pdbx_connectCategory. has a category pdbx_connect. pdbx_connectItem Abstract datatype property for pdbx_connect items. reference_to_pdbx_connect cross-reference to pdbx_connect. referenced_by_pdbx_connect cross-reference from pdbx_connect. pdbx_connect.class_1 Internal classification type 1. pdbx_connect.class_2 Internal classification type 2. pdbx_connect.date Date added. pdbx_connect.formal_charge Formal charge if nonzero pdbx_connect.formul Place-holder for PDB record FORMUL pdbx_connect.hetgroup_chemical_name Place-holder for PDB record HETNAM pdbx_connect.hetgroup_name Place-holder for PDB record HET pdbx_connect.modified_date Date of last modification. pdbx_connect.parent_residue Parent residue pdbx_connect.status Release status associated with this component. pdbx_connect.type Approximately corresponds to attribute type in category chem_comp pdbx_connect.res_name Unique (typically 3-letter code) identifier for chemical group. 0 pdbx_connect_atom Local data items describing ligand and monomer atom names and connectivity. 0 1 0 1 1 1 1 1 1 1 1 pdbx_connect_atomCategory This property indicates that datablock has a category holder pdbx_connect_atomCategory. pdbx_connect_atomCategory This property indicates that pdbx_connect_atomCategory. has a category pdbx_connect_atom. pdbx_connect_atomItem Abstract datatype property for pdbx_connect_atom items. reference_to_pdbx_connect_atom cross-reference to pdbx_connect_atom. referenced_by_pdbx_connect_atom cross-reference from pdbx_connect_atom. pdbx_connect_atom.align_pos Starting column of atom name in PDB atom field. pdbx_connect_atom.bond_type Bond type. pdbx_connect_atom.charge Charge pdbx_connect_atom.type_symbol Element symbol pdbx_connect_atom.atom_name Uniquely identifies the atom within the component. pdbx_connect_atom.connect_to Identifies a connected atom within the component. pdbx_connect_atom.res_name Unique (typically 3-letter code) identifier for chemical group. 0 pdbx_connect_modification Local data items describing ligand and monomer modifications. 1 1 1 pdbx_connect_modificationCategory This property indicates that datablock has a category holder pdbx_connect_modificationCategory. pdbx_connect_modificationCategory This property indicates that pdbx_connect_modificationCategory. has a category pdbx_connect_modification. pdbx_connect_modificationItem Abstract datatype property for pdbx_connect_modification items. reference_to_pdbx_connect_modification cross-reference to pdbx_connect_modification. referenced_by_pdbx_connect_modification cross-reference from pdbx_connect_modification. pdbx_connect_modification.modification Type of modification pdbx_connect_modification.res_name Unique (typically 3-letter code) identifier for chemical group. 0 pdbx_connect_type Local data items describing ligand and monomer type information. 0 1 0 1 1 pdbx_connect_typeCategory This property indicates that datablock has a category holder pdbx_connect_typeCategory. pdbx_connect_typeCategory This property indicates that pdbx_connect_typeCategory. has a category pdbx_connect_type. pdbx_connect_typeItem Abstract datatype property for pdbx_connect_type items. reference_to_pdbx_connect_type cross-reference to pdbx_connect_type. referenced_by_pdbx_connect_type cross-reference from pdbx_connect_type. pdbx_connect_type.modified Indicates a modified chemical component. pdbx_connect_type.ndbTokenType Internal chemical type identifier used by NDB. pdbx_connect_type.res_name Unique (typically 3-letter code) identifier for chemical group. 0 pdbx_construct Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that attribute id in category pdbx_construct would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition). Example 1 - hypothetical example <PDBx:pdbx_constructCategory> <PDBx:pdbx_construct id="1"> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:seq> gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg # - - - - data truncated for brevity - - - -</PDBx:seq> <PDBx:type>DNA</PDBx:type> </PDBx:pdbx_construct> </PDBx:pdbx_constructCategory> 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 pdbx_constructCategory This property indicates that datablock has a category holder pdbx_constructCategory. pdbx_constructCategory This property indicates that pdbx_constructCategory. has a category pdbx_construct. pdbx_constructItem Abstract datatype property for pdbx_construct items. reference_to_pdbx_construct cross-reference to pdbx_construct. referenced_by_pdbx_construct cross-reference from pdbx_construct. plasmid protein insert primer transcript The primary function of the construct. This should be considered as a guideline only. pdbx_construct.date The date that the sequence was determined. 