Improving the accuracy of macromolecular structure refinement at 7 Å resolution.
Improving the accuracy of macromolecular structure refinement at 7 Å resolution.
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DOI：
10.1016/j.str.2012.04.020
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发表时间：
2012-06-06
期刊：
影响因子：
5.7
通讯作者：
Schroeder, Gunnar F.
中科院分区：
文献类型：
--
作者：
Brunger, Axel T.;Adams, Paul D.;Fromme, Petra;Fromme, Raimund;Levitt, Michael;Schroeder, Gunnar F.
在X射线晶体学中，分子置换和随后的细化在低分辨率下具有挑战性。我们比较了细化方法，使用同步辐射衍射数据的光系统I在7.4 μ m的分辨率，从不同的初始模型与已知的高分辨率结构的偏差增加。标准细化破坏了初始模型，使其进一步远离真实结构，并导致高Rfree值。相比之下，DEN细化改进了即使是最遥远的起始模型，如通过Rfree、与真实结构的原子均方根差异、初始模型中未包括的特征的重要性以及电子密度的连通性所判断的。最好的协议是DEN细化与初始分段刚体细化。对于最远的初始模型，在真实结构的2 μ m内的原子分数从24%提高到60%。我们还发现Rfree值与模型的准确性之间存在显著相关性，这表明Rfree即使在低分辨率下也很有用。
In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models moving them further away from the true structure and leading to high Rfree-values. In contrast, DEN-refinement improved even the most distant starting model as judged by Rfree, atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN-refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between Rfree-values and the accuracy of the model, suggesting that Rfree is useful even at low resolution.
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DOI：
10.1107/s0907444909029436
发表时间：
2009-10-01
影响因子：
2.2
作者：
Moriarty, Nigel W.;Grosse-Kunstleve, Ralf W.;Adams, Paul D.
通讯作者：
Adams, Paul D.
影响因子：
5.7
作者：
Schroeder, Gunnar F.;Brunger, Axel T.;Levitt, Michael
通讯作者：
Levitt, Michael
DOI：
10.1107/s0108767386099622
发表时间：
1986-05-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION A
影响因子：
--
作者：
READ, RJ
通讯作者：
READ, RJ
DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH
影响因子：
64.8
作者：
DiMaio, Frank;Terwilliger, Thomas C.;Read, Randy J.;Wlodawer, Alexander;Oberdorfer, Gustav;Wagner, Ulrike;Valkov, Eugene;Alon, Assaf;Fass, Deborah;Axelrod, Herbert L.;Das, Debanu;Vorobiev, Sergey M.;Iwai, Hideo;Pokkuluri, P. Raj;Baker, David
通讯作者：
Baker, David