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模拟解析大分子衍射。

Interpreting macromolecular diffraction through simulation.

机构信息

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States.

出版信息

Methods Enzymol. 2023;688:195-222. doi: 10.1016/bs.mie.2023.06.011. Epub 2023 Aug 10.

DOI:10.1016/bs.mie.2023.06.011
PMID:37748827
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11801407/
Abstract

This chapter discusses the use of diffraction simulators to improve experimental outcomes in macromolecular crystallography, in particular for future experiments aimed at diffuse scattering. Consequential decisions for upcoming data collection include the selection of either a synchrotron or free electron laser X-ray source, rotation geometry or serial crystallography, and fiber-coupled area detector technology vs. pixel-array detectors. The hope is that simulators will provide insights to make these choices with greater confidence. Simulation software, especially those packages focused on physics-based calculation of the diffraction, can help to predict the location, size, shape, and profile of Bragg spots and diffuse patterns in terms of an underlying physical model, including assumptions about the crystal's mosaic structure, and therefore can point to potential issues with data analysis in the early planning stages. Also, once the data are collected, simulation may offer a pathway to improve the measurement of diffraction, especially with weak data, and might help to treat problematic cases such as overlapping patterns.

摘要

这一章讨论了使用衍射模拟器来提高大分子晶体学实验结果的质量，特别是对于未来旨在研究漫散射的实验。即将到来的数据采集的重要决定包括选择同步加速器或自由电子激光 X 射线源、旋转几何形状或连续晶体学，以及纤维耦合面探测器技术与像素阵列探测器。希望模拟器能够提供更多的见解，使这些选择更加有信心。模拟软件，特别是那些专注于基于物理计算的衍射的软件包，可以帮助根据基本物理模型预测布拉格斑点和漫散射模式的位置、大小、形状和轮廓，包括对晶体镶嵌结构的假设，因此可以在早期规划阶段指出数据分析中潜在的问题。此外，一旦收集到数据，模拟可能为提高衍射的测量提供途径，特别是对于弱数据，并且可能有助于处理重叠模式等有问题的情况。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92b3/11801407/66c89ebe0dda/nihms-2048956-f0011.jpg
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本文引用的文献

1
Crystal diffraction prediction and partiality estimation using Gaussian basis functions.使用高斯基函数进行晶体衍射预测和偏性估计。
Acta Crystallogr A Found Adv. 2023 Mar 1;79(Pt 2):145-162. doi: 10.1107/S2053273323000682. Epub 2023 Feb 17.
2
Beyond integration: modeling every pixel to obtain better structure factors from stills.超越整合：对每个像素进行建模以从静态图像中获得更好的结构因子。
IUCrJ. 2020 Oct 24;7(Pt 6):1151-1167. doi: 10.1107/S2052252520013007. eCollection 2020 Nov 1.
3
Diffuse X-ray scattering from correlated motions in a protein crystal.
蛋白质晶体中相关运动的漫散射 X 射线。
Nat Commun. 2020 Mar 9;11(1):1271. doi: 10.1038/s41467-020-14933-6.
4
Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.通过详细建模 XFEL 晶体学衍射，实现金属蛋白电荷态的空间分辨率。
Acta Crystallogr D Struct Biol. 2020 Feb 1;76(Pt 2):176-192. doi: 10.1107/S2059798320000418. Epub 2020 Feb 4.
5
Intermolecular correlations are necessary to explain diffuse scattering from protein crystals.分子间相关性对于解释蛋白质晶体的漫散射是必要的。
IUCrJ. 2018 Feb 21;5(Pt 2):211-222. doi: 10.1107/S2052252518001124. eCollection 2018 Mar 1.
6
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.
7
Bringing diffuse X-ray scattering into focus.将漫散射 X 射线聚焦。
Curr Opin Struct Biol. 2018 Jun;50:109-116. doi: 10.1016/j.sbi.2018.01.009. Epub 2018 Feb 16.
8
X-ray Scattering Studies of Protein Structural Dynamics.蛋白质结构动力学的X射线散射研究。
Chem Rev. 2017 Jun 28;117(12):7615-7672. doi: 10.1021/acs.chemrev.6b00790. Epub 2017 May 30.
9
Imperfection and radiation damage in protein crystals studied with coherent radiation.利用相干辐射研究蛋白质晶体中的缺陷与辐射损伤。
J Synchrotron Radiat. 2016 Jan;23(1):228-37. doi: 10.1107/S1600577515019700. Epub 2016 Jan 1.
10
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.通过多温度和X射线自由电子激光晶体学绘制动态酶的构象图谱。
Elife. 2015 Sep 30;4:e07574. doi: 10.7554/eLife.07574.