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具有平移无序的晶体衍射的从头算相位分析。

Ab initio phasing of the diffraction of crystals with translational disorder.

作者信息

Morgan Andrew J, Ayyer Kartik, Barty Anton, Chen Joe P J, Ekeberg Tomas, Oberthuer Dominik, White Thomas A, Yefanov Oleksandr, Chapman Henry N

机构信息

Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Department of Physics, Arizona State University, Tempe, AZ, 85287, USA.

出版信息

Acta Crystallogr A Found Adv. 2019 Jan 1;75(Pt 1):25-40. doi: 10.1107/S2053273318015395.

DOI:10.1107/S2053273318015395
PMID:30575581
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6302929/
Abstract

To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined against the set of observed Bragg reflections from a protein crystal. The resolution of the refined protein structure is limited by the highest angle at which Bragg reflections can be observed. In addition, the Bragg reflections alone are typically insufficient (by a factor of two) to determine the structure ab initio, and so prior information is required. Crystals formed from an imperfect packing of the protein molecules may also exhibit continuous diffraction between and beyond these Bragg reflections. When this is due to random displacements of the molecules from each crystal lattice site, the continuous diffraction provides the necessary information to determine the protein structure without prior knowledge, to a resolution that is not limited by the angular extent of the observed Bragg reflections but instead by that of the diffraction as a whole. This article presents an iterative projection algorithm that simultaneously uses the continuous diffraction as well as the Bragg reflections for the determination of protein structures. The viability of this method is demonstrated on simulated crystal diffraction.

摘要

迄今为止,X射线蛋白质晶体学是用于确定生物分子及其复合物高分辨率三维结构的最成功技术。在X射线蛋白质晶体学中,蛋白质的结构是根据从蛋白质晶体观察到的一组布拉格反射进行精修的。精修后的蛋白质结构分辨率受可观察到布拉格反射的最高角度限制。此外,仅布拉格反射通常不足以(相差两倍)从头确定结构,因此需要先验信息。由蛋白质分子不完全堆积形成的晶体在这些布拉格反射之间及之外也可能表现出连续衍射。当这是由于分子从每个晶格位点的随机位移导致时,连续衍射提供了无需先验知识即可确定蛋白质结构的必要信息,其分辨率不受观察到的布拉格反射角度范围的限制,而是受整个衍射的角度范围限制。本文提出了一种迭代投影算法,该算法同时使用连续衍射和布拉格反射来确定蛋白质结构。该方法的可行性在模拟晶体衍射上得到了证明。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/95789d1f063c/a-75-00025-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/c4c176eedb22/a-75-00025-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/d4eb563d638e/a-75-00025-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/be045edff05b/a-75-00025-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/7a5c99c41fb7/a-75-00025-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/8e5da35cfec6/a-75-00025-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/95789d1f063c/a-75-00025-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/c4c176eedb22/a-75-00025-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/d4eb563d638e/a-75-00025-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/be045edff05b/a-75-00025-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/7a5c99c41fb7/a-75-00025-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/8e5da35cfec6/a-75-00025-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ed8/6302929/95789d1f063c/a-75-00025-fig6.jpg

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2
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3
Macromolecular diffractive imaging using imperfect crystals.使用非完美晶体的大分子衍射成像
Struct Dyn. 2021 Jul 8;8(4):044701. doi: 10.1063/4.0000087. eCollection 2021 Jul.
4
Macromolecular phasing using diffraction from multiple crystal forms.多晶型物衍射的大分子相分析。
Acta Crystallogr A Found Adv. 2021 Jan 1;77(Pt 1):19-35. doi: 10.1107/S2053273320013650. Epub 2021 Jan 5.
5
A fixed-target platform for serial femtosecond crystallography in a hydrated environment.用于在水合环境中进行串行飞秒晶体学的固定靶平台。
IUCrJ. 2020 Jan 1;7(Pt 1):30-41. doi: 10.1107/S2052252519014003.
6
An outlook on using serial femtosecond crystallography in drug discovery.展望药物研发中连续的飞秒晶体学的应用。
Expert Opin Drug Discov. 2019 Sep;14(9):933-945. doi: 10.1080/17460441.2019.1626822. Epub 2019 Jun 11.
Nature. 2016 Feb 11;530(7589):202-6. doi: 10.1038/nature16949.
4
Uniqueness of the macromolecular crystallographic phase problem.大分子晶体学相位问题的独特性。
Acta Crystallogr A Found Adv. 2015 Nov;71(Pt 6):592-8. doi: 10.1107/S2053273315015387. Epub 2015 Oct 6.
5
Direct phasing of protein crystals with high solvent content.高溶剂含量蛋白质晶体的直接相位分析
Acta Crystallogr A Found Adv. 2015 Jan;71(Pt 1):92-8. doi: 10.1107/S2053273314024097. Epub 2015 Jan 1.
6
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Acta Crystallogr A. 2012 Mar;68(Pt 2):256-65. doi: 10.1107/S0108767311053815. Epub 2012 Feb 7.
7
Reconstruction of an object from the modulus of its Fourier transform.根据傅里叶变换模量对物体进行重建。
Opt Lett. 1978 Jul 1;3(1):27-9. doi: 10.1364/ol.3.000027.
8
Characterization of Solanum tuberosum multicystatin and its structural comparison with other cystatins.马铃薯多聚半胱氨酸蛋白酶抑制剂的特性及其与其他半胱氨酸蛋白酶抑制剂的结构比较。
Plant Cell. 2009 Mar;21(3):861-75. doi: 10.1105/tpc.108.064717. Epub 2009 Mar 20.
9
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.自由R值:一种用于评估晶体结构准确性的新型统计量。
Nature. 1992 Jan 30;355(6359):472-5. doi: 10.1038/355472a0.
10
Analysis of solvent content and oligomeric states in protein crystals--does symmetry matter?蛋白质晶体中溶剂含量和寡聚状态的分析——对称性重要吗?
Protein Sci. 2008 Apr;17(4):623-32. doi: 10.1110/ps.073360508.