2003-12-25 2003-12-25:09:00 pdbx_construct.details Additional details about the construct that cannot be represented in the category _pdbx_construct_feature. pdbx_construct.entity_id In cases where the construct IS found in the co-ordinates then this item provides a pointer to attribute id in category entity in the ENTITY category for the corresponding molecule. pdbx_construct.entry_id The value of attribute entry_id in category pdbx_construct uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. pdbx_construct.name attribute name in category pdbx_construct provides a placeholder for the local name of the construct, for example the plasmid name if this category is used to list plasmids. pdbx_construct.organisation attribute organisation in category pdbx_construct describes the organisation in which the attribute id in category pdbx_construct is unique. This will normally be the lab in which the constrcut originated. It is envisaged that this item will permit a globally unique identifier to be constructed in cases where this is not possible from the attribute id in category pdbx_construct alone. pdbx_construct.robot_id In cases where the sequence has been determined by a robot this data item provides a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category for the robot responsible pdbx_construct.seq sequence expressed as string of one-letter base codes or one letter amino acid codes. Unusual residues may be represented either using the appropriate one letter code wild cards or by the three letter code in parentheses. gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg DNA RNA cDNA mRNA tRNA protein The type of nucleic acid sequence in the construct. Note that to find all the DNA molecules it is necessary to search for DNA + cDNA and for RNA, RNA + mRNA + tRNA. pdbx_construct.id The value of attribute id in category pdbx_construct must uniquely identify a record in the PDBX_CONSTRUCT list and should be arranged so that it is composed of a site-speicific prefix combined with a value that is unique within a given site.Note that this item need not be a number; it can be any unique identifier. 0 pdbx_construct_feature Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production. Example 1 - vector pUC28 <PDBx:pdbx_construct_featureCategory> <PDBx:pdbx_construct_feature construct_id="1" id="1"> <PDBx:details>pKK84-1 ClaI 5260bp 5247..5247 ptac11 TaqI-TaqI 192bp, -35 trp promoter -&gt; pEA300 5452bp</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="2"> <PDBx:details>pKK84-1 1..5246 5246bp ClaI = AT^CGAT TaqI = T^CGA cgact...</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="3"> <PDBx:details>ptac11 190bp ...cat TaqI = T^CGA ClaI = AT^CGAT</PDBx:details> <PDBx:end_seq>5436</PDBx:end_seq> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq>5247</PDBx:start_seq> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="4"> <PDBx:details>pKK84-1 5247..5260 14bp</PDBx:details> <PDBx:end_seq>5450</PDBx:end_seq> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq>5437</PDBx:start_seq> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="5"> <PDBx:details>SIT unique EcoRI-ClaI-HindIII-BamHI-PvuII</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>misc_binding</PDBx:type> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="6"> <PDBx:details>ORI E. coli pMB1 (ColE1 and pBR322)</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>rep_origin</PDBx:type> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="7"> <PDBx:details>PRO E. coli trp</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>promoter</PDBx:type> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="8"> <PDBx:details>ANT E. coli beta-lactamase gene (bla) ampicillin resistance gene (apr/amp)</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>CDS</PDBx:type> </PDBx:pdbx_construct_feature> </PDBx:pdbx_construct_featureCategory> 