|
International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 15.1, p. 318
Section 15.1.2.6. Atomization
a
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA 90109, USA,bDepartment of Chemistry, University of York, York YO1 5DD, England, and cDepartment of Physics, University of York, York YO1 5DD, England |
The atomization method uses the fact that the structure underlying the map consists of discrete atoms. It attempts to interpret the map by automatically placing atoms and refining their positions.
Agarwal & Isaacs (1977)![[link]](/graphics/greenarr.gif)
proposed a method for the extension of phases to higher resolutions by interpreting an electron-density map in terms of `dummy' atoms. These are so called because at the initial resolution of 3.0 Å, true atom peaks could not be resolved. The placement of `dummy atoms' is subject to constraints of bonding distance and the number of neighbours. The coordinates and temperature factors of these dummy atoms may then be refined against all the available diffraction amplitudes. Structure factors may then be calculated from the refined coordinates to provide phases for the high-resolution reflections and to improve the phases of the starting set.
The atomization approach has been extended in the ARP program (Lamzin & Wilson, 1997) by the use of difference-map criteria to test dummy-atom assignments, with the aim of removing wrong atoms and introducing missing atoms. With modern refinement algorithms, this technique has become very effective for the solution of structures at high resolution from a poor molecular-replacement model, or even directly from an MIR/MAD map.
Map improvement has also been demonstrated at intermediate resolutions by Perrakis et al. (1997) using a multi-solution variant of the ARP method, and by Vellieux (1998).
The interpretation of an approximately phased map has also been applied very successfully as part of the `Shake n' Bake' direct-methods procedure (Miller et al., 1993; Weeks et al., 1993). The alternating application of phase refinement by the minimum principle in reciprocal space (`Shake') and atomization in real space (`Bake') has proved to be a very powerful method for solving small protein structures at atomic resolution using only structure-factor amplitudes.
References
Agarwal, R. C. & Isaacs, N. W. (1977). Method for obtaining a high resolution protein map starting from a low resolution map. Proc. Natl Acad. Sci. USA, 74(7), 2835–2839.Google Scholar
Lamzin, V. S. & Wilson, K. S. (1997). Automated refinement for protein crystallography. Methods Enzymol. 277, 269–305.Google Scholar
Miller, R., DeTitta, G. T., Jones, R., Langs, D. A., Weeks, C. M. & Hauptman, H. A. (1993). On the application of the minimal principle to solve unknown structures. Science, 259, 1430–1433.Google Scholar
Perrakis, A., Sixma, T. K., Wilson, K. S. & Lamzin, V. S. (1997). wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Cryst. D53, 448–455.Google Scholar
Vellieux, F. M. D. (1998). A comparison of two algorithms for electron-density map improvement by introduction of atomicity: skeletonization, and map sorting followed by refinement. Acta Cryst. D54, 81–85.Google Scholar
Weeks, C. M., DeTitta, G. T., Miller, R. & Hauptman, H. A. (1993). Applications of the minimal principle to peptide structures. Acta Cryst. D49, 179–181.Google Scholar
