Anomalous signal indicators in protein crystallography - PubMed (original) (raw)
. 2005 Nov;61(Pt 11):1437-48.
doi: 10.1107/S0907444905023589. Epub 2005 Oct 19.
Affiliations
- PMID: 16239720
- DOI: 10.1107/S0907444905023589
Anomalous signal indicators in protein crystallography
P H Zwart. Acta Crystallogr D Biol Crystallogr. 2005 Nov.
Abstract
A Monte Carlo procedure is described that generates random structure factors with simulated errors corresponding to an X-ray data set of a protein of a specific size and given heavy-atom content. The simulated data set can be used to estimate Bijvoet ratios and figures of merit as obtained from SAD phasing routines and can be used to gauge the feasibility of solving a structure via the SAD method. In addition to being able to estimate results from phasing, the simulation allows the estimation of the correlation coefficient between |DeltaF|, the absolute Bijvoet amplitude difference, and FA, the structure-factor amplitude of the heavy-atom model. As this quantity is used in various substructure-solution routines, the estimate provides a rough estimate of the ease of substructure solution. Furthermore, the Monte Carlo procedure provides an easy way of estimating the number of significant Bijvoet intensity differences, denoted as the measurability, and is proposed as an intuitive measure of the quality of anomalous data.
Similar articles
- Recent advances in direct phasing methods for heavy-atom substructure determination.
Xu H, Hauptman HA. Xu H, et al. Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):897-900. doi: 10.1107/S0907444906012704. Epub 2006 Jul 18. Acta Crystallogr D Biol Crystallogr. 2006. PMID: 16855306 - Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data.
Hatti KS, McCoy AJ, Read RJ. Hatti KS, et al. Acta Crystallogr D Struct Biol. 2021 Jul 1;77(Pt 7):880-893. doi: 10.1107/S2059798321004538. Epub 2021 Jun 18. Acta Crystallogr D Struct Biol. 2021. PMID: 34196615 Free PMC article. - Rapid and automated substructure solution by Shake-and-Bake.
Xu H, Weeks CM. Xu H, et al. Acta Crystallogr D Biol Crystallogr. 2008 Feb;64(Pt 2):172-7. doi: 10.1107/S0907444907058659. Epub 2008 Jan 16. Acta Crystallogr D Biol Crystallogr. 2008. PMID: 18219117 - Protein structure determination by x-ray crystallography.
Ilari A, Savino C. Ilari A, et al. Methods Mol Biol. 2008;452:63-87. doi: 10.1007/978-1-60327-159-2_3. Methods Mol Biol. 2008. PMID: 18563369 Review. - ACORN: a review.
Yao JX, Dodson EJ, Wilson KS, Woolfson MM. Yao JX, et al. Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):901-8. doi: 10.1107/S0907444906008122. Epub 2006 Jul 18. Acta Crystallogr D Biol Crystallogr. 2006. PMID: 16855307 Review.
Cited by
- Design of High Affinity Binders to Convex Protein Target Sites.
Yang W, Hicks DR, Ghosh A, Schwartze TA, Conventry B, Goreshnik I, Allen A, Halabiya SF, Kim CJ, Hinck CS, Lee DS, Bera AK, Li Z, Wang Y, Schlichthaerle T, Cao L, Huang B, Garrett S, Gerben SR, Rettie S, Heine P, Murray A, Edman N, Carter L, Stewart L, Almo S, Hinck AP, Baker D. Yang W, et al. bioRxiv [Preprint]. 2024 May 2:2024.05.01.592114. doi: 10.1101/2024.05.01.592114. bioRxiv. 2024. PMID: 38746206 Free PMC article. Preprint. - Tetramerization is essential for the enzymatic function of the Pseudomonas aeruginosa virulence factor UDP-glucose pyrophosphorylase.
Dirr L, Cleeves S, Ramón Roth I, Li L, Fiebig T, Ve T, Häussler S, Braun A, von Itzstein M, Führing JI. Dirr L, et al. mBio. 2024 Apr 10;15(4):e0211423. doi: 10.1128/mbio.02114-23. Epub 2024 Mar 12. mBio. 2024. PMID: 38470050 Free PMC article. - Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway.
González L, Díaz L, Pous J, Baginski B, Duran-Corbera A, Scarpa M, Brun-Heath I, Igea A, Martin-Malpartida P, Ruiz L, Pallara C, Esguerra M, Colizzi F, Mayor-Ruiz C, Biondi RM, Soliva R, Macias MJ, Orozco M, Nebreda AR. González L, et al. Nat Commun. 2023 Jun 12;14(1):3318. doi: 10.1038/s41467-023-39051-x. Nat Commun. 2023. PMID: 37308482 Free PMC article. - Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family.
Yun JH, Ohki M, Park JH, Ishimoto N, Sato-Tomita A, Lee W, Jin Z, Tame JRH, Shibayama N, Park SY, Lee W. Yun JH, et al. Sci Adv. 2020 Feb 7;6(6):eaay2042. doi: 10.1126/sciadv.aay2042. eCollection 2020 Feb. Sci Adv. 2020. PMID: 32083178 Free PMC article. - Bayesian machine learning improves single-wavelength anomalous diffraction phasing.
Garcia-Bonete MJ, Katona G. Garcia-Bonete MJ, et al. Acta Crystallogr A Found Adv. 2019 Nov 1;75(Pt 6):851-860. doi: 10.1107/S2053273319011446. Epub 2019 Oct 7. Acta Crystallogr A Found Adv. 2019. PMID: 31692460 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Research Materials