A new generation of crystallographic validation tools for the Protein Data Bank

Randy J. Read, Paul D. Adams, W. Bryan Arendall, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas Lütteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend, Peter H. Zwart

Research output: Contribution to journalArticle

276 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1395-1412
Number of pages18
JournalStructure
Volume19
Issue number10
DOIs
StatePublished - Oct 12 2011

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Databases
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Proteins
X-Rays

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

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Read, R. J., Adams, P. D., Arendall, W. B., Brunger, A. T., Emsley, P., Joosten, R. P., ... Zwart, P. H. (2011). A new generation of crystallographic validation tools for the Protein Data Bank. Structure, 19(10), 1395-1412. https://doi.org/10.1016/j.str.2011.08.006

A new generation of crystallographic validation tools for the Protein Data Bank. / Read, Randy J.; Adams, Paul D.; Arendall, W. Bryan; Brunger, Axel T.; Emsley, Paul; Joosten, Robbie P.; Kleywegt, Gerard J.; Krissinel, Eugene B.; Lütteke, Thomas; Otwinowski, Zbyszek; Perrakis, Anastassis; Richardson, Jane S.; Sheffler, William H.; Smith, Janet L.; Tickle, Ian J.; Vriend, Gert; Zwart, Peter H.

In: Structure, Vol. 19, No. 10, 12.10.2011, p. 1395-1412.

Research output: Contribution to journalArticle

Read, RJ, Adams, PD, Arendall, WB, Brunger, AT, Emsley, P, Joosten, RP, Kleywegt, GJ, Krissinel, EB, Lütteke, T, Otwinowski, Z, Perrakis, A, Richardson, JS, Sheffler, WH, Smith, JL, Tickle, IJ, Vriend, G & Zwart, PH 2011, 'A new generation of crystallographic validation tools for the Protein Data Bank', Structure, vol. 19, no. 10, pp. 1395-1412. https://doi.org/10.1016/j.str.2011.08.006
Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP et al. A new generation of crystallographic validation tools for the Protein Data Bank. Structure. 2011 Oct 12;19(10):1395-1412. https://doi.org/10.1016/j.str.2011.08.006
Read, Randy J. ; Adams, Paul D. ; Arendall, W. Bryan ; Brunger, Axel T. ; Emsley, Paul ; Joosten, Robbie P. ; Kleywegt, Gerard J. ; Krissinel, Eugene B. ; Lütteke, Thomas ; Otwinowski, Zbyszek ; Perrakis, Anastassis ; Richardson, Jane S. ; Sheffler, William H. ; Smith, Janet L. ; Tickle, Ian J. ; Vriend, Gert ; Zwart, Peter H. / A new generation of crystallographic validation tools for the Protein Data Bank. In: Structure. 2011 ; Vol. 19, No. 10. pp. 1395-1412.
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