Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.
Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.
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DOI：
10.1107/s2059798323008793
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发表时间：
2023-12-01
期刊：
影响因子：
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通讯作者：
Murshudov GN
中科院分区：
文献类型：
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作者：
Catapano L;Long F;Yamashita K;Nicholls RA;Steiner RA;Murshudov GN
来自CCP4套件的大分子精炼包REFMAC5通过合并中子晶体学算法进行了扩展。氢(H)原子在大分子中含量丰富，在酶催化、配体识别过程和蛋白质-蛋白质相互作用中起着关键作用。然而，通过衍射技术直接可视化它们是具有挑战性的。大分子x射线晶体学只能在（亚）原子分辨率下（约1.2 Å或更高）定位最有序的氢原子。然而，许多具有生物化学意义的氢原子仍然无法通过这种方法检测到。相比之下，中子衍射方法能够以更常见的分辨率值（优于2.5 Å）可视化大多数H原子，通常以氘（2H）原子的形式。因此，中子晶体学虽然在技术上要求很高，但在寻求质子化态的直接信息时，通常是选择的方法。来自协作计算项目4号（CCP4）的REFMAC5是一个针对x射线晶体学和低温电镜数据改进大分子模型的程序。这篇文章描述了它的扩展，包括从中子晶体学数据中获得的结构模型的改进。具有H原子与其母原子核之间精确键距的立体化学约束现在是CCP4单体库的一部分，这是精炼中使用的先前化学信息的来源。REFMAC5中子数据分析的一个新功能是改进了质子/氘（1H/2H）分数。该参数描述氢同位素对中子散射的相对1H/2H贡献。新开发的REFMAC5算法通过使用(i)中子数据或（ii）中子数据补充参考x射线晶体结构的外部约束，对PDB中可用的几个条目和一种新结构（FutA）进行（重新）改进来进行测试。用REFMAC5进行再细化，得到的模型的r因子值与最初沉积的值一致，在某些情况下优于最初沉积的值。在精化过程中使用外部参考结构约束已被观察到是一种有价值的策略，特别是对于中低分辨率的结构。
The macromolecular refinement package REFMAC5 from the CCP4 suite has been extended by the incorporation of algorithms for neutron crystallography. Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein–protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium–low resolution.
影响因子：
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作者：
Liebschner D;Afonine PV;Urzhumtsev AG;Adams PD
通讯作者：
Adams PD