McCoy Airlie J, Read Randy J
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 OXY, England.
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. doi: 10.1107/S0907444910006335. Epub 2010 Mar 24.
Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real-imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods.
本文综述了通过实验相位法测定蛋白质晶体结构的进展，重点强调了实验相位法、密度修正、模型构建和精修之间的理论连续性。讨论了亚结构组成的传统概念以及生成图谱的最佳系数。详细讨论了诸如确定对映体、识别亚结构中的中心对称（或伪对称）以及晶体孪晶等陷阱。附录介绍了用于单波长反常散射（SAD）相位法的实部-虚部对数似然梯度图谱系数，以及它们在软件Phaser中用于亚结构完成的应用。补充材料包括动画概率哈克图，展示了基于最大似然的相位法如何用于单同晶置换（SIR）和多同晶置换（MIR）情况下的参数精修；希望这些对教授实验相位法最佳实践的人员有所帮助。
