Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering
文献类型：期刊论文
| 作者 | Ockwell, DM ; Hough, MA ; Grossmann, JG ; Hasnain, SS ; Hao, Q |
| 刊名 | ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
 |
| 出版日期 | 2000 |
| 卷号 | 56页码:1002 |
| 关键词 | SMALL-ANGLE SCATTERING DIRECT SHAPE DETERMINATION COMPLEX PACKAGE |
| ISSN号 | 0907-4449 |
| 通讯作者 | Hao, Q: De Montfort Univ, Dept Chem, Leicester LE1 9BH, Leics, England. |
| 中文摘要 | Solution of the phase problem is central to crystallographic structure determination. The conventional methods of isomorphous replacement (MIR or SIR) and molecular replacement are ineffective in the absence of a suitable isomorphous heavy-atom derivative or knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has shown to be successful in locating the molecular shape within the crystallographic unit cell in the case of the trimer nitrite reductase (NiR, 105 kDa) [Hao et al. (1999), Acta Cryst. D55, 243-246]. This was achieved by performing a direct real-space search for orientation and translation using knowledge of the orientation of the polar angles of the non-crystallographic axis obtained by performing a self-rotation on crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle and three translational parameters). In the case of NiR, the direct four-dimensional search produced a clear solution that was in good agreement with the known structure. The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups and in particular those in possession of non-crystallographic symmetry. However, the method employed was initially unsuccessful when applied to the small dimeric molecule superoxide dismutase (SOD, 32 kDa) owing to the absence of strong reflections at low resolution caused by saturation at the detector. The determined solution deviated greatly from that of the known structure [Hough & Hasnain (1999), J. Mol. Biol. 287, 579-592]. It was found that once these absent reflections were replaced by a series of randomly generated intensity values and cluster analysis was performed on the output, the signal-to-noise ratio was improved and a most probable solution was found. The electron-density map of the stochastically determined solution agrees well with the known structure; the phase error calculated from this map was 67 degrees within 14 Angstrom resolution. |
| 收录类别 | SCI |
| 语种 | 英语 |
| 公开日期 | 2013-09-17 |
| 源URL | [http://ir.iphy.ac.cn/handle/311004/39640]  |
| 专题 | 物理研究所_物理所公开发表论文_物理所公开发表论文_期刊论文 |
| 推荐引用方式 GB/T 7714 | Ockwell, DM,Hough, MA,Grossmann, JG,et al. Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering[J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY,2000,56:1002. |
| APA | Ockwell, DM,Hough, MA,Grossmann, JG,Hasnain, SS,&Hao, Q.(2000).Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering.ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY,56,1002. |
| MLA | Ockwell, DM,et al."Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering".ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 56(2000):1002. |
入库方式： OAI收割
来源：物理研究所
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