Adams P D, Pannu N S, Read R J, Brunger A T
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):181-90. doi: 10.1107/S0907444998006635. Epub 1999 Jan 1.
Phases determined by the molecular-replacement method often suffer from model bias. In extreme cases, the refinement of the atomic model can stall at high free R values when the resulting electron-density maps provide little indication of how to correct the model, sometimes rendering even a correct solution unusable. Here, it is shown that several recent advances in refinement methodology allow productive refinement, even in cases where the molecular-replacement-phased electron-density maps do not allow manual rebuilding. In test calculations performed with a series of homologous models of penicillopepsin using either backbone atoms, or backbone atoms plus conserved core residues, model bias is reduced and refinement can proceed efficiently, even if the initial model is far from the correct one. These new methods combine cross-validation, torsion-angle dynamics simulated annealing and maximum-likelihood target functions. It is also shown that the free R value is an excellent indicator of model quality after refinement, potentially discriminating between correct and incorrect molecular-replacement solutions. The use of phase information, even in the form of bimodal single-isomorphous-replacement phase distributions, greatly improves the radius of convergence of refinement and hence the quality of the electron-density maps, further extending the limits of molecular replacement.
由分子置换法确定的相位常常存在模型偏差。在极端情况下，当所得电子密度图几乎无法指示如何校正模型时，原子模型的精修可能会在高自由R值处停滞，有时甚至会使正确的解也无法使用。本文表明，精修方法学的几项最新进展能够实现有效的精修，即使在分子置换相位电子密度图不允许手动重建的情况下也是如此。在用一系列青霉胃蛋白酶同源模型进行的测试计算中，使用主链原子或主链原子加保守核心残基，即使初始模型与正确模型相差甚远，模型偏差也会减小，精修能够有效进行。这些新方法结合了交叉验证、扭转角动力学模拟退火和最大似然目标函数。本文还表明，自由R值是精修后模型质量的一个极佳指标，有可能区分正确和错误的分子置换解。即使以双峰单同晶置换相位分布的形式使用相位信息，也能极大地提高精修的收敛半径，从而提高电子密度图的质量，进一步扩展分子置换的极限。
