A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model
| Autor: | Sean McSweeney, Sine Larsen, Demet Araç, Matthew W. Bowler, Harm Otten, André Hoelz, Gordon A. Leonard, Navraj S. Pannu, Pavol Skubák, Christoph Mueller-Dieckmann, Ana R. Correia, Gabriel S. Salzman, Andrew A. McCarthy |
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| Přispěvatelé: | Leiden University, Department of Biochemistry and Molecular Biology The University of Chicago, University of Chicago, European Molecular Biology Laboratory [Grenoble] (EMBL), Division of Chemistry and Chemical Engineering (DCCE-Caltech), California Institute of Technology (CALTECH), European Synchrotron Radiation Facility (ESRF) |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Diffraction multivariate statistics Computer science membrane proteins single-wavelength anomalous diffraction Biochemistry Set (abstract data type) 03 medical and health sciences multi-protein complexes [CHIM]Chemical Sciences General Materials Science refinement X-ray crystallography Complex data type Structure (mathematical logic) Quantitative Biology::Biomolecules Crystallography Resolution (electron density) Process (computing) General Chemistry Function (mathematics) Condensed Matter Physics Research Papers model bias structure determination Data set 030104 developmental biology QD901-999 Algorithm low resolution |
| Zdroj: | International Union of Crystallography journal International Union of Crystallography journal, International Union of Crystallography 2018, 5 (2), pp.166-171. ⟨10.1107/S2052252517017961⟩ Skubak, P, Arac, D, Bowler, M W, Correia, A R, Hoelz, A, Larsen, S, Leonard, G A, McCarthy, A A, McSweeney, S, Mueller-Dieckmann, C, Otten, H, Salzman, G & Pannu, N S 2018, ' A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model ', I U Cr J, vol. 5, no. Part 2, pp. 166-171 . https://doi.org/10.1107/S2052252517017961 IUCrJ IUCrJ, Vol 5, Iss 2, Pp 166-171 (2018) 'IUCrJ ', vol: 5, pages: 166-171 (2018) |
| ISSN: | 2052-2525 |
| DOI: | 10.1107/S2052252517017961⟩ |
| Popis: | A new algorithm automatically determines the structures of large macromolecules of unknown fold from low-resolution single-wavelength anomalous X-ray data and a partial model that failed with other methods. Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F1-ATPase data set and a 4.5 Å resolution SecYEG–SecA complex data set. All of the models were automatically built by the method to R free values of between 28.9 and 39.9% and were free from the initial model bias. |
| Databáze: | OpenAIRE |
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