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首页> 美国卫生研究院文献>Acta Crystallographica Section D: Biological Crystallography >Improving macromolecular atomic models at moderate resolution by automated iterative model building statistical density modification and refinement
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Improving macromolecular atomic models at moderate resolution by automated iterative model building statistical density modification and refinement

机译：通过自动迭代模型构建统计密度修改和细化来改善中等分辨率的大分子原子模型

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摘要

An iterative process for improving the completeness and quality of atomic models automatically built at moderate resolution (up to about 2.8 Å) is described. The process consists of cycles of model building interspersed with cycles of refinement and combining phase information from the model with experimental phase information (if any) using statistical density modification. The process can lead to substantial improvements in both the accuracy and completeness of the model compared with a single cycle of model building. For eight test cases solved by MAD or SAD at resolutions ranging from 2.0 to 2.8 Å, the fraction of models built and assigned to sequence was 46–91% (mean of 65%) after the first cycle of building and refinement, and 78–­95% (mean of 87%) after 20 cycles. In an additional test case, an incorrect model of gene 5 protein (PDB code 2gn5; r.m.s.d. of main-chain atoms from the more recent refined structure 1vqb at 1.56 Å) was rebuilt using only structure-factor amplitude information at varying resolutions from 2.0 to 3.0 Å. Rebuilding was effective at resolutions up to about 2.5 Å. The resulting models had 60–­80% of the residues built and an r.m.s.d. of main-chain atoms from the refined structure of 0.20 to 0.62 Å. The algorithm is useful for building preliminary models of macromolecules suitable for an experienced crystallographer to extend, correct and fully refine.
机译：描述了一种迭代过程，该过程可提高以中等分辨率（最大约2.8Å）自动建立的原子模型的完整性和质量。该过程包括模型构建的周期和精细化的周期，并使用统计密度修正将模型的相信息与实验相信息（如果有）组合在一起。与建立模型的单个周期相比，该过程可以大大提高模型的准确性和完整性。对于通过MAD或SAD在2.0至2.8？Å分辨率范围内求解的八个测试用例，在第一个构建和完善周期之后，构建并分配给序列的模型的比例为46–91％（平均值为65％），而78– 20个循环后达到95％（平均值为87％）。在另一个测试案例中，仅使用结构因子振幅信息以不同的分辨率（从2.0到1.5）重建了不正确的基因5蛋白模型（PDB代码2gn5；来自最新精制结构1vqb的主链原子的均方根均方根值在1.56Å）。 3.0Å。重建在高达约2.5Å的分辨率下有效。生成的模型具有60-­80％的残留物残留量和r.m.s.d.主链原子从0.20到0.620.6Å的精细结构。该算法可用于建立适合有经验的晶体学家扩展，校正和完全精炼的大分子的初步模型。

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