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Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive

Shao, Chenghua ; Yang, Huanwang ; Westbrook, John D. ; Young, Jasmine Y. ; Zardecki, Christine ; Burley, Stephen K.

Structure (London), 2017-03, Vol.25 (3), p.458-468 [Periódico revisado por pares]

United States: Elsevier Ltd

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  • Título:
    Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive
  • Autor: Shao, Chenghua ; Yang, Huanwang ; Westbrook, John D. ; Young, Jasmine Y. ; Zardecki, Christine ; Burley, Stephen K.
  • Assuntos: Crystallography, X-Ray ; Databases, Protein - standards ; Models, Molecular ; multivariate analysis ; Nuclear Magnetic Resonance, Biomolecular ; OneDep ; PDB ; principal component analysis ; Protein Conformation ; protein crystal structure ; Proteins - chemistry ; RCSB ; structure quality ; structure validation ; wwPDB
  • É parte de: Structure (London), 2017-03, Vol.25 (3), p.458-468
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    USDOE
    DBI-1338415
  • Descrição: Following deployment of an augmented validation system by the Worldwide Protein Data Bank (wwPDB) partnership, the quality of crystal structures entering the PDB has improved. Of significance are improvements in quality measures now prominently displayed in the wwPDB validation report. Comparisons of PDB depositions made before and after introduction of the new reporting system show improvements in quality measures relating to pairwise atom-atom clashes, side-chain torsion angle rotamers, and local agreement between the atomic coordinate structure model and experimental electron density data. These improvements are largely independent of resolution limit and sample molecular weight. No significant improvement in the quality of associated ligands was observed. Principal component analysis revealed that structure quality could be summarized with three measures (Rfree, real-space R factor Z score, and a combined molecular geometry quality metric), which can in turn be reduced to a single overall quality metric readily interpretable by all PDB archive users. [Display omitted] •Improved structure quality from the wwPDB OneDep system versus legacy PDB systems•Little change in ligand quality from the OneDep system versus legacy systems•Principal component analyses allow streamlining of OneDep quality metrics Two years after deployment of the wwPDB OneDep Deposition/Annotation/Validation system and official wwPDB validation report, Shao et al. analyzed the individual and condensed structure quality measures, revealing quality improvements in protein crystal structures deposited to the PDB, but little improvement in the quality of bound ligands.
  • Editor: United States: Elsevier Ltd
  • Idioma: Inglês
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