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Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.面向非晶体学家的蛋白质晶体学,或如何从已发表的大分子结构中获取最佳(而非更多)信息。
FEBS J. 2008 Jan;275(1):1-21. doi: 10.1111/j.1742-4658.2007.06178.x. Epub 2007 Nov 23.
2
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3
You are lost without a map: Navigating the sea of protein structures.没有地图你就会迷失方向:探索蛋白质结构的海洋。
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Integrative/Hybrid Methods Structural Biology: Role of Macromolecular Crystallography.综合/混合方法结构生物学:大分子晶体学的作用。
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本文引用的文献

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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.
2
Triclinic lysozyme at 0.65 A resolution.分辨率为0.65埃的三斜晶系溶菌酶。
Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1254-68. doi: 10.1107/S0907444907054224. Epub 2007 Nov 16.
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Structural basis for catalysis by onconase.癌酶催化作用的结构基础。
J Mol Biol. 2008 Jan 4;375(1):165-77. doi: 10.1016/j.jmb.2007.09.089. Epub 2007 Oct 4.
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Reexamination of the Three-Dimensional Structure of the Small Subunit of RuBisCo from Higher Plants.高等植物 Rubisco 小亚基的三维结构再研究。
Science. 1989 May 12;244(4905):702-5. doi: 10.1126/science.244.4905.702.
5
Quality of protein crystal structures.蛋白质晶体结构的质量。
Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):941-50. doi: 10.1107/S0907444907033847. Epub 2007 Aug 17.
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Separating model optimization and model validation in statistical cross-validation as applied to crystallography.在应用于晶体学的统计交叉验证中分离模型优化和模型验证。
Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):939-40. doi: 10.1107/S0907444907033458. Epub 2007 Aug 17.
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Crystallography: crystallographic evidence for deviating C3b structure.晶体学:偏离C3b结构的晶体学证据。
Nature. 2007 Aug 9;448(7154):E1-2; discussion E2-3. doi: 10.1038/nature06102.
8
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?重新审视立体化学限制:精修目标的准确性如何,以及蛋白质结构应被允许与其偏离多少?
Acta Crystallogr D Biol Crystallogr. 2007 May;63(Pt 5):611-20. doi: 10.1107/S090744490700978X. Epub 2007 Apr 21.
9
Growth of novel protein structural data.新型蛋白质结构数据的增长。
Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3183-8. doi: 10.1073/pnas.0611678104. Epub 2007 Feb 20.
10
Structure of a bacterial multidrug ABC transporter.一种细菌多药ABC转运蛋白的结构。
Nature. 2006 Sep 14;443(7108):180-5. doi: 10.1038/nature05155. Epub 2006 Aug 30.

面向非晶体学家的蛋白质晶体学,或如何从已发表的大分子结构中获取最佳(而非更多)信息。

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.

作者信息

Wlodawer Alexander, Minor Wladek, Dauter Zbigniew, Jaskolski Mariusz

机构信息

Macromolecular Crystallography Laboratory, NCI, Frederick, MD 21702, USA.

出版信息

FEBS J. 2008 Jan;275(1):1-21. doi: 10.1111/j.1742-4658.2007.06178.x. Epub 2007 Nov 23.

DOI:10.1111/j.1742-4658.2007.06178.x
PMID:18034855
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4465431/
Abstract

The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45,000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.

摘要

蛋白质数据库中储存的大分子结构数量现已超过45000个,其中绝大多数是用晶体学方法测定的。数千篇描述此类结构的研究已发表在科学文献中,并且已有14位蛋白质晶体学家获得了诺贝尔化学奖或医学奖。尽管这些结构对于理解生物体中发生的过程以及药物设计等实际应用非常重要,但许多非晶体学家在对结构文献数据进行批判性评估时仍存在问题。本综述试图简要概述晶体学的技术方面,并解释一些参数的含义,大分子结构的使用者应评估这些参数,以便解释而非过度解读坐标文件及其描述中所呈现的信息。本文还讨论了从不同分辨率解析的结构坐标中可收集到的信息范围,以及结构测定和解释中遇到的问题与陷阱。