RCSB PDB Data Validation and Deposition Services


wwPDB Deposition | SF-Tool | pdb_extract | Ligand Expo | Validation | ADIT 2.0 | Deposition FAQ

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Depositing large structures?

If your structure exceeds the size of the traditional PDB file format limits (>62 chains or >99,999 atoms), please prepare your deposition as a single PDBx/mmCIF file using recent versions of CCP4 (REFMAC > 5.8) or Phenix (> 1.8.2) before submitting your structure with the wwPDB Deposition System.



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Depositing X-ray Data? Try the new wwPDB Deposition System at http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon).

The following data deposition tools and instructions can make your structure deposition easy, complete and accurate:

  1. Review wwPDB Policies and Procedures to be familiar with the latest format and deposition policy.
  2. Gather information about the proteins/nucleic acids in your structure from sequence databases (e.g. using UniProtKB 1 or BLAST 2 ) or about your ligand (using Ligand Expo 3 ). Instructions will be provided during deposition to deposit new ligands. Collect log files from data processing, scaling, MR, refinement, etc. (pdb_extract can parse these files for you and gather sequence information for what was in the sample.)
  3. Convert and Check crystallographic structure factors with SF-Tool. The deposited structure factor file should be the one that was used for the final refinement. It can either be in mmCIF, ASCII, or mtz formats and should at least include h, k, l, F, SigmaF (and/or I and SigmaI) and test flags. Definitions and format are available in DOC (48 KB) and PDF (24 KB) format.
  4. Prepare your structural data for deposition using pdb_extract 4, which can extract information from log files and/or the desktop version of ADIT.

  5. THEN

  6. Validate your structure using the new X-ray Validation Server or the older Validation Server for NMR/EDEM..
  7. Deposit your structure using the new wwPDB Deposition system (X-ray only), ADIT, ADIT-NMR, or EMDB.


The Validation Server can also be used to monitor improvements made to your structural model before you begin the deposition process.

Detailed step-by-step instructions for individual structural methods are available.

  • Instructions for X-ray crystallography structure depositions
  • Instructions for NMR structure depositions
  • Instructions for EM structure depositions
  • More information on deposition of structures determined by other methods
    (including Electron diffraction, Fiber diffraction)

Tutorials:
Policies and Procedures

Questions, comments and suggestions should be sent to deposit@deposit.rcsb.org


1 The UniProt Consortium. (2008) "The Universal Protein Resource (UniProt)." Nucleic Acids Res. 36:D190-D195.
2 Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.
3 Feng, Z., Chen, L., Maddula, H., Akcan, O., Oughtred, R., Berman, H.M., & Westbrook, J. (2004) " Ligand Depot: a data warehouse for ligands bound to macromolecules " Bioinformatics 20:2153-2155.
4 Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H.M., & Westbrook, J.D. (2004) " Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. " Acta Cryst. D60, 1833-1839.