Automated refinement for protein crystallography.

Publisher Summary This chapter discusses an automated refinement procedure (ARP) for proteins. The basis of ARP is the iterative use of unrestrained least-squares minimization coupled with constant updating of the model. This is comparable to the iterative least-squares/Fourier synthesis approach for small molecules. It requires X-ray data to 2.0 A, or better, to allow unrestrained refinement and improvement of the whole content of the unit cell. At lower resolutions, as a rule, only unrestrained parts of the model are expected to be improved. The quality of data and the initