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

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

doi:10.1016/j.str.2017.01.013

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

Structure. 2017 Mar 7;25(3):458-468. doi: 10.1016/j.str.2017.01.013. Epub 2017 Feb 16.

Authors

Chenghua Shao¹, Huanwang Yang², John D Westbrook³, Jasmine Y Young², Christine Zardecki², Stephen K Burley⁴

Affiliations

¹ RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers University, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA. Electronic address: chenghua.shao@rcsb.org.
² RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers University, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
³ RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers University, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers University, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁴ RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers University, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers University, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08903, USA; RCSB Protein Databank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.

Abstract

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.

Keywords: OneDep; PDB; RCSB; multivariate analysis; principal component analysis; protein crystal structure; structure quality; structure validation; wwPDB.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Crystallography, X-Ray
Databases, Protein / standards*
Models, Molecular
Nuclear Magnetic Resonance, Biomolecular
Protein Conformation
Proteins / chemistry*

Substances

Proteins

Grants and funding

R01 GM133198/GM/NIGMS NIH HHS/United States