Updating direct methods II. Reduction of the structural complexity when triplet invariants are estimated via the Patterson map

IF 5.2 3区 材料科学 Q2 CHEMISTRY, MULTIDISCIPLINARY
Maria Cristina Burla, Carmelo Giacovazzo, Giampiero Polidori
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Abstract

Direct methods have practically solved the phase problem for small–medium-size molecules but have substantially failed in macromolecular crystallography. They have two main limitations: a strong dependence on structural complexity and the need to work with atomic-resolution data. Many attempts have been made to broaden their field of applicability, for example the use of some a priori information to make the estimate of the triplet invariant phases more effective. Unfortunately none of these new approaches allowed the successful application of direct methods to proteins and nucleic acids. Direct methods are still a niche tool in macromolecular crystallography. In a recent publication [Giacovazzo (2019). Acta Cryst. A75, 142–157] the method of joint probability distributions has been modified to take into account new sources of prior information, one of which is relevant to this article: the Patterson map. In practice, it has been shown that with prior knowledge of the interatomic vectors one is able to modify the classic Cochran reliability parameter for estimating the triplet invariant phases. The article was essentially theoretical in nature, and no attempt was described to test the practical usefulness of the new probabilistic formulas. This work is therefore the first application of the new method. It is shown that the use of the Patterson map as prior information substantially improves the Cochran estimate of triplet phases; the phase error distribution for the new estimates, even if it is related to macromolecular structures, becomes similar to that obtained for medium-size structures. In some ways, it is as if the use of the Patterson information reduces the structural complexity, thus allowing a more general use of direct methods in macromolecular crystallography. Atomic resolution no longer seems to be a necessary ingredient for the applicability of direct methods; tests show that the apparent reduction in structural complexity also occurs in macromolecular structures with experimental data having a resolution of 2.3 Å. A number of test structures have been used to show the potential of the new technique.

Abstract Image

更新直接方法 II.通过帕特森图估算三重不变式时结构复杂性的降低
直接方法实际上解决了中小尺寸分子的相问题,但在大分子晶体学方面却严重失败。它们有两个主要的局限性:对结构复杂性的强烈依赖,以及需要使用原子分辨率数据。人们曾多次尝试扩大其适用范围,例如使用一些先验信息来更有效地估计三重不变相。遗憾的是,这些新方法都无法将直接方法成功应用于蛋白质和核酸。直接方法仍然是大分子晶体学中的一个小众工具。最近发表的一篇文章 [Giacovazzo (2019). Acta Cryst. A75, 142-157] 对联合概率分布方法进行了修改,以考虑新的先验信息源,其中一个与本文相关:帕特森图。实践证明,有了原子间矢量的先验知识,就能修改用于估计三重不变相的经典科克兰可靠性参数。这篇文章基本上是理论性的,并没有试图测试新概率公式的实用性。因此,这项工作是新方法的首次应用。结果表明,使用帕特森图作为先验信息,大大改进了三重相的科克兰估算;新估算的相位误差分布,即使与大分子结构有关,也变得与中型结构的相位误差分布相似。在某些方面,帕特森信息的使用仿佛降低了结构的复杂性,从而使直接方法在大分子晶体学中得到更广泛的应用。原子分辨率似乎不再是直接方法适用性的必要因素;测试表明,结构复杂性的明显降低也发生在实验数据分辨率为 2.3 Å 的大分子结构中。一些测试结构被用来展示新技术的潜力。
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来源期刊
Journal of Applied Crystallography
Journal of Applied Crystallography CHEMISTRY, MULTIDISCIPLINARYCRYSTALLOGRAPH-CRYSTALLOGRAPHY
CiteScore
7.80
自引率
3.30%
发文量
178
期刊介绍: Many research topics in condensed matter research, materials science and the life sciences make use of crystallographic methods to study crystalline and non-crystalline matter with neutrons, X-rays and electrons. Articles published in the Journal of Applied Crystallography focus on these methods and their use in identifying structural and diffusion-controlled phase transformations, structure-property relationships, structural changes of defects, interfaces and surfaces, etc. Developments of instrumentation and crystallographic apparatus, theory and interpretation, numerical analysis and other related subjects are also covered. The journal is the primary place where crystallographic computer program information is published.
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