data_template # # PDB X-RAY DEPOSITION FORM # # This mmCIF form can be used to submit X-ray structures to the Protein # Data Bank (PDB; http://www.rcsb.org/). It is an alternative to the # Web-based deposition tool, ADIT (http://pdb.rutgers.edu/adit/). # # An optional data format precheck is available at # http://pdb.rutgers.edu/validate/ # # After this form is completed, please send it to deposit@rcsb.rutgers.edu or # ftp the file to pdb.rutgers.edu/private and send a message notifying the # PDB that your structure has been submitted to deposit@rcsb.rutgers.edu. # # The information in this form is divided into the following sections: # # # Deposition # Citation # Chemical/Biological Features # Structure Features # Crystallization # Crystal Data # Data Collection # Refinement # Software # Coordinates # # Each section contains definitions and examples of the data items to be # entered. Lines begining with a "#" are comments. Your data should replace # the question marks found in the portions of the file between lines of # "~" symbols. # # If the requested information is not relevant to your structure, the question # mark should be left in the form. # # In mmCIF format, identifiers (tokens with the extension _id, such as # _citation_author.citation_id) are used to differentiate between parallel # entries within a category. Multiple equivalent entries can be entered by # the use of loops. For example in the category citation_author, multiple # authors for two different citations (primary and 1) can be included in a # loop: # # loop_ # _citation_author.citation_id # _citation_author.name # primary 'Holtz, K.M.' # primary 'Stec, B.' # primary 'Kantrowitz, E.R.' # 1 'Murphy, J.E.' # 1 'Stec, B.' # 1 'Ma, L.' # 1 'Kantrowitz, E.R.' # # Please see http://ndbserver.rutgers.edu/mmcif/examples/index.html # for examples of mmCIF format files. # #***************************************************************************** # # Deposition # #***************************************************************************** # # # Category = audit_contact_author # # Enter the name, address, e-mail, and phone # numbers for the contact person for this deposition. # # ==> Contact name (_audit_contact_author.name) # # # The name of the author to whom correspondence should be # addressed. The names should be in the format: # Smith, J.H. or Jones Jr., B.T. # # For example: Parkinson, G. # # ==> Contact e-mail (_audit_contact_author.email) # # The electronic mail address of the corresponding author. # # For example: parkinson@rutchem.rutgers.edu # # ==> Contact address (_audit_contact_author.address) # # The mailing address of the corresponding author. # # For example: # # Department of Chemistry # Rutgers, The State University of New Jersey # 610 Taylor Road # Piscataway, New Jersey 08854-8087 # USA # # ==> Contact phone number (_audit_contact_author.phone) # # The phone number of the corresponding author. # # The recommended style includes the international dialing prefix, # the area code in parentheses, followed by the local number with # no spaces. # # For example: 1(732)4450103 # # ==> Contact fax number (_audit_contact_author.fax) # # The facsimile number of the corresponding author. # # The recommended style includes the international dialing prefix, # the area code in parentheses, followed by the local number with # no spaces. # # For example: 1(732)4454230 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Replace the question marks in the template below with your data. # # _audit_contact_author.name ? _audit_contact_author.email ? _audit_contact_author.address ? _audit_contact_author.phone ? _audit_contact_author.fax ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Category = rcsb_database_related # If this deposition is one of a group of related entries, you may enter the # ID codes that are related to the current deposition in this section. If this # deposition is related to an entry in another database (other than sequence) # this information may also be entered. # # ==> Database name (_rcsb_database_related.db_name) # # Enter the name of the database containing the related entry. # # For example: PDB - Protein Data Bank # NDB - Nucleic Acid Database # BMRB - BioMagResBank # BMCD - Biological Macromolecule Crystallization Database # # ==> Database ID code (_rcsb_database_related.db_id) # # Enter the identifying code in the related database. # # For example: 1ABC # # ==> Related entry description (_rcsb_database_related.details) # # Enter a description of the related entry. # # For example: 1ABC contains the same protein complexed with Netropsin. # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _rcsb_database_related.db_name _rcsb_database_related.db_id _rcsb_database_related.details ? ? ? #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Category = status # # Choose the manner in which you would like your deposited data to be released. # Please note that unless you select otherwise, your data will be RELEASED # IMMEDIATELY. # # ==> Release status for coordinates # ==> (_ndb_database_status.dep_release_code_coordinates) # # Choose the manner in which you would like the coordinates for this # deposition to be released. Please note that unless you select otherwise, # your coordinates will be RELEASED IMMEDIATELY. # # For example: RELEASE NOW = Release immediately # HOLD FOR PUBLICATION = Hold until primary citation is published # HOLD FOR 6 MONTHS = Hold for 6 months # HOLD FOR 1 YEAR = Hold for 1 year # # ==> Release status for structure factors # ==> (_ndb_database_status.dep_release_code_struct_fact) # # Choose the manner in which you would like the structure factors for this # deposition to be released. Please note that unless you select otherwise, # your structure factors will be RELEASED IMMEDIATELY. # # For example RELEASE NOW = Release immediately # HOLD FOR PUBLICATION = Hold until primary citation is published # HOLD FOR 6 MONTHS = Hold for 6 months # HOLD FOR 1 YEAR = Hold for 1 year # HOLD FOR 2 YEARS = Hold for 2 years # HOLD FOR 3 YEARS = Hold for 3 years # HOLD FOR 4 YEARS = Hold for 4 years #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Replace the question marks in the template below with your data. # # _ndb_database_status.dep_release_code_coordinates ? _ndb_database_status.dep_release_code_struct_fact ? # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Category = struct # # Enter a title for the deposition and any remarks related to this structure # deposition that are not included elsewhere in this deposition. # # ==> Deposition Title (_struct.title) # # Enter a title for this deposition. The author should attempt to convey # the essence of the structure and to distinguish this structural result # from others. # # For example: Crystal Structure Analysis of the B-DNA Dodecamer CGTGAATTCACG # # ==> Other Structure Details (_struct.ndb_details) # # # Enter additional remarks related to this structure deposition that have not # been included elsewhere in the deposition. # # For example: # # Hydrogen bonds between peptide chains follow the Rich and Crick # model II for collagen. # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _struct.title ? _struct.ndb_details ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Citation # #***************************************************************************** # # # Category = citation_author # # Enter the authors names for the publications associated with this deposition. # # The primary citation is the article in which the deposited # coordinates were first reported. # # Other related citations may be provided, and are identified as citations # 1 through 5. # # For the primary citation, enter the authors listed in the primary # citation in the order in which they appear in the citation article. # # For the other related citations, enter the authors that correspond # to other citations. # # ==> Citation identifier (_citation_author.citation_id) # # A unique identifier for each citation related to this deposition. # # For example: primary # # ==> Author names (_citation_author.name) # # Enter each author's name individually into a text box in the order in which # they appear in the citation article. # # Names should be in the format: # # Smith, J.H. # van der Marel, G.A. # # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _citation_author.citation_id _citation_author.name ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = citation # # In the following tables, enter the information about each of the citations. # # If the details about the publication are unavailable, select # "To be published" as the journal abbreviation. # # The citation which is labeled "primary" is the citation in which the # deposited coordinates were first reported. Other related citations may be # provided. These are identified as 1 through 5. # # Please note that the authors for each citation are listed separately. # # ==> Citation Identifier (_citation.id) # # A unique identifier for each citation related to this deposition. # # For example: primary # # ==> Year (_citation.year) # # The year in which the citation was published. # # For example: 1981 # # ==> Journal abbreviation (_citation.journal_abbrev) # # # Abbreviated name of the journal in which the citation is published. # # For example: J. Am. Chem. Soc. # # ==> Journal volume (_citation.journal_volume) # # Volume number of the journal in which the citation is published. # # For example: 100 # # ==> First page (_citation.page_first) # # The first page of the citation. # # For example: 101 # # ==> Last page (_citation.page_last) # # The last page of the citation. # # For example: 122 # # ==> Title (_citation.title) # # The title of the citation. # # For example: Crystal Structure Analysis of the B-DNA Dodecamer CGTGAATTCACG # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _citation.id _citation.year _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.title ? ? ? ? ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Chemical/Biological Features # #***************************************************************************** # # # Category = entity # # Enter information about the molecules that are in the asymmetric unit. Each # chemically unique molecule is called an entity and must have a unique id. # # For example, a double stranded nucleic acid molecule would be one entity if # both strands were of identical sequence, but would be two entities if the two # strands were of different sequence. # # ==> Entity identifier (_entity.id) # # This is an identifier for each unique molecule in the asymmetric unit. # Each entity is assigned a numerical ID. # # For example: 1 # # ==> Entity description (_entity.ndb_description) # # The names of the entities. Proteins and biological nucleic acids # (such as t-RNA) are identified by their common names, short NA strands by # their nucleotide sequences, and non-polymer compounds by their chemical or # trivial names. # # Polymer compounds (proteins and nucleic acids) are expected to have # their sequences entered under the category entity_poly. # # For example: # # HIV-1 integrase # HAEIII METHYLTRANSFERASE # FACTOR FOR INVERSION STIMULATION (FIS) # ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN # PHAGE LAMBDA CRO # DIPTHERIA TOXIN REPRESSOR (DTXR) # CATABOLITE GENE ACTIVATOR PROTEIN (CAP) # HIV-1 REVERSE TRANSCRIPTASE (RT) # 5'-EXONUCLEASE (3.1.11.3) # FYN TYROSINE KINASE # PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) # AVIAN SARCOMA VIRUS (ASV) INTEGRASE # ALPHA-THROMBIN (RESIDUES 37 - 259) # LIVER ALCOHOL DEHYDROGENASE # ENDOGLUCANASE V CELLOBIOSE COMPLEX # FLAVODOXIN # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _entity.id _entity.ndb_description ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = entity_keywords # # Enter additional information about the entities in the asymmetric unit such # as whether a protein is a fragment or whether it is a mutant. # # ==> Entity identifier (_entity_keywords.entity_id) # # This is an identifier for each unique molecule in the asymmetric unit. # Each entity is assigned a numerical ID. # # For example: 1 # # ==> Fragment name (_entity_keywords.ndb_fragment) # # Give the name of the fragment if the protein or nucleic acid is a part of a # larger molecule with well established biological function. # # For example: REPLICASE OPERATOR HAIRPIN # # ==> Mutation type (_entity_keywords.ndb_mutation) # # Specify mutation of the protein entity. # # For example: C280S # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _entity_keywords.entity_id _entity_keywords.ndb_fragment _entity_keywords.ndb_mutation ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = entity_poly # # For each polymeric entity identified in the entity category, # give the amino acid or nucleic acid sequence using standard one letter # nomenclature. # # Also enter the chain identifiers from your PDB format coordinate file # corresponding to each entity. A single entity may have multiple chain_id's # if there are multiple molecules of the same sequence in the asymmetric unit. # # The one-letter code sequence derived from your coordinates is displayed # when using the Pre-Deposition Data Format Check at # http://pdb.rutgers.edu/validate/. You may edit this as necessary and # copy the result into the sequence item below. # # ==> Entity identifier (_entity_poly.entity_id) # # This is an identifier for each unique molecule in the asymmetric unit. # Each entity is assigned a numerical ID. # # For example: 1 # # ==> One-letter sequence code (_entity_poly.ndb_seq_one_letter_code) # # Sequence is expressed as string of one-letter amino or nucleic acid codes. # # Letter should not be separated by commas or spaces. # # The one-letter code sequence derived from your coordinates is displayed # by Pre-Deposition Data Format Check. You may edit this as necessary and # copy the result into the sequence item below. # # For example: # # 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 # # ==> Chain identifiers (_entity_poly.ndb_chain_id) # # The chain_id(s) in your PDB format coordinate file which correspond to this # polymer entity. # # A single entity may have multiple chain_ids if there are multiple molecules # of the same sequence in the asymmetric unit. Separate multiple chain_ids by # commas. # # For example: # # For a single polymer in the asymmetric unit, the chain identifier is A. # For a homodimer in the asymmetric unit, the chain identifiers are A and