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New wwPDB X-ray structure validation reports

As of August 1, 2013, the wwPDB sites that process depositions of X-ray crystal structures (PDBe, PDBj, and RCSB PDB) provide depositors with new detailed reports (as PDF files) that include the results of model and experimental data validation, as part of the curation process (announcement).

As these wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, the wwPDB partners strongly encourage journal editors and referees to request them from authors as part of the manuscript submission and review process. The reports are date-stamped and display the logo of the wwPDB site where the entry was curated. They contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by the Journal of Biological Chemistry and the International Union of Crystallography (IUCr) journals as part of their manuscript-submission process.

The validation reports continue to be developed and improved as we receive recommendations from the expert Validation Task Forces (VTF) for X-ray, NMR, and EM, as we develop the new wwPDB Deposition & Annotation (D&A) system, and as we collect feedback from depositors and users.

Depositors of X-ray crystal structures receive the new validation reports in addition to the old-style annotation reports produced by the current deposition systems (ADIT and AUTODEP). A brief user guide that describes and explains the contents of the new X-ray validation reports is available on the wwPDB website. We encourage depositors to submit the new X-ray validation reports to journals along with their manuscripts.

Useful links and resources

  • X-ray VTF: Homepage and report
  • NMR VTF: Homepage (report is in press, Structure)
  • EMDataBank 3DEM VTF: Homepage and report
  • New Validation Report announcement
  • New Validation Report User Guide
  • Sample validation report PDFs for:
    • 1CBS, a 1.8Å structure of a small protein and a ligand, an entry with better overall quality relative to all X-ray structures
    • 1FCC, a 3.2Å structure with worse overall quality relative to all X-ray structures
    • 1EG1, a 3.6Å structure with possible ligand geometry and fit to density issues
  • Deposit a crystal structure now at PDBe, PDBj or RCSB PDB

Please send any comments, questions or suggestions on these new reports to validation@mail.wwpdb.org

Summary Validation Report FAQ

Question 1: What information will be made available about a deposited structure before the coordinates and experimental data are released?

Similar to a typical manuscript submission process (where information is confidential until a paper is published), only limited information is made publicly available prior to release of a PDB entry (see also Question 2).

The validation reports are sent only to the depositors (who may choose to submit them with their manuscripts). They include the results of geometry checks, structure factor validation, and ligand validation. Coordinates and experimental data are not included in the validation report.

Mandatory submission of wwPDB validation reports has not had an impact on the number of submissions to IUCr journals.

Question 2: What is the timing on making information about a deposited structure publicly available? What is the timing for releasing the coordinates, etc.?

The new validation reports are generated for X-ray crystal structures as part of the current wwPDB curation pipelines, and do not affect any timings.

When a structure has been deposited, only the author list, entry title, and release status (along with the pre-release sequence, if allowed by the depositor) are made publicly available with the next weekly PDB update. The entry title may be suppressed upon request.

Once a PDB entry is finalised and approved by the authors, structures can be released as close to the publication date as our update procedures allow.

Question 3: How much control do authors have over the release of information?

The validation reports are only provided to the depositors, not to journals or other third parties. Depositors thus maintain complete control over the distribution of their validation reports to any journals, co-authors, or other individuals or third parties. Depositors also determine the entry's release status at the time of deposition, typically subject to requirements of the journal in which they aim to publish.

Question 4: I have deposited a structure with the PDB but not received a report. Why not?

The new style validation reports are only provided for new depositions of X-ray crystal structures and subject to the successful completion of the underlying calculations. For instance, no reports are created for NMR or 3DEM structures, and occasionally a software problem may preclude generation of a report for an X-ray structure (we endeavour to fix any such problems as soon as possible, where needed in collaboration with the authors of the software).

Question 5: The validation report only lists up to 5 outliers - what if I want to see more?

In the future, in addition to the summary reports in PDF form, wwPDB will also provide an XML file for every entry that contains exhaustive information on all statistics, complete lists of outliers, etc.

Question 6: Can I get a validation report for an existing X-ray structure in the PDB?

Early in 2014, validation reports (PDF and XML files) for all existing X-ray crystal structures in the PDB archive will be made publicly available through the wwPDB ftp sites.

In the future, wwPDB plans to recalculate statistical distributions as well as validation reports for all entries once a year. All these data will be made publicly available to encourage downstream use by software developers, bioinformaticians and other PDB users.

In addition, wwPDB expects to reconvene VTFs once every 5 years or so to assess the validation pipelines, reports and protocols and to recommend any changes, updates or additions.

Question 7: Can I get a validation report for my own intermediate or unpublished structure?

Later this year, wwPDB will launch a separate web service, which can be used to run the validation software pipeline on your own structures, prior to deposition.


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