中国物理B ›› 2019, Vol. 28 ›› Issue (7): 76108-076108.doi: 10.1088/1674-1056/28/7/076108

• CONDENSED MATTER: STRUCTURAL, MECHANICAL, AND THERMAL PROPERTIES • 上一篇    下一篇

Enhancement of MAD/MIR phasing at low resolution and a new procedure for automatic phase extension

Pu Han(韩普), Yuan-Xin Gu(古元新), Wei Ding(丁玮), Hai-Fu Fan(范海福)   

  1. 1 Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
    2 School of Physics Science, University of Chinese Academy of Sciences, Beijing 100049, China
  • 收稿日期:2019-05-05 修回日期:2019-05-20 出版日期:2019-07-05 发布日期:2019-07-05
  • 通讯作者: Wei Ding, Hai-Fu Fan E-mail:dingwei@iphy.ac.cn;fan@iphy.ac.cn
  • 基金资助:

    Project supported by the National Basic Research Program of China (Grant No. 2011CB911100) of the Ministry of Science and Technology of China.

Enhancement of MAD/MIR phasing at low resolution and a new procedure for automatic phase extension

Pu Han(韩普)1,2, Yuan-Xin Gu(古元新)1, Wei Ding(丁玮)1, Hai-Fu Fan(范海福)1   

  1. 1 Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
    2 School of Physics Science, University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2019-05-05 Revised:2019-05-20 Online:2019-07-05 Published:2019-07-05
  • Contact: Wei Ding, Hai-Fu Fan E-mail:dingwei@iphy.ac.cn;fan@iphy.ac.cn
  • Supported by:

    Project supported by the National Basic Research Program of China (Grant No. 2011CB911100) of the Ministry of Science and Technology of China.

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摘要：

To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction (MAD) and multiple isomorphous replacement (MIR) phasing can be powerful tools to obtain low-resolution initial phases from heavy-atom derivative datasets, then phase extension is needed against high-resolution data to obtain accurate structures. In this context, we propose a direct-methods procedure here that could improve the initial low-resolution MAD/MIR phase quality. And accordingly, an automated process for extending initial phases to high resolution is also described. These two procedures are both implanted in the newly released IPCAS pipeline. Three cases are used to perform the test, including one set of 4.17 Å MAD data from a membrane protein and two sets of MAD/MIR data with derivatives truncated down to 6.80 Å and 6.90 Å, respectively. All the results have shown that the initial phases generated from the direct-methods procedure are better than that from the conventional MAD/MIR methods. The automated phase extensions for the latter two cases starting from 6.80 Å to 3.00 Å and 6.90 Å to 2.80 Å are proved to be successful, leading to complete models. This may provide convenient and reliable tools for phase improvement and phase extension in difficult low-resolution tasks.

关键词: direct methods, multi-wavelength anomalous diffraction (MAD)/multiple isomorphous replacement (MIR) phasing, phase extension, low-resolution

Abstract:

To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction (MAD) and multiple isomorphous replacement (MIR) phasing can be powerful tools to obtain low-resolution initial phases from heavy-atom derivative datasets, then phase extension is needed against high-resolution data to obtain accurate structures. In this context, we propose a direct-methods procedure here that could improve the initial low-resolution MAD/MIR phase quality. And accordingly, an automated process for extending initial phases to high resolution is also described. These two procedures are both implanted in the newly released IPCAS pipeline. Three cases are used to perform the test, including one set of 4.17 Å MAD data from a membrane protein and two sets of MAD/MIR data with derivatives truncated down to 6.80 Å and 6.90 Å, respectively. All the results have shown that the initial phases generated from the direct-methods procedure are better than that from the conventional MAD/MIR methods. The automated phase extensions for the latter two cases starting from 6.80 Å to 3.00 Å and 6.90 Å to 2.80 Å are proved to be successful, leading to complete models. This may provide convenient and reliable tools for phase improvement and phase extension in difficult low-resolution tasks.

Key words: direct methods, multi-wavelength anomalous diffraction (MAD)/multiple isomorphous replacement (MIR) phasing, phase extension, low-resolution

中图分类号:  (Techniques for structure determination)

  • 61.05.-a