New parameters for the refinement of nucleic acid-containing structures
New parameters for the refinement of nucleic acid-containing structures
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DOI：
10.1107/s0907444995011115
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发表时间：
1996-01-01
期刊：
影响因子：
--
通讯作者：
Berman, HM
中科院分区：
文献类型：
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作者：
Parkinson, G;Vojtechovsky, J;Berman, HM
从核酸数据库或剑桥结构数据库中选择含有碱基、糖或磷酸二酯键的原子分辨率（高达1.0埃）的结构，以从X射线精细结构构建核酸字典。字典由键距、键角和二面角的平均值组成。样本的方差用于提供有关预期均方根的信息。精确参数的偏差。在X-PLOR中构建了用于精化试验的字典。字典包括RNA和DNA在C2 '-endo和C3'-endo糖折叠构象，以及骨干二面角的值。使用三种结构对字典进行测试：B-DNA，Z-DNA和蛋白质-DNA复合物。在改进过程中，所有三种结构都显示出显著的改进，如通过r.m.s.与之前的DNA词典相比，偏差和R因子。
Structures at atomic resolution (up to 1.0 Angstrom) which contain bases, sugars or the phosphodiester linkage, were selected from the Nucleic Acid Database or the Cambridge Structural Database to build a nucleic acid dictionary from X-ray refined structures. The dictionary consists of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information about the expected r.m.s. deviations of the refined parameters. A dictionary was constructed for refinement trials in X-PLOR. The dictionary includes RNA and DNA in C2'-endo and C3'-endo sugar pucker conformations, as well as values for the backbone dihedrals. Tests were performed on the dictionary using three structures: a B-DNA, a Z-DNA and a protein-DNA complex. During the course of refinement, all three structures showed significant improvements as measured by r.m.s. deviations and R factors when compared to the previous DNA dictionary.