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 usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward 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. Structure. >17, 1316). 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 conformation dependent library 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 usage 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 modelling accuracy.
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机译：用作外部约束的键角和长度的理想值对于除最高分辨率外的所有蛋白晶体结构的成功细化都是至关重要的。如今，在通常使用的约束条件是基于以下假设而设计的：每种键或角度类型都具有独立于上下文的单个理想值。但是，最近的工作表明，理想值实际上对局部构象敏感，作为使用此类信息构建更准确模型的第一步，超高分辨率蛋白质晶体结构已用于推导构象，蛋白质骨架约束的依赖库（CDL）（Berkholz et al。2009. Structure。> 17 ，1316）。在这里，我们报告了该CDL在Phenix软件包中的引入，以及在各种分辨率下对数千种结构进行测试改进的结果。这些测试表明，使用依赖于构象的文库可产生与理想主链键角和长度具有更好的一致性的模型，并且平均而言，对X射线数据的拟合度略有提高。没有发现使用主干CDL的缺点。在Phenix中，只需指定cdl = True选项就可以选择CDL的用法。这种成功的实现为理想几何图形的上下文相关性的进一步方面奠定了基础，并为提高实验和预测建模精度提供了依据。
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