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Evaluation of Structure Quality Using RCSB PDB Tools

Evaluation of Structure Quality Using RCSB PDB Tools. Kyle Burkhardt, Data Annotation Leader The RCSB PDB at Rutgers University. www.pdb.org deposit@rcsb.org. Workshop format. In class Learn how to use the RCSB PDB Validation Server and evaluate the results Homework

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Evaluation of Structure Quality Using RCSB PDB Tools

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  1. Evaluation of Structure Quality Using RCSB PDB Tools Kyle Burkhardt, Data Annotation Leader The RCSB PDB at Rutgers University www.pdb.org deposit@rcsb.org

  2. Workshop format • In class • Learn how to use the RCSB PDB Validation Server and evaluate the results • Homework • Follow the RCSB PDB Validation Server tutorial for a particular structure • Answer questions about the structure and evaluate it

  3. Why assess structure quality? • Over 39,000 PDB structures (October 2006) • 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?

  4. 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

  5. Steps to validate structural data • Download mmCIF coordinate & sf file • Upload to the RCSB PDB Validation Server • Validate • Evaluate the reports (think!)

  6. Validation Reports Contain • Close contacts • Bond and angle deviations • Chirality errors • Sequence/coordinate alignment • Missing atoms or residues • Distant waters • NUCheck, PROCHECK1, SFCHECK2 ,MolProbity3 Reports 1. 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. 26:283-291. 2. 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. D55:191-205. 3. Lovell SC, Davis IW, Arendall III WB, de Bakker, PIW, Word JM,Prisant MG, Richardson JS, Richardson DC (2003). Structure Validation by C-alpha Geometry: phi, psi and C-beta Deviation. PROTEINS: Structure, Function, and Genetics, 50, 437-450.

  7. Online Validation Tutorial Go to: http://pdb-linux-37.rutgers.edu/validemo/index.html

  8. 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 MolProbity plot • Your evaluation of the SFCHECK report • What you’re studying

  9. 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 • 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) • National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) • The worldwide PDB (wwPDB) is a collaboration between • RCSB • MSD/EBI • PDBj

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