B. # # ==> Sequence database name (_entity_poly.rcsb_seq_db_name) # # The name of the sequence data base containing a database entry # for this sequence. # # For example: GenBank # # ==> Sequence database code (_entity_poly.rcsb_seq_db_id) # # The identifier for this sequence in the sequence data base. # # For example: P00730 # # ==> Beginning sequence position (_entity_poly.rcsb_seq_align_begin) # # The sequence position in the database sequence at which the # alignment with your sequence begins. # # ==> Ending sequence position (_entity_poly.rcsb_seq_align_end) # # The sequence position in the database sequence at which the # alignment with your sequence ends. # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _entity_poly.entity_id _entity_poly.ndb_seq_one_letter_code _entity_poly.ndb_chain_id _entity_poly.rcsb_seq_db_name _entity_poly.rcsb_seq_db_id _entity_poly.rcsb_seq_align_begin _entity_poly.rcsb_seq_align_end ? ? ? ? ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = entity_src_nat # # In the table below, give the natural sources of each molecule (entity) in the # asymmetric unit. # # ==> Entity identifier (_entity_src_nat.entity_id) # # This is an identifier for each unique molecule in the asymmetric unit. # Each entity is assigned a numerical ID. # # For example: 1 # # ==> Natural source (_entity_src_nat.common_name) # # Common name of the organism from which the biological polymer was # isolated. # # For example: monkey # # ==> Natural source description (_entity_src_nat.details) # # Give the scientific description of the natural source of each biomolecule. # Use the order: organism, genus, species, organ, tissue, cell, organelle. # # For example: Homo, Sapiens, brain, neuron # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _entity_src_nat.entity_id _entity_src_nat.common_name _entity_src_nat.details ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = entity_src_gen # # In the table below describe the entities in the asymmetric unit # that were genetically manipulated. There are two types of information # required: the name of the source of the gene, and the name of the # expression system. Additional information about the vector system # may also be entered. # # ==> Entity identifier (_entity_src_gen.entity_id) # # This is an identifier for each unique molecule in the asymmetric unit. # Each entity is assigned a numerical ID. # # For example: 1 # # ==> Source of gene (_entity_src_gen.gene_src_common_name) # # Common name of the organism from which the gene for the expression product # originates. # # For example: yeast # # ==> Gene source description (_entity_src_gen.gene_src_details) # # Give the scientific names for the natural source of the gene of the # expression product. # # Use the order: Genus, species, organ, tissue, cell, organelle. # # For example: Homo, sapiens, brain # # ==> Expression system name (_entity_src_gen.host_org_common_name) # # Common name of the expression system. # # For example: bacteria # # ==> Expression system description (_entity_src_gen.rcsb_host_org_details) # # The scientific description of the expression system host. # # For example: Escherichia Coli # # ==> Vector description (_entity_src_gen.rcsb_host_org_vector_details) # # The description of the vector system used to transfer the gene. # # For example: Plasmid PET3 # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _entity_src_gen.entity_id _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_details _entity_src_gen.host_org_common_name _entity_src_gen.rcsb_host_org_details _entity_src_gen.rcsb_host_org_vector_details ? ? ? ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Category = rcsb_entity_src_syn # # In the table below enter information about each chemically # synthesized molecule (entity) in the asymmetric unit. # # ==> _rcsb_entity_src_syn.entity_id # # This data item is a pointer to _entity.id in the ENTITY category. # # ==> Synthetic source description (_rcsb_entity_src_syn.details) # # A description of special aspects of the source for the # synthetic entity. # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _rcsb_entity_src_syn.entity_id _rcsb_entity_src_syn.details ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Structure Features # #***************************************************************************** # # # Category = struct_keywords # # Give a list of keywords that describe important features of the deposited # structure. The keywords entered here should provide information about # special structural features such as beta-alpha-barrels, or helix-turn-helix. # # ==> Keywords (_struct_keywords.text) # # Keywords describing this structure. # # For example: BETA BARREL, PROTEIN-DNA COMPLEX, DOUBLE HELIX # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _struct_keywords.text ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Crystallization # #***************************************************************************** # # # Category = exptl_crystal_grow # # # Enter information about the crystallization method and the # crystallization conditions which produced the crystal(s) used # in this experiment. # # ==> Crystal identifier (_exptl_crystal_grow.crystal_id) # # This data item uniquely identifies each crystal that was used to # measure data agains which the structure was refined. # # For example: 1 # # ==> Method (_exptl_crystal_grow.method) # # Select the method used to grow the crystals (evaporation, # evaporation/recrystallization, liquid diffusion, microdialysis, # slow cooling, small tubes, vapor diffusion, vapor diffusion/hanging # drop, vapor diffusion/sitting drop). # # If the method used is not listed, please enter it in the space provided. # # For example: EVAPORATION # # ==> pH (_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. # # For example: 7.4 # # ==> Temperature (_exptl_crystal_grow.temp) # # The temperature in Kelvin at which the crystal was grown. # If more than one temperature was employed during the # crystallization process, the final temperature should be noted # here. # # For example: 298.0 # # ==> Crystallization components (_exptl_crystal_grow.rcsb_details) # # Give the key components in the crystallization. Use the following order: primary # precipitating agent, secondary precipitating agent, other chemicals used in # crystallization drop. # # For example: PEG 4000, potassium phosphate, magnesium chloride, cacodylate # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.pH _exptl_crystal_grow.temp _exptl_crystal_grow.rcsb_details ? ? ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Crystal Data # #***************************************************************************** # # # Category = cell # # # Enter the crystallographic cell parameters for this structure. # # ==> Length a (_cell.length_a) # # Unit-cell length a in Angstroms of the structure reported. # # For example: 44.710 # # ==> Length b (_cell.length_b) # # Unit-cell length b in Angstroms of the structure reported. # # For example: 44.710 # # ==> Length c (_cell.length_c) # # Unit-cell length c in Angstroms of the structure reported. # # For example: 44.710 # # ==> Angle alpha (_cell.angle_alpha) # # Unit-cell angle alpha in degrees for the reported structure. # # For example: 90.00 # # ==> Angle beta (_cell.angle_beta) # # Unit-cell angle beta in degrees for the reported structure. # # For example: 90.00 # # ==> Angle gamma (_cell.angle_gamma) # # Unit-cell angle gamma in degrees for the reported structure. # # For example: 90.00 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _cell.length_a ? _cell.length_b ? _cell.length_c ? _cell.angle_alpha ? _cell.angle_beta ? _cell.angle_gamma ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = symmetry # # Select the space-group for this structure. # # ==> Space-group name (_symmetry.space_group_name_H-M) # # Hermann-Mauguin space-group symbol. Note that the H-M symbol does # not necessarily contain complete information about the symmetry # and the space-group origin. In such a case, supply a full space # group name from International Tables for Crystallography, # Vol. A (1987). # # For example: P 2 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _symmetry.space_group_name_H-M ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Data Collection # #***************************************************************************** # # # Category = exptl # # # Enter the number of crystals used to collect data that were used # in the refinement of the deposited coordinates. # # ==> Number of crystals (_exptl.crystals_number) # # The total number of crystals used to measure the native data set. # # For example: 1 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _exptl.crystals_number ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Category = diffrn_source # # For each experiment used to collect the native data set, # enter the details of the source of radiation or the X-ray generator used. # # ==> Diffraction experiment (_diffrn_source.diffrn_id) # # Identifier for each data collection experiment which contributed to # the native data set. # # For example: 1 # # ==> Source (_diffrn_source.source) # # # Select the type of radiation source: # rotating anode, sealed tube, or synchrotron. # # For example: sealed tube # # ==> Source type (_diffrn_source.type) # # Select the make, model, name or beamline of the source of radiation. # # For example: NSLS beamline X8C # # ==> Wavelength (_diffrn_source.rcsb_wavelength) # # # Give the wavelength of the radiation used to collect the native data set # (Angstroms). # # For example: 1.5418 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.rcsb_wavelength ? ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = diffrn_detector # # # For each native diffraction data set named enter details about the detector # used. Also enter the initial date of data collection in the format yyyy-mm-dd. # # ==> Diffraction experiment (_diffrn_detector.diffrn_id) # # Identifier for each data collection experiment which contributed to the # native data set. # # For example: 1 # # ==> Detector (_diffrn_detector.detector) # # The general class of detector: area detector, CCD, diffractometer, # film, image plate, oscillation camera, etc. # # For example: IMAGE PLATE # # ==> Detector type (_diffrn_detector.type) # # The make, model or name of the detector device used. # # For example: ENRAF-NONIUS # # ==> Data collection date (_diffrn_detector.ndb_collection_date) # # For each experiment used to collect the native data set # enter the initial date of data collection in the format yyyy-mm-dd. # # For example: 1996-11-27 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.ndb_collection_date ? ? ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Category = diffrn # # For each native diffraction data set enter the temperature # (in Kelvin) at which the diffraction data were measured. # # ==> Diffraction experiment (_diffrn.id) # # Identifier for each data collection experiment which contributed to the # native data set. # # For example: 1 # # ==> Ambient temperature (_diffrn.ambient_temp) # # The mean temperature (in Kelvin) at which the intensities were # measured. # # For example: 298.0 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _diffrn.id _diffrn.ambient_temp ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = reflns # # Enter the details about the unique set of reflection # data used to produce the coordinate set in this deposition. # # You may choose to provide the sigma criterion for observed # reflections in either F or I. # # Note the observed criterion on sigma(F) and the observed criterion # on sigma(I) are different from the sigma(F) and sigma(I) cut-offs # specified in the refine category. # # ==> Observed criterion sigma(F) (_reflns.observed_criterion_sigma_F) # # The criterion used to classify a reflection as observed, # expressed as a multiple of the value of sigma(F). # # This is the cutoff used for data collection, not refinement. # # For example: 2.0 # # ==> Observed criterion sigma(I) (_reflns.observed_criterion_sigma_I) # # # The criterion used to classify a reflection as observed, # expressed as a multiple of the value of sigma(I). # # This is the cutoff used for data collection, not refinement. # # For example: 2.0 # # ==> Resolution (high) (_reflns.d_resolution_high) # # The highest resolution for the reflection data (in Angstroms). # This is the smaller value. # # For example: 2.0 # # ==> Resolution (low) (_reflns.d_resolution_low) # # The lowest resolution for the reflection data (in Angstroms). # This is the larger value. # # For example: 8.0 # # ==> Number reflections (all) (_reflns.number_all) # # The total number of unique measured reflections. # # For example: 4500 # # ==> Number reflections (observed) (_reflns.number_obs) # # The total number of unique measured reflections that are # labeled as observed by the criterion on sigma(I) or # or sigma(F). # # For example: 2300 # # ==> Percent possible (observed) (_reflns.percent_possible_obs) # # The percentage of measured reflections classified as observed # compared with reflections which are geometrically possible within # the resolution limits. # # For example: 75.0 # # ==> R-merge I (observed) (_reflns.ndb_Rmerge_I_obs) # # Residual factor Rmerge for reflections that satisfy the # resolution limits and the observation limit (F or I). # # For example: 0.084 # # ==> Net I over average sigma(I) (_reflns.ndb_netI_over_av_sigmaI) # # The ratio of the mean of all the intensities classified # as 'observed' to the mean of the standard uncertainties # of the intensities of the 'observed' reflections. # # For example: 11.4 # # ==> B(isotropic) from Wilson plot (_reflns.B_iso_Wilson_estimate) # # The value of the overall isotropic temperature factor # estimated from the slope of the Wilson plot. # # For example: 14.7 # # ==> Redundancy (_reflns.ndb_redundancy) # # The number of all measured reflections divided by the number of the # unique reflections. # # For example: 6.7 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high ? _reflns.d_resolution_low ? _reflns.number_all ? _reflns.number_obs ? _reflns.percent_possible_obs ? _reflns.ndb_Rmerge_I_obs ? _reflns.ndb_netI_over_av_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.ndb_redundancy ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = reflns_shell # # Enter the details about the reflection # data in the highest resolution shell. # # ==> Resolution (high) (_reflns_shell.d_res_high) # # The highest resolution for this shell (in Angstroms). This is the smaller value. # # For example: 1.90 # # ==> Resolution (low) (_reflns_shell.d_res_low) # # The lowest resolution for this shell (in Angstroms). This is the larger value. # # For example: 1.96 # # ==> Percent possible (all) (_reflns_shell.percent_possible_all) # # The percentage of the unique measured reflections compared with # the number of geometrically possible reflections in the shell. # # For example: 93.6 # # ==> R-merge I (observed) (_reflns_shell.Rmerge_I_obs) # # Residual factor R-merge(I) for reflections that are within the # resolution limits of the shell and are labeled as observed. # # For example: 0.127 # # ==> Redundancy (_reflns_shell.ndb_redundancy) # # The number of all reflections measured in a shell divided by # the number of the unique measured reflections in the shell. # # For example: 4.3 # # ==> Number unique reflections (all) (_reflns_shell.number_unique_all) # # The number of unique measured reflections within the shell. # # For example: 647 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _reflns_shell.d_res_high ? _reflns_shell.d_res_low ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.ndb_redundancy ? _reflns_shell.number_unique_all ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Refinement # #***************************************************************************** # # # Category = refine # # Enter the refinement parameters of the deposited structure. # # ==> Resolution (high) (_refine.ls_d_res_high) # # The highest resolution for the reflection data used in the refinement # (in Angstroms). This is the smaller value. # # For example: 2.8 # # ==> Resolution (low) (_refine.ls_d_res_low) # # The lowest resolution for the reflection data used in the refinement # (in Angstroms). This is the larger value. # # For example: 15.0 # # ==> Cut-off sigma(F) (_refine.ndb_ls_sigma_F) # # The cut-off limit for structure factors used in refinement in units of # their estimated standard deviations. # # This is the cutoff used for refinement, not data collection. # # For example: 2.0 # # ==> Cut-off sigma(I) (_refine.ndb_ls_sigma_I) # # The limit for cut-off of reflection intensities in units # of their estimated standard deviations. # # This is the cutoff used for refinement, not data collection. # # For example: 2.0 # # ==> Number reflections (all) (_refine.ls_number_reflns_all) # # The number of reflections that satisfy the resolution limit established # by the high and low resolution cut-offs. # # This number includes reflections set aside for cross-validation # in a "free" R-factor set. # # For example: 1089 # # ==> Number reflections (observed) (_refine.ls_number_reflns_obs) # # The number of reflections that satisfy the resolution and observation # limits. # # This number includes reflections set aside # for cross-validation in a "free" R-factor set. # # For example: 6453 # # ==> Number rerlections (R-free) (_refine.ls_number_reflns_R_free) # # The number of reflections that satisfy the resolution limit established # by high and low resolution cut-offs, the # observation limit established by sigma(F) or # sigma(I) cut-offs, and that were excluded from refinement for # cross-validation in a "free" R-factor set. # # Details of how reflections were assigned to the working and test sets are # given in R-free selection details. # # For example: 150 # # ==> Percent reflections observed (_refine.ls_percent_reflns_obs) # # The percentage of observable reflections that satisfy the # resolution and observation limits. # # This number includes reflections set aside # for cross-validation in a "free" R-factor set. # # For example: 87.4 # # ==> R-factor (all) (_refine.ls_R_factor_all) # # Residual factor R for all reflections that satisfy the limits # established by high and low resolution cut-offs. # # It includes reflections which do not satisfy the sigma cutoff criteria # as well as those set aside for cross-validation in a "free" R-factor set. # # For example: 0.247 # # ==> R-factor (observed) (_refine.ls_R_factor_obs) # # Residual factor R for reflections that satisfy the resolution and # observation limits. # # This quantity includes reflections set aside # for cross-validation in a "free" R-factor set. # # The R-factor (obs) should not be confused with # R-factor (R-work) which does not contain these reflections. # # For example: 0.231 # # ==> R-factor (R-work) (_refine.ls_R_factor_R_work) # # Residual factor R for reflections that satisfy the resolution and observation # limits and that were used as the working reflections in the refinement. # # This quantity does not include reflections set aside for # cross-validation in a "free" R-factor set. # # For example: 0.226 0.169 # # ==> R-factor (R-free) (_refine.ls_R_factor_R_free) # # Residual