Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a dominant phasing method for the crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database for finding suitable templates for phasing. However, such sequence information is not always available such as when proteins are crystallized with unknown binding partner proteins or when the crystal is that of a contaminant. The recent development of AlphaFold has resulted in the availability of predicted protein structures for all proteins from twenty species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough for sequence-independent phasing of diffraction data from two crystallization contaminants for which we had not identified the protein. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained which allowed the identification and structure determination of both structures, YncE and YadF. Our results advocate a general utility of AlphaFold-predicted structure database with respect to crystallographic phasing.

中文翻译：

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用于序列无关分子置换的 AlphaFold 蛋白质结构数据库

晶体定相恢复衍射实验中丢失的相位信息。分子置换是蛋白质数据库中晶体结构的主要定相方法。在一种形式中，它使用蛋白质序列来搜索结构数据库以寻找合适的定相模板。然而，这样的序列信息并不总是可用的，例如当蛋白质与未知的结合伴侣蛋白质结晶时或当晶体是污染物时。AlphaFold 的最新发展已经使来自 20 个物种的所有蛋白质的预测蛋白质结构变得可用。在这项工作中，我们测试了 AlphaFold 预测的大肠杆菌蛋白质结构对于来自我们尚未鉴定蛋白质的两种结晶污染物的衍射数据的序列独立定相足够准确。使用超过 4000 个预测结构中的每一个作为搜索模型，获得了强大的分子置换解决方案，允许识别和结构确定 YncE 和 YadF 两种结构。我们的结果提倡 AlphaFold 预测结构数据库在晶体定相方面的通用性。