****************************************************************************** ****************************************************************************** ****************************************************************************** April 15, 1999: Structures can be deposited to the NDB using the AutoDep Input Tool, a Web-based tool developed by the RCSB. ADIT is available at http://pdb.rutgers.edu/adit/. ****************************************************************************** ****************************************************************************** ****************************************************************************** Deposition Form for Nucleic Acid Crystal Structures To deposit data for a nucleic acid crystal structure, complete the following deposition form as completely as possible. The form is a shortened version of the PDB deposition form (Version 3.40) and does not include the items SSBOND, SITE, HELIX, SHEET, and TURN. Send this form, along with the coordinate file, to deposit@ndbserver.rutgers.edu. Structure factors, if submitted, may be submitted in any format. The paper manuscript should also be sent via facsimile or air mail. Questions and manuscripts should be sent to: deposit@ndbserver.rutgers.edu The Nucleic Acid Database Rutgers, the State University Wright-Reiman Laboratories Chemistry 610 Taylor Road Piscataway, NJ 08854-8087 Phone: 732-445-0103 Fax: 732-445-4320 ****************************************************************************** CONTACT INFORMATION Primary Contact The primary contact has authority to grant approval for release of the completed entry. The prepared entry, validation diagnostics, and approval request will be sent to the primary contact. Typically this is the Principal Investigator. First name: Middle name or initial: Family name: e-mail address: Department and institution: Mailing address: Fax number: Telephone number: Secondary Contact First name: Middle name or initial: Family name: e-mail address: Department and institution: Mailing address: Fax number: Telephone number: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- AUTHORS, TITLE AND REFERENCE(S) Please, specify authors and title(s) of this entry. Cite both the primary reference which identifies the deposited set of coordinates as well as other important references. Repeat block as many times as necessary. Is this the primary citation reporting this structure? [ ] No [ ] Yes Author(s): Journal or book name: Year: Volume number: Page numbers (first-last): Article or chapter title: Thesis title: Publisher, for non-journals: Editor(s), for non-journals: Place of publication, for non-journals: Series info: Other info: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- CRYSTAL GROWTH Give the crystal's solvent content and crystallization conditions. Crystallization method (hanging/sitting drop...): pH of crystallization: Temperature of crystallization: Percent solvent content (Vs): Matthews coefficient (Vm): Crystallization conditions: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- CRYSTAL DATA Unit-cell data and coordinate system information. All PDB coordinate entries are released in an orthogonal coordinate frame, in Angstroms. All submissions must have this section completed. Unit Cell and Crystal Data Provide the unit cell information for your crystal. a (Angstroms): b (Angstroms): c (Angstroms): alpha (degrees): beta (degrees): gamma (degrees): space group: Is this a non-standard space group or setting? [ ] No [ ] Yes Z-value: If this is a non-standard space group or setting, choose Yes above, and provide the symmetry operators here. Symmetry operators for non-standard space group or setting, separated by semicolons: Explain any unusual unit cell data: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- EXPERIMENTAL DETAILS [ ] X-ray diffraction type of radiation used [ ] monochromatic [ ] laue sample type [ ] single crystal [ ] fiber [ ] polycrystalline fiber Number of crystals used in the experiment: X-RAY SOURCE if laboratory source: x-ray generator type (e.g. rotating anode) and model: if synchrotron: name of synchrotron and beamline [ ] APS [ ] CHESS [ ] DESY-EMBL,HAMBURG [ ] ESRF [ ] LURE [ ] NSLS [ ] PHOTON FACTORY [ ] SRS [ ] SSRL [ ] OTHER (specify beamline) Monochromator: Optics: Detector type (e.g. image plate): Detector manufacturer: Date of data collection: Temperature of experiment, in Kelvin: Wavelength(s) or wavelength range (A): -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- DATA COLLECTION Total number of unique reflections collected: Number of unique reflections collected with I or F higher than the specified rejection limit: Rejection criteria (sigma(I)): Rejection criteria (sigma(F)): Completeness for range (%): Resolution range high (A): Resolution range low (A): Merging R value (I): Data redundancy: -------------------------------------------------------------------------------- Information on the highest Resolution Shell Resolution range high (A): Resolution range low (A): Percent possible reflections (%): Merging R value (I): Data redundancy: Total number of unique reflections collected in the shell: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- COMPOUND AND SOURCE Please, describe the molecular contents of the entry, including the macromolecules and their biological sources. Keyword(s) describing the entry: Name and describe each unique macromolecule, repeating the block for each molecule of a macromolecular complex. Molecule name: Chain name(s): Domain or fragment: Synonyms: Mutations: Biological unit: Compound, other details: -------------------------------------------------------------------------------- Please, describe the biological source. Scientific name of organism: Common name of organism: Source, other details: Was the molecule chemically synthesized? [ ] No [ ] Yes optional remark describing the synthetic sequence: Was the molecule made using recombinant techniques? [ ] No [ ] Yes If this is an engineered molecule, also describe the experiment. Expression system organism: Expression system strain: Expression system plasmid: Expression system organelle: Optional comment on the experiment: -------------------------------------------------------------------------------- SEQUENCE Describe any non-standard residues. These may have arisen due to post-translational or chemical modifications. Repeat block as many times as necessary. 1) MODIFIED RESIDUES Non-standard residue name, as used in the submitted coordinates: Standard residue name: Description of the modification: -------------------------------------------------------------------------------- 2) HETEROGENS Are there any non-water hetero atoms included in this structure? [ ] No [ ] Yes If yes, please, describe prosthetic groups, inhibitors, solvents (except water), and/or ions. Repeat this block for each unique HET group. HET residue name used in this deposition: HET group trivial name: HET group systematic name: Synonyms for HET group: Empirical formula: Charge: Other details: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- SOFTWARE USED Intensity-integration software: Data scaling software: Structure solution program: Details: -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- REFINEMENT Quality of fit and data used for refinement R value (all reflections): R value (working + test set): R value (working set): Resolution range high (Angstroms): Resolution range low (Angstroms): Number of observed reflections: Completeness for range (%): Total number of reflections (no cutoff): Data cutoff (sigma(F)): Data cutoff (sigma(I)): Cross Validation Free R value: Free R value test set count: Free R value test set size (%): Free R value test set selection: RMS deviations from ideal values Bond lengths (A): Bond angles (degrees): Bond angles (A): Number of non-hydrogen refined atoms Protein atoms: Nucleic acid atoms: Heterogen atoms: Solvent atoms: -------------------------------------------------------------------------------- REFINEMENT PROGRAM NOTE: If you have a complete X-PLOR, CNS or SHELXL-97 output file in PDB format, you may send this file and ignore the remaining part of this deposition form. [ ] X-PLOR Version of X-PLOR used for the refinement: [ ] CNS Version of CNS used for the refinement: [ ] TNT Version of TNT used for the refinement: [ ] PROLSQ and related Indicate which program/extension was used [ ] PROLSQ [ ] CCP4 [ ] PROFFT [ ] REFMAC [ ] GPRLSA [ ] Other (please, specify program name and authors): [ ] SHELX Version of SHELX used for the refinement: [ ] NUCLSQ [ ] Other Refinement program name: Refinement program authors: --------------------------------------------------------------------------------