factor R for reflections that satisfy the resolution and observation # limits and that were excluded from refinement to be used for cross validation # in a "free" R-factor set. # # Details of how reflections were assigned to the working and test sets # can be given in R-free selection details data item. # # For example: 0.339 # # ==> R-free selection details (_refine.ndb_R_free_selection_details) # # Details of how the cross validation reflections were selected. # # For example: RANDOM # # ==> Stereochemistry target values (_refine.ndb_stereochemistry_target_values) # # The library of standard bond lengths and bond angles # used during refinement. # # For example: Engh & Huber # # ==> _refine.details # # Description of special aspects of the refinement process. # # For example: Used weighted full matrix least squares procedure. # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _refine.ls_d_res_high ? _refine.ls_d_res_low ? _refine.ndb_ls_sigma_F ? _refine.ndb_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_R_free ? _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ndb_R_free_selection_details ? _refine.ndb_stereochemistry_target_values ? _refine.details ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Category = refine_ls_restr # # For the given parameter type, enter the root-mean-square deviation # between the ideal values used as restraints in the least-squares # refinement and the values obtained by refinement. For instance, # bond distances may deviate by 0.018 Angstroms from ideal values # in the current model. # # ==> Parameter type (_refine_ls_restr.type) # # The type of the parameter being restrained, 1) bond # length in angstroms, and 2) bond angle expressed in # either degrees or distance. Select the type of # restraint from the list, appropriate for the refinement # method used: # # X-PLOR: x_, CNS: x_, NUCLSQ: n_, PROLSQ: p_, SHELX: s_, and # TNT: t_ # # For example: # # x_bond_d for X-PLOR bond distance # x_angle_d for X-PLOR bond angle expressed as a distance # x_angle_deg for X-PLOR bond angle degree # c_bond_d for CNS bond distance # c_angle_d for CNS bond angle expressed as a distance # c_angle_deg for CNS bond angle degree # n_bond_d for NUCLSQ bond distance # n_angle_d for NUCLSQ bond angle expressed as a distance # p_bond_d for PROLSQ bond distance # p_angle_d for PROLSQ bond angle expressed as a distance # s_bond_d for SHELXL bond distance # s_angle_d for SHELXL bond angle expressed as a distance # t_bond_d for TNT bond distance # t_angle_deg for TNT bond angle degree # # ==> Deviation from ideal (_refine_ls_restr.dev_ideal) # # The root-mean-square deviation, according to parameter type, # between the dictionary target values used as restraints in the # least-squares refinement and the values obtained by refinement. # # For example: .020 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # The question marks in the template below are placeholders for one row # of data in this category. Replace the question marks with your data and # add as many rows as required. # # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal ? ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Software # #***************************************************************************** # # # Category = computing # # Select the computer programs used in the crystal # structure analysis. If several programs were used at any step, enter # the final one utilized. # # ==> Data collection (_computing.data_collection) # # Software used for data collection. # # For example: DENZO # # ==> Data reduction (_computing.data_reduction) # # Software used for data reduction. # # For example: DIFDAT # # ==> Structure solution (_computing.structure_solution) # # Software used for solution of the structure. # # For example: AMoRE # # ==> Structure refinement (_computing.structure_refinement) # # Software used for refinement of the structure. # # For example: X-PLOR 3.1 # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Replace the question marks in the template below with your data. # # _computing.data_collection ? _computing.data_reduction ? _computing.structure_solution ? _computing.structure_refinement ? # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # #***************************************************************************** # # Coordinates # #***************************************************************************** # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # # Please enter your coordinate data here. # ? # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # After this form is completed, please send it to deposit@rcsb.rutgers.edu or # ftp the file to pdb.rutgers.edu/private and send a message notifying the # PDB that your structure has been submitted to deposit@rcsb.rutgers.edu. # #END OF FILE