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使用Python进行微晶数据组装。

: microcrystal data assembly using Python.

作者信息

Takemaru Lina, Guo Gongrui, Zhu Ping, Hendrickson Wayne A, McSweeney Sean, Liu Qun

机构信息

Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

Photon Sciences Division, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.

出版信息

J Appl Crystallogr. 2020 Feb 1;53(Pt 1):277-281. doi: 10.1107/S160057671901673X.

DOI:10.1107/S160057671901673X
PMID:32047415
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6998775/
Abstract

The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation damaged with incomplete data per microcrystal and with unit-cell variations. A multi-stage data assembly method has previously been designed for microcrystal synchrotron crystallography. Here the strategy has been implemented as a Python program for microcrystal data assembly (). optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, may be applicable for assembling data sets from larger crystals for improved data quality.

摘要

微衍射X射线束线的最新进展使大分子微晶成为常规结构分析的诱人对象。在同步加速器微衍射束线收集的微晶衍射数据可能会受到辐射损伤,每个微晶的数据不完整且晶胞存在变化。此前已设计了一种多阶段数据组装方法用于微晶同步辐射晶体学。在这里,该策略已被实现为一个用于微晶数据组装的Python程序()。它通过迭代的晶体和帧拒绝来优化微晶数据质量,包括微弱的反常信号。除了微晶,它可能适用于组装来自较大晶体的数据集以提高数据质量。

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本文引用的文献

1
Synchrotron microcrystal native-SAD phasing at a low energy.低能量同步辐射微晶天然单波长反常散射法相位测定
IUCrJ. 2019 May 3;6(Pt 4):532-542. doi: 10.1107/S2052252519004536. eCollection 2019 Jul 1.
2
Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays.利用低能X射线从微晶进行硫-SAD相位分析。
IUCrJ. 2019 Jun 28;6(Pt 4):503-504. doi: 10.1107/S2052252519008698. eCollection 2019 Jul 1.
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Direct measurement of X-ray-induced heating of microcrystals.直接测量 X 射线诱导的微晶体加热。
IUCrJ. 2022 Oct 21;9(Pt 6):768-777. doi: 10.1107/S205225252200971X. eCollection 2022 Nov 1.
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FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II.FMX - 国家同步辐射光源 II 上的前沿微聚焦大分子晶体学光束线。
J Synchrotron Radiat. 2021 Mar 1;28(Pt 2):650-665. doi: 10.1107/S1600577520016173. Epub 2021 Feb 25.
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Long-wavelength native-SAD phasing: opportunities and challenges.长波长天然单波长反常散射法相位测定:机遇与挑战
IUCrJ. 2019 Apr 1;6(Pt 3):373-386. doi: 10.1107/S2052252519002756. eCollection 2019 May 1.
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Long-wavelength Mesh&Collect native SAD phasing from microcrystals.长波长网格&收集微晶体的原生 SAD 相。
Acta Crystallogr D Struct Biol. 2019 Feb 1;75(Pt 2):192-199. doi: 10.1107/S2059798319002031. Epub 2019 Feb 11.
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In situ serial crystallography for rapid de novo membrane protein structure determination.用于快速从头测定膜蛋白结构的原位连续晶体学。
Commun Biol. 2018 Aug 27;1:124. doi: 10.1038/s42003-018-0123-6. eCollection 2018.
7
High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner.采用高精度压电扫描仪的高速光栅扫描同步辐射串行微晶学
J Synchrotron Radiat. 2018 Sep 1;25(Pt 5):1362-1370. doi: 10.1107/S1600577518010354. Epub 2018 Aug 23.
8
Sample manipulation and data assembly for robust microcrystal synchrotron crystallography.用于稳健微晶同步辐射晶体学的样品处理与数据组装
IUCrJ. 2018 Apr 19;5(Pt 3):238-246. doi: 10.1107/S2052252518005389. eCollection 2018 May 1.
9
KAMO: towards automated data processing for microcrystals.卡莫:实现微晶体自动化数据处理。
Acta Crystallogr D Struct Biol. 2018 May 1;74(Pt 5):441-449. doi: 10.1107/S2059798318004576. Epub 2018 Apr 24.
10
DIALS: implementation and evaluation of a new integration package.DIALS:一个新集成包的实现和评估。
Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):85-97. doi: 10.1107/S2059798317017235.