Evaluation of Structure Quality Using RCSB PDB Tools

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Evaluation of Structure Quality Using RCSB PDB
Tools
Kyle Burkhardt, Lead Data Annotator The RCSB PDB
at Rutgers University
www.pdb.org info_at_rcsb.org
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Workshop format

• First section
• Learn how to use the RCSB PDB Validation Server
  and evaluate the results
• Second section
• Follow the RCSB PDB Validation Server tutorial
  for a particular structure (with a partner)
• Answer questions about the structure and evaluate
  it

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Why assess structure quality?

• Over 26,000 PDB structures (August 2004)
• Many structures have multiple entries
  (redundancy)
• Some structures are represented only once
• Is the structure well determined?
• Is the overall or detailed information derived
  from it reliable?

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How to assess structure quality?

• RCSB PDB Validation Server
• No single standard (magic number) that all
  structures must meet to be of acceptable quality
• Quality is dependent on
• experimental data
• method of structure solution
• agreement with available geometrical and chemical
  standards

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Steps to validate structural data

• Download mmCIF coordinate sf file
• Upload to the RCSB PDB Validation Server
• Validate
• Evaluate the reports (think!)

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Validation Reports Contain

• Close contacts
• Bond and angle deviations
• Chirality errors
• Sequence/coordinate alignment
• Missing atoms or residues
• Distant waters
• NUCheck1, PROCHECK2, and SFCHECK3 reports

1. Feng Z, Westbrook J, Berman HM.(1998) NUCheck
Rutgers University, New Brunswick, NJ. Report
No. NDB-407. 2. Laskowski, R.A., McArthur,
M.W., Moss, D.S., et al. (1993) PROCHECK a
program to check the stereochemical quality of
protein structures. J. Appl. Cryst. 26283-291.
3. Vaguine A.A., Richelle J., Wodak S.J. (1999)
SFCHECK a unified set of procedures for
evaluating the quality of macromolecular
structure-factor data and their agreement with
the atomic model. Acta Crystallogr. D55191-205.
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What is the overall quality of a structure?

• Dependent on
• The size of the structure
• The resolution and R-factor
• Your evaluation of the validation letter
• Your evaluation of the Ramachandran plot
• Your evaluation of the SFCHECK report
• What youre studying

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Acknowledgements

• The Protein Data Bank (PDB) is operated by
• Rutgers, The State University of New Jersey
• San Diego Supercomputer Center at the
• University of California, San Diego
• Center for Advanced Research in
  Biotechnology/UMBI/NIST
• The RCSB PDB is supported by funds from
• National Science Foundation (NSF)
• National Institute of General Medical Sciences
  (NIGMS)
• Office of Science, Department of Energy (DOE)
• National Library of Medicine (NLM)
• National Cancer Institute (NCI)
• National Center for Research Resources (NCRR)
• National Institute of Biomedical Imaging and
  Bioengineering (NIBIB)
• National Institute of Neurological Disorders and
  Stroke (NINDS)
• The worldwide PDB (wwPDB) is a collaboration
  between
• RCSB
• MSD/EBI