Validation of ligands in macromolecular structures determined by X-ray crystallography

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Validation of ligands in macromolecular structures determined by X-ray crystallography. Acta Crystallographica Section D. 2018, vol. 74, No 3, p. 228-236. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798318002541.

Basic information

• Original name: Validation of ligands in macromolecular structures determined by X-ray crystallography
• Authors: SMART, Oliver S. (826 United Kingdom of Great Britain and Northern Ireland), Vladimír HORSKÝ (203 Czech Republic, belonging to the institution), Swanand GORE (826 United Kingdom of Great Britain and Northern Ireland), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, guarantor, belonging to the institution), Veronika BENDOVÁ (203 Czech Republic, belonging to the institution), Gerard J. KLEYWEGT (528 Netherlands) and Sameer VELANKAR (826 United Kingdom of Great Britain and Northern Ireland).
• Edition: Acta Crystallographica Section D, 2018, 2059-7983.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 3.227
• RIV identification code: RIV/00216224:14740/18:00102379
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1107/S2059798318002541
• UT WoS: 000427362000006
• Keywords in English: PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. In this article, the ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

Links

• LM2015047, research and development project: Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

• LQ1601, research and development project: Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

• MUNI/A/1204/2017, interní kód MU: Name: Matematické statistické modelování 2 (Acronym: MaStaMo2)

Investor: Masaryk University, Category A

• 676559, interní kód MU: Name: ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences (Acronym: ELIXIR-EXCELERATE)

Investor: European Union, RI Research Infrastructures (Excellent Science)