Considerations for the refinement of low-resolution crystal structures
Considerations for the refinement of low-resolution crystal structures
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DOI：
10.1107/s0907444906012650
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发表时间：
2006-08-01
影响因子：
2.2
通讯作者：
Brunger, Axel T.
中科院分区：
文献类型：
--
作者：
DeLaBarre, Byron;Brunger, Axel T.
通常认为晶体结构必须以足够高的分辨率获得，以便进行大分子的细化。在最近的几个结构中，被认为是“可接受”的阈值已被推到较低的衍射分辨率。本文描述了用于解决和改进ATPase p97/VCP的一组特定低分辨率结构的标准改进协议的注意事项和修改。发现在细化后，包括实验相信息以及在低至4.7埃的衍射极限下明智地使用约束，可以获得合理的无r值和良好的几何形状。在这一分辨率下，拓扑结构和主链轨迹大部分被定义，一些侧链的位置可以明确地分配，并且可以识别已知结合位点内的配体。此外，当不同状态的结构可用时，可以识别出大的构象变化，这些信息不易通过其他方法获得。
It is often assumed that crystal structures have to be obtained at sufficiently high resolution in order to perform macromolecular refinement. In several recent structures, the threshold of what is considered `acceptable' has been pushed to lower diffraction resolutions. Here, considerations and modifications to standard refinement protocols are described that were used to solve and refine a particular set of lowresolution structures for the ATPase p97/VCP. It was found that reasonable R-free values and good geometry can be achieved upon refinement that includes experimental phase information along with judicious use of restraints at diffraction limits as low as 4.7 angstrom. At this resolution, the topology and the backbone- chain trace are mostly defined, some side- chain positions can be unambiguously assigned and ligands within known binding sites can be identified. Furthermore, large conformational changes can be discerned when structures in different states are available, information that is not easily obtainable by other means.