0 1 0 1 1 1 0 1 0 1 1 1 pdbx_construct_featureCategory This property indicates that datablock has a category holder pdbx_construct_featureCategory. pdbx_construct_featureCategory This property indicates that pdbx_construct_featureCategory. has a category pdbx_construct_feature. pdbx_construct_featureItem Abstract datatype property for pdbx_construct_feature items. reference_to_pdbx_construct_feature cross-reference to pdbx_construct_feature. referenced_by_pdbx_construct_feature cross-reference from pdbx_construct_feature. pdbx_construct_feature.details Details that describe the feature pdbx_construct_feature.end_seq The sequence position at which the feature ends pdbx_construct_feature.entry_id The value of attribute entry_id in category pdbx_construct_feature uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. pdbx_construct_feature.start_seq The sequence position at which the feature begins pdbx_construct_feature.type The type of the feature pdbx_construct_feature.construct_id The value of attribute construct_id in category pdbx_construct_feature uniquely identifies the construct with which the feature is associated. This is a pointer to attribute id in category pdbx_construct This item may be a site dependent bar code. pdbx_construct_feature.id The value of attribute id in category pdbx_construct_feature must uniquely identify a record in the PDBX_CONSTRUCT_FEATURE list. Note that this item need not be a number; it can be any unique identifier. 0 pdbx_contact_author Data items in the PDBX_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. This category atomizes information to a greater degree than the standard AUDIT_CONTACT_AUTHOR category. Example 1 - <PDBx:pdbx_contact_authorCategory> <PDBx:pdbx_contact_author id="1"> <PDBx:address_1>Department of Biophysical Chemistry</PDBx:address_1> <PDBx:address_2>Merck Research Laboratories</PDBx:address_2> <PDBx:address_3>P. O. Box 2000, Ry80M203</PDBx:address_3> <PDBx:city>Rahway</PDBx:city> <PDBx:country>UNITED STATES</PDBx:country> <PDBx:email>paula_fitzgerald@merck.com</PDBx:email> <PDBx:fax>908 594 6645</PDBx:fax> <PDBx:name_first>Paula</PDBx:name_first> <PDBx:name_last>Fitzgerald</PDBx:name_last> <PDBx:name_mi>M.D.</PDBx:name_mi> <PDBx:name_salutation>Dr.</PDBx:name_salutation> <PDBx:organization_type>commercial</PDBx:organization_type> <PDBx:phone>908 594 5510</PDBx:phone> <PDBx:postal_code>07065</PDBx:postal_code> <PDBx:role>principal investigator/group leader</PDBx:role> <PDBx:state_province>New Jersey</PDBx:state_province> </PDBx:pdbx_contact_author> </PDBx:pdbx_contact_authorCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_contact_authorCategory This property indicates that datablock has a category holder pdbx_contact_authorCategory. pdbx_contact_authorCategory This property indicates that pdbx_contact_authorCategory. has a category pdbx_contact_author. pdbx_contact_authorItem Abstract datatype property for pdbx_contact_author items. reference_to_pdbx_contact_author cross-reference to pdbx_contact_author. referenced_by_pdbx_contact_author cross-reference from pdbx_contact_author. pdbx_contact_author.address_1 The mailing address of the author of the data block to whom correspondence should be addressed, line 1 of 3. 610 Taylor Road pdbx_contact_author.address_2 The mailing address of the author of the data block to whom correspondence should be addressed, line 2 of 3. Department of Chemistry and Chemical Biology pdbx_contact_author.address_3 The mailing address of the author of the data block to whom correspondence should be addressed, line 3 of 3. Busch Campus pdbx_contact_author.city The mailing address of the author of the data block to whom correspondence should be addressed, city. Piscataway AFRICA ANTARTICA ASIA AUSTRALIA EUROPE NORTH AMERICA SOUTH AMERICA The continent of the author of the data block to whom correspondence should be addressed. AFRICA ANTARTICA ASIA AUSTRALIA EUROPE NORTH AMERICA SOUTH AMERICA pdbx_contact_author.country The country/region of the author of the data block to whom correspondence should be addressed. UNITED STATES UNITED KINGDOM AUSTRALIA pdbx_contact_author.email The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognisable to international networks. name@host.domain.country bm@iucr.ac.uk pdbx_contact_author.fax The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number with no spaces. 