Zhou G, Wang J, Blanc E, Chapman M S
Department of Chemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-3015, USA.
Acta Crystallogr D Biol Crystallogr. 1998 May 1;54(Pt 3):391-9. doi: 10.1107/s0907444997011530.
Several real-space indices and temperature factors are compared with respect to their correlation with atomic positional error and their ability to indicate atoms and residues with the worst of subtle errors. The best index, rED, is a correlation coefficient between model and map electron densities, similar to one proposed earlier, but incorporating two improvements. Firstly, resolution is accounted for explicitly by calculating the model electron density by Fourier transformation of resolution-truncated scattering factors. Secondly, the deviation between model and map electron densities is assigned to neighboring atoms according to their contribution to the electron density of each grid point. With maps of various qualities, rED is the single index with best correlation to atomic error with grouped or individual atoms, and it is the most reliable indicator of poor residues. With poorer omit maps, imprecision of individual atoms is best diagnosed by a combination of low rED or high B factor. With the improved methods, 60-70% of the least precise atoms can detected in a fully refined structure. Similarly, 40-80% of the least precise atoms of an unrefined model can be detected by comparison with an isomorphous replacement map. This is useful in assessing and improving the quality of a model, but not sufficient to confidently validate all atoms of a structure at sub-atomic resolution.
比较了几种实空间指标和温度因子与原子位置误差的相关性，以及它们指示存在最细微误差的原子和残基的能力。最佳指标rED是模型与电子密度图之间的相关系数，与之前提出的一个指标类似，但有两点改进。首先，通过对分辨率截断的散射因子进行傅里叶变换来计算模型电子密度，从而明确考虑了分辨率。其次，根据模型与电子密度图之间的电子密度偏差对相邻原子的贡献，将其分配给相邻原子。对于各种质量的电子密度图，rED是与成组或单个原子的原子误差相关性最好的单一指标，也是残基质量差的最可靠指标。对于质量较差的省略图，通过低rED或高B因子的组合可以最好地诊断单个原子的不精确性。采用改进方法后，在完全精修的结构中可以检测到60%-70%最不精确的原子。同样，通过与同晶置换图比较，可以检测到未精修模型中40%-80%最不精确的原子。这对于评估和提高模型质量很有用，但不足以在亚原子分辨率下可靠地验证结构中的所有原子。
