Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

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Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common use today have been designed on the assumption that each type of bond or angle has a single ideal value that is independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and, as a first step towards using such information to build more accurate models, ultra-high-resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone [Berkholz et al. (2009) Structure17, 1316–1325]. Here, we report the introduction of this CDL into the phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the CDL yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In phenix, use of the CDL can be selected by simply specifying the cdl = True option. This successful implementation paves the way for further aspects of the context dependence of ideal geometry to be characterized and applied to improve experimental and predictive modeling accuracy.Ultra-high resolution protein crystal structures have revealed inadequacies of current covalent geometry restraints. Here, a novel library defining ø,ψ and residue-type dependent backbone bond angle and length restraints is incorporated into all geometry-based Phenix programs. Refinement using this library yields models with substantially better agreement with ideal backbone geometry and, on average, slightly enhanced fits to the X-ray data.

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