12(34) 947 7334 732 445 0103 pdbx_contact_author.identifier_ORCID The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X pdbx_contact_author.legacy_address The mailing address of the author of the data block to whom correspondence should be addressed transfered from attribute address in category audit_contact_author Busch Campus pdbx_contact_author.name_first The first name of the author of the data block to whom correspondence should be addressed. Percival Loyd Susan pdbx_contact_author.name_last The last name of the author of the data block to whom correspondence should be addressed. Samuels Rodgers pdbx_contact_author.name_mi The middle initial(s) of the author of the data block to whom correspondence should be addressed. T. M.F. Dr. Prof. Mr. Ms. Mrs. The salutation of the author of the data block to whom correspondence should be addressed. Dr. Prof. Mr. Ms. Mrs. academic commercial government other The organization type to which this author is affiliated. academic commercial government other pdbx_contact_author.phone The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. 12 (34) 947 7330 947 732 0103 x8320 pdbx_contact_author.postal_code The mailing address of the author of the data block to whom correspondence should be addressed, zip code. 08854 principal investigator/group leader responsible scientist investigator The role of this author in the project depositing this data. principal investigator/group leader responsible scientist investigator pdbx_contact_author.state_province The mailing address of the author of the data block to whom correspondence should be addressed, state or province. New Jersey 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 A unique integer identifier for this author 1 2 3 0 pdbx_coord Gives information about what kind of coordinates are available. 1 1 1 1 1 1 1 1 1 pdbx_coordCategory This property indicates that datablock has a category holder pdbx_coordCategory. pdbx_coordCategory This property indicates that pdbx_coordCategory. has a category pdbx_coord. pdbx_coordItem Abstract datatype property for pdbx_coord items. reference_to_pdbx_coord cross-reference to pdbx_coord. referenced_by_pdbx_coord cross-reference from pdbx_coord. Y P NA Gives information if the coordinates for the main chain atoms are available. Y Y N Gives information if the coordinates for hydrogen atoms are available. Y Y N Gives information if the coordinates for solvent atoms are available. Y Y P N H Gives information if the structure factors for this entry are available. Y pdbx_coord.entry_id The entry identifier. 0 pdbx_coordinate_model The details of the composition of the coordinate model. Example 1 - <PDBx:pdbx_coordinate_modelCategory> <PDBx:pdbx_coordinate_model asym_id="A"> <PDBx:type>CA ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> <PDBx:pdbx_coordinate_model asym_id="B"> <PDBx:type>CA ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> <PDBx:pdbx_coordinate_model asym_id="X"> <PDBx:type>P ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> <PDBx:pdbx_coordinate_model asym_id="Y"> <PDBx:type>P ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> </PDBx:pdbx_coordinate_modelCategory> 1 1 1 pdbx_coordinate_modelCategory This property indicates that datablock has a category holder pdbx_coordinate_modelCategory. pdbx_coordinate_modelCategory This property indicates that pdbx_coordinate_modelCategory. has a category pdbx_coordinate_model. pdbx_coordinate_modelItem Abstract datatype property for pdbx_coordinate_model items. reference_to_pdbx_coordinate_model cross-reference to pdbx_coordinate_model. referenced_by_pdbx_coordinate_model cross-reference from pdbx_coordinate_model. CA ATOMS ONLY P ATOMS ONLY A classification of the composition of the coordinate model. CA ATOMS ONLY P ATOMS ONLY pdbx_coordinate_model.asym_id A reference to attribute id in category struct_asym. 1 A 0 pdbx_crystal_alignment Data in the PDBX_CRYSTAL_ALIGNMENT are produced by log files from programs during indexing 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_crystal_alignmentCategory This property indicates that datablock has a category holder