6SIM

SAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry data collection and univariate analysis

6SIM の概要

• エントリーDOI: 10.2210/pdb6sim/pdb
• 分子名称: Lysozyme C, 1,2-ETHANEDIOL, ACETATE ION, ... (6 entities in total)
• 機能のキーワード: univariate analysis, single-wavelength x-ray anomalous diffraction, inverse beam geometry collection, hen egg white lysozyme, hydrolase
• 由来する生物種: Gallus gallus (Chicken)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16868.57

構造登録者

Garcia-Bonete, M.J.,Katona, G. (登録日: 2019-08-10, 公開日: 2019-11-06, 最終更新日: 2024-10-16)

主引用文献

Garcia-Bonete, M.J.,Katona, G.
Bayesian machine learning improves single-wavelength anomalous diffraction phasing.
Acta Crystallogr.,Sect.A, 75:851-860, 2019

PubMed Abstract: Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.

PubMed: 31692460
DOI: 10.1107/S2053273319011446

実験手法

X-RAY DIFFRACTION (1.6101802385 Å)