Ice in biomolecular cryocrystallography.
Ice in biomolecular cryocrystallography.
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DOI：
10.1107/s2059798321001170
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发表时间：
2021-04-01
期刊：
影响因子：
--
通讯作者：
Thorne RE
中科院分区：
文献类型：
--
作者：
Moreau DW;Atakisi H;Thorne RE
三种蛋白质的衍射数据分析表明，在晶体内部溶剂中形成的冰是堆积无序的。从蛋白质结构因子数据中检测冰的修正度量和算法的应用表明，大约3.9%的PDB条目表现出主要是六边形的冰，11.7%表现出堆叠无序的冰。从低温冷却的蛋白质晶体获得的衍射数据通常包括来自冰的衍射。三种蛋白质晶体的冰衍射分析表明，在快速冷却过程中形成的溶剂空腔内的冰是由六方和立方平面的堆叠无序混合物，立方平面分数随着冷冻保护剂浓度的增加和冷却速率的增加而增加。基于Thorn及其同事的工作[Thorn et al.（2017），Acta Cryst. D 73，729-727]，定义了一种用于从沉积的蛋白质结构因子数据中检测冰的修订指标，并使用来自大分子晶体学再现综合资源的全帧衍射数据验证了该指标。使用此修订后的度量和改进的算法，从一个随机样本的89 827 PDB条目在低温下收集的结构因子数据的分析表明，大约16%的冰污染的证据，这部分增加溶剂含量和最大溶剂腔的大小。 通过检查冰衍射峰的位置，在那里观察到的结构因子扰动，它被发现，大约25%的晶体表现出冰主要是六边形的字符，这表明，不充分的冷却速率和/或冷冻保护剂浓度使用，而其余的75%显示冰与堆叠无序或立方字符。
Analysis of diffraction data from three proteins indicates that the ice formed in internal crystal solvent is stacking-disordered. Application of a revised metric and algorithm for detecting ice from protein structure-factor data indicates that roughly 3.9% of PDB entries exhibit ice that is primarily hexagonal and 11.7% exhibit stacking-disordered ice. Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thorn et al. (2017), Acta Cryst. D73, 729–727], a revised metric is defined for detecting ice from deposited protein structure-factor data, and this metric is validated using full-frame diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography. Using this revised metric and improved algorithms, an analysis of structure-factor data from a random sample of 89 827 PDB entries collected at cryogenic temperatures indicates that roughly 16% show evidence of ice contamination, and that this fraction increases with increasing solvent content and maximum solvent-cavity size. By examining the ice diffraction-peak positions at which structure-factor perturbations are observed, it is found that roughly 25% of crystals exhibit ice with primarily hexagonal character, indicating that inadequate cooling rates and/or cryoprotectant concentrations were used, while the remaining 75% show ice with a stacking-disordered or cubic character.