Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen
Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen
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DOI：
10.1107/s1744309112008421
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发表时间：
2012-04-01
影响因子：
0.9
通讯作者：
Rupp, Bernhard
中科院分区：
文献类型：
--
作者：
Rupp, Bernhard
物理上不可能的功能，在模型中的桦树花粉结构Bet v 1d（PDB条目3k78）忠实地再现电子密度产生的沉积结构的因素，但这些结构因素本身表现出的特性，是从一个简单的模型计算的数据，并通过实验测量获得的数据和误差模型不一致。针对这些结构因子的3k78模型的细化导致与沉积模型不同的同晶结构，其具有令人难以置信的小R值（0.019）。将异常细化与Bet v 11的同构变体结构的正常细化（PDB条目1fm4）进行比较。各种分析工具，包括应用Diederichs图，R西格玛图和散装溶剂分析进行了讨论，作为有前途的艾滋病验证。对Bet v 1d结构的检查还警告不要通过零占位符指示定义不佳的蛋白质链残基。对保存衍射图像的建议进行了放大。
Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78 model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4). A variety of analytical tools, including the application of Diederichs plots, R sigma plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified.