Macromolecular refinement by model morphing using non-atomic parameterizations.
Macromolecular refinement by model morphing using non-atomic parameterizations.
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DOI：
10.1107/s205979831701350x
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发表时间：
2018-02-01
期刊：
影响因子：
--
通讯作者：
Agirre J
中科院分区：
文献类型：
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作者：
Cowtan K;Agirre J
描述了一种根据一组不依赖于原子参数的结构因素观测来改进电子密度模型的方法。可以改变参数化中的有效细节级别，以确保在数据支持的任何分辨率下很好地确定细化。精炼是确定模型的关键步骤，该模型解释了结晶学观察，从而最好地解释了缺失的相成分。散射密度通常用原子参数来描述；然而，在大分子结晶学中，数据的分辨率通常不足以确定单个原子的这些参数的值。立体化学和几何约束用于提供附加信息，但会产生参数之间的相互关系，从而减缓收敛速度，导致更长的精化时间。提出了另一种方法，其中参数不是附加到原子，而是附加到电子密度图的区域。这些参数可以改变密度或改变局部温度因子，以更好地解释结构因素。改变确定地图中特定位置的参数的区域的大小允许在不使用约束的情况下以不同的分辨率应用该方法。潜在的应用包括用域运动对分子置换模型进行初始改进，以及潜在地使用来自其他来源的电子密度作为改进模型，例如电子冷冻显微镜(Cryo-EM)。
A method is described for the refinement of an electron-density model against a set of structure-factor observations which does not rely on atomic parameters. The effective level of detail in the parameterization can be varied to ensure that the refinement is well determined at any resolution supported by the data. Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.