Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Summer 2011
Number 50
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Data Deposition
Deposition Statistics
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Validate Entries Before Deposition
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Deposition Statistics

From April 1-June 30, 2011, 2336 experimentally-determined structures were deposited to the PDB archive. The entries were processed and annotated by wwPDB teams at the RCSB PDB, PDBe, and PDBj. 4542 have been deposited overall in 2011.

Of the structures deposited in the first half of 2011 (Jan 1-June 30), 79.8% were deposited with a release status of "hold until publication"; 17.8% were released as soon as annotation of the entry was complete; and 2.4% were held until a particular date. 92.8% of these entries were determined by X-ray crystallographic methods; 6.3% were determined by NMR methods.

During the same time period (April 1-June 30), 2068 structures were released in the PDB.

wwPDB News

PDB Archive Version 4.0 to be Released July 13, 2011

As announced previously, the wwPDB has performed an ambitious review of the PDB archive resulting in a new set of corrected files that follow the PDB Exchange Dictionary v.4.0. These files will be released on July 13, 2011.

The review involved remediating complex problems, including the representation of biological assemblies, residual B factors, peptide inhibitors and antibiotics, and entries in nonstandard crystal frames. A description of the review and resulting changes and corrections is available as a PDF from the wwPDB website (PDF). Versioning and revision logs will be introduced with this release.

For PDB format files, only the entries that have been changed during this remediation will be updated (<17000). These changes will be identified as version 3.3 of the PDB file format. All files in PDBx/mmCIF and PDBML/XML formats will be updated to reflect the new schema updates. Any changes made to the data will be recorded in the PDBX_VERSION data category and a revision log made for this release that will be available from the wwPDB FTP site.

From July 13, 2011 onward, all new releases and modified entries released will follow the updated formats (PDBx/PDBML v 4.0 and PDB File Format 3.3). Revisions to released entries will be tracked and numbered in the PDBx/mmCIF formatted files.

Users who maintain local copies of the wwPDB FTP can download the new files via rsync (see for more).

A time-stamped snapshot of the PDB archive before this release will be available from

Validate Entries Before Deposition

The Validation Server (

Depositors are encouraged to run data validation checks to monitor improvements made to structural models before deposition. The RCSB PDB's online Validation Server ( can be used to create validation reports outside of the deposition pipeline. Two options are available:

• In the plain text report option, the server first checks the format consistency of the coordinates in the PRECHECK step. The precheck will produce a brief report identifying any changes that need to be made in your data files in order to obtain a validation report. In the validation step, the server produces an Atlas entry, a summary report, and a collection of structural diagnostics including bond distance and angle comparisons, torsion angle comparisons, base morphology comparisons (for nucleic acids), and molecular graphic images. Reports from PROCHECK1, NUCheck2, SFCheck3, and MolProbity4 are made available.

• A new PDF report option produces a report that contains high-level geometric and experimental checking results without listing the detailed geometry. This unofficial report is similar to the wwPDB's PDF report generated during the annotation process for depositors to include with their journal submissions.

The Validation Server is available from the RCSB PDB Deposition Services page at

1. R.A. Laskowski, M.W. McArthur, D.S. Moss, J.M. Thornton (1993) J. Appl. Cryst. 265:283-291.

2. Z. Feng, J. Westbrook, H.M. Berman (1998) NUCheck. NDB-407 Rutgers University, New Brunswick, NJ.

3. A.A. Vaguine, J. Richelle, S.J. Wodak (1999) Acta Crystallogr. D55:191-205.

4. S.C. Lovell, I.W. Davis, B.W. Arendall, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson (2003) Protein Struct. Funct. Genet. 50:437-450.

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