(1) Department of Chemistry, Purdue University, West Lafayette, IN, 47907, U.S.A.
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
virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation).
On the other hand, unfavorable
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.
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