IUCr journals

Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins

Acta Cryst. (2010). D66, 834-842 (doi.org/10.1107/S0907444910019207)

[Stereochemical libraries] Plots of the main chain (left panel) and N—Ca—C (right panel) r.m.s. bond angle deviation from ideality as a function of the restraint library in test refinements at 1.7 Å and 2.4 Å resolution. CSD-X is the Engh & Huber library and CDL is the new conformation-dependent library. The improved geometry agreement was obtained with no significant change in R factors.

A conceptually novel restraint library with ideal geometry targets parameterized by φ,ψ strongly outperformed the commonly used Engh & Huber library and approached the performance of a 'perfect' library derived from a 1.05 Å resolution model of the test case protein. The results imply that more accurate protein structures at all resolutions will be obtained when refinement packages are modified to account for this new paradigm of ideal geometry functions.

D. E. Tronrud, D. S. Berkholz and P. A. Karplus