Abstract
SummaryThis 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.
Highlights
Validation arose as a major issue in the structural biology community when it became apparent that some published structures contained serious errors (Branden and Jones, 1990)
The community developed a number of validation criteria, and tools to assess these criteria were implemented by the Protein Data Bank (PDB) (Bernstein et al, 1977; Berman et al, 2000), which later expanded to become the Worldwide PDB (Berman et al, 2003)
This paper reports conclusions drawn by the X-ray Validation Task Force (VTF) of the Worldwide PDB
Summary
Validation arose as a major issue in the structural biology community when it became apparent that some published structures contained serious errors (Branden and Jones, 1990). The VTF recommends that the summary validation for each PDB entry containing a protein include the residue category– specific Ramachandran outlier frequency at the level of 1:2000 ($3.5s), available from MolProbity, expressed both as a percent of total residues and as percentile ranks globally and within the resolution class.
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