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Updated X-ray Validation Reports for Archived PDB Structures Now Available

03/15

The wwPDB partners are pleased to announce that updated validation reports for all X-ray crystal structures deposited in the PDB archive were made available on March 9, 2016.

The updates include:

  • New percentile statistics reflecting the state of the PDB archive on December 30th 2015
  • Updated versions for component software packages:
    • CCP4 V6.5 (Refmac 5.8.0135)
    • Mogul 2015 (CSD archive as536be)
  • Improvements in the way that Mogul analysis of ligand geometry is performed
  • Clearer graphical elements for representing quality of macromolecular chains
  • Improvements to make the report text clearer
  • Updated user guide and FAQs

The updated reports are accessible from the following FTP sites:

  • ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
  • ftp://ftp.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
  • ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
  • ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

A copy of the previous version is archived at RCSB PDB and PDBj.

These updated wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, recommended by community experts serving in the Validation Task Force. 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 wwPDB logo, and contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by eLife, The Journal of Biological Chemistry, the International Union of Crystallography (IUCr) journals, FEBS journals, and the Journal of Immunology as part of their manuscript-submission process.

Validation reports are also provided to depositors in the new wwPDB Deposition and Annotation System. Depositors are required to review and accept the reports as part of the data submission process. Going forward validation reports will be further developed and improved as we receive recommendations from the expert Validation Task Forces (VTF) for X-ray, NMR, and EM, as we develop the wwPDB Deposition & Annotation (D&A) system, and as we collect feedback from depositors and users.

The earlier version of the X-ray structure-validation reports have been provided to depositors as part of the structure-annotation process since August 2013. They were first made public in March 2014.

Similar reports for structures determined by Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) will become available in May 2016.

Further information and sample X-ray validation reports are available.

Your feedback, comments, and questions are welcome at validation@mail.wwpdb.org.



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