A new generation of crystallographic validation tools for the protein data bank

Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006.


This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Advisory Committees
  • Crystallography, X-Ray / standards*
  • Databases, Protein / standards*
  • Hydrogen Bonding
  • Protein Conformation
  • Proteins / chemistry*
  • Quality Control
  • Sequence Analysis, Protein
  • Software
  • X-Ray Diffraction / standards


  • Proteins