The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the phi/psi angle of the residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm.
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机译：主要的大分子晶体精致包约束模型的理想几何目标定义为单一值是独立的分子构象。然而,超高分辨率x射线的模型蛋白质是不符合这个概念理想,用于开发一个图书馆理想的主链键的长度和角度由φ和ψ角参数化的残留[Berkholz et al。(2009),结构,17日1316 - 1325年)。conformation-dependent图书馆不受与超高分辨率从贫穷的协议结构,而当前图书馆问题。然后表明,蛋白质结构细化使用这个conformation-dependent图书馆的结果在模型有更好的协议图书馆的键角值几乎没有变化在R值。修改细化软件账户新的范例。
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