Journal of Biomolecular NMR

, Volume 33, Issue 2, pp 83–93

Estimating the Accuracy of Protein Structures using Residual Dipolar Couplings

Authors

  • Katya Simon
    • Department of ChemistryPurdue University
  • Jun Xu
    • Department of ChemistryPurdue University
  • Chinpal Kim
    • Department of ChemistryPurdue University
    • Department of ChemistryPurdue University
Article

DOI: 10.1007/s10858-005-2601-7

Cite this article as:
Simon, K., Xu, J., Kim, C. et al. J Biomol NMR (2005) 33: 83. doi:10.1007/s10858-005-2601-7

Abstract

It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H–15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable values \(\tilde{R}\) virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable \(\tilde{R}\) values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.

Keywords

NMRPALES softwarePDZ2 domain from human phosphatase hPTP1Eprecision and accuracy of protein structuresresidual dipolar couplingsX-ray crystallography

Supplementary material

supp.pdf (181 kb)
Supplementary material

Copyright information

© Springer 2005