Molding atomic structures into intermediate-resolution Cryo-EM density maps of ribosomal complexes using real-space refinement
Molding atomic structures into intermediate-resolution Cryo-EM density maps of ribosomal complexes using real-space refinement
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DOI：
10.1016/j.str.2005.01.004
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发表时间：
2005-03-01
期刊：
影响因子：
5.7
通讯作者：
Frank, J
中科院分区：
文献类型：
--
作者：
Gao, HX;Frank, J
实空间细化之前已被引入作为一种灵活的拟合方法，用于根据原子结构解释中等分辨率冷冻电镜密度图。通过这种方式，可以在分子水平上分析与功能过程相关的构象变化。在将该技术应用于核糖体时，衍生出了准原子模型，这增进了我们对易位的理解。在本文中，讨论了拟合过程的参数选择。拟合的质量主要取决于模型被划分为的刚性部分的数量。合适的质量指标是互相关、R 因子和密度残差，所有这些指标也可以局部应用。核糖体的例子可以为现实空间细化到灵活拟合问题的一般应用提供一些指导。
Real-space refinement has been previously introduced as a flexible fitting method to interpret medium-resolution cryo-EM density maps in terms of atomic structures. In this way, conformational changes related to functional processes can be analyzed on the molecular level. In the application of the technique to the ribosome, quasiatomic models have been derived that have advanced our understanding of translocation. In this article, the choice of parameters for the fitting procedure is discussed. The quality of the fitting depends critically on the number of rigid pieces into which the model is divided. Suitable quality indicators are crosscorrelation, R factor, and density residual, all of which can also be locally applied. The example of the ribosome may provide some guidelines for general applications of real-space refinement to flexible fitting problems.