pdbx_crystal_alignmentCategory. pdbx_crystal_alignmentCategory This property indicates that pdbx_crystal_alignmentCategory. has a category pdbx_crystal_alignment. pdbx_crystal_alignmentItem Abstract datatype property for pdbx_crystal_alignment items. reference_to_pdbx_crystal_alignment cross-reference to pdbx_crystal_alignment. referenced_by_pdbx_crystal_alignment cross-reference from pdbx_crystal_alignment. pdbx_crystal_alignment.crossfire_x Angular spread (in degrees) of incident X-ray along the horizontal (x) direction. Default is 0. pdbx_crystal_alignment.crossfire_x_esd The estimated deviation of angular spread (in degrees) of incident X-ray along the horizontal (x) direction. pdbx_crystal_alignment.crossfire_xy Correlated xy component of the beam spread. This tends to be zero within error (in degrees^2). pdbx_crystal_alignment.crossfire_xy_esd The estimated deviation of correlated xy component of the beam spread (in degrees^2). pdbx_crystal_alignment.crossfire_y Angular spread (in degrees) of incident X-ray along the vertical (y) direction. Default is 0. pdbx_crystal_alignment.crossfire_y_esd The estimated deviation of angular spread (in degrees) of incident X-ray along the vertical (y) direction. pdbx_crystal_alignment.crystal_to_detector_distance Distance (mm) from crystal to detector. pdbx_crystal_alignment.crystal_to_detector_distance_esd The estimated deviation of distance (mm) from crystal to detector. pdbx_crystal_alignment.crysx_spindle Crystal mis-orientation angle (in degree) on x axis (spindle). pdbx_crystal_alignment.crysx_spindle_esd The estimated deviation of orientation angle (in degree) on x axis. pdbx_crystal_alignment.crysy_vertical Crystal mis-orientation angle (in degree) on y axis (vertical). pdbx_crystal_alignment.crysy_vertical_esd The estimated deviation of orientation angle (in degree) on y axis. pdbx_crystal_alignment.crysz_beam Crystal mis-orientation angle (in degree) on z axis (in beam). pdbx_crystal_alignment.crysz_beam_esd The estimated deviation of orientation angle (in degree) on yzaxis. pdbx_crystal_alignment.oscillation_end Ending oscillation angle (in degrees) (default end = start + range). pdbx_crystal_alignment.oscillation_range The actual oscillation angle (normally <1.0 degree). pdbx_crystal_alignment.oscillation_start Starting oscillation angle (in degrees) . pdbx_crystal_alignment.overall_beam_divergence Isotropic distribution of photon angles from the source impacting on the crystal in degrees. Note this is typically a derived quantity, inferred from measuring the radial profile of the measured reflections, and it may be convolved with effects from the bandpass. pdbx_crystal_alignment.overall_beam_divergence_esd The uncertainty in the beam divergence estimate. pdbx_crystal_alignment.xbeam Distance (mm) from the edge of data to beam spot (in X direction). pdbx_crystal_alignment.xbeam_esd The estimated deviation of xbeam (mm). pdbx_crystal_alignment.ybeam Distance from (mm) the edge of data to beam spot (in Y direction). pdbx_crystal_alignment.ybeam_esd The estimated deviation of ybeam (mm). pdbx_crystal_alignment.crystal_id The identifer of the crystal. 0 pdbx_data_processing_cell Crystallographic cell specifications used in data processing. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 pdbx_data_processing_cellCategory This property indicates that datablock has a category holder pdbx_data_processing_cellCategory. pdbx_data_processing_cellCategory This property indicates that pdbx_data_processing_cellCategory. has a category pdbx_data_processing_cell. pdbx_data_processing_cellItem Abstract datatype property for pdbx_data_processing_cell items. reference_to_pdbx_data_processing_cell cross-reference to pdbx_data_processing_cell. referenced_by_pdbx_data_processing_cell cross-reference from pdbx_data_processing_cell. pdbx_data_processing_cell.a Unit cell length A 58.39 pdbx_data_processing_cell.a_tolerance Tolerance in unit cell length A 0.04 pdbx_data_processing_cell.alpha Unit cell angle alpha. 90.0 pdbx_data_processing_cell.alpha_tolerance Tolerance in unit cell angle alpha. 0.04 pdbx_data_processing_cell.b Unit cell length B 58.39 pdbx_data_processing_cell.b_tolerance Tolerance in unit cell length B 0.04 pdbx_data_processing_cell.beta Unit cell angle beta. 90.0