4xan的重新优化：鸡蛋清溶菌酶与卡铂在溴化钠溶液中的反应，包括溶质、溶剂、离子和氨基酸电子密度的证据
Re-refinement of 4xan: hen egg white lysozyme with carboplatin in sodium bromide solution including details of solute, solvent, ion and split occupancy amino acid electron density evidence
摘要：
已对4xan（含卡铂的鸡蛋清溶菌酶（HEWL）在NaBr溶液中结晶）进行了重新精制（Tanley et al 2016）。这是我们对Shabalin et al 2015的评论文章的回应文章（Tanley et al 2015），表明需要对4xan中电子密度的一些溶质分子解释进行校正，并去除有机部分作为与His 15配位的铂离子的配体。我们注意到Shabalin等人（2015年）的模型，即氯的密度和溴的部分占据来解释形状。然而，由于溴化物浓度远远超过氯化物（20倍），我们认为4 yem Shabalin等人2015年的解释极不可能，但尽管如此，我们仍然无法对该形状提供解释，证实了Tanley等人（2014）中描述的早期分析。在Shabalin等人（2015）对4g 4a的原始衍射数据进行再处理后，我们还使用EVAL（Schreurs等人，2010）将4xan的衍射数据处理重新调整为更高的分辨率，得出的结论是支持1.3埃作为分辨率限值，这是我们修订的4xan（5 HMJ）PDB文件的基础。非常有趣的是，存在1.47至1.30埃分辨率的额外X射线衍射数据，例如在最终壳层中<I/sigma（I）> =0.39和CCl/2 = 0.181（1.30至1.322埃）。在这篇arXiv文章中，我们详细记录了我们不同的溶剂和分裂占据侧链电子密度解释，作为我们在回应文章中声明方法的证据（Tanley et al 2015）。我们的关键重新检查包括比较的基础上的4xan衍射数据图像再处理与三个不同的软件包，以评估的可能性，由于电子密度解释的变化。总的来说，我们的最终模型（PDB代码5 HMJ）现在比4xan有所改进。
英文摘要：
A re-refinement of 4xan, hen egg white lysozyme (HEWL) with carboplatin crystallised in NaBr solution, has been made (Tanley et al 2016). This follows our Response article (Tanley et al 2015) to the Critique article of Shabalin et al 2015, suggesting the need for corrections to some solute molecule interpretations of electron density in 4xan and removal of an organic moiety as a ligand to the platinum ion coordinated to His15. We note Shabalin et al (2015) model of a chlorine in that density and a close by bromine at partial occupancy to explain the shape. However, as the bromide concentration is in huge excess over chloride (by 20 fold), we think that the 4yem Shabalin et al 2015 interpretation highly unlikely, but nevertheless we still cannot offer an explanation for that shape, confirming our earlier analysis described in Tanley et al (2014). Following Shabalin et al (2015) reprocessing of the raw diffraction data for 4g4a, we also redid the diffraction data processing for 4xan to a higher resolution using EVAL (Schreurs et al 2010) concluding in favour of 1.3 Angstrom as the resolution limit and which is the basis for our revised PDB file for 4xan (5HMJ). It is very interesting that there is extra X-ray diffraction data from 1.47 to 1.30 Angstrom resolution e.g. with <I/sigma(I)> =0.39 and CC1/2 = 0.181 in the final shell (1.30 to 1.322 Angstrom). In this arXiv article we document in detail our different solvent and split occupancy side chain electron density interpretations as evidence for our statement of approach in our Response article (Tanley et al 2015). Our critical re-examination includes comparisons based on the 4xan diffraction data images reprocessing with three different software packages so as to evaluate the possibility of variations in electron density interpretations due to that. Overall our finalised model (PDB code 5HMJ) is now improved over 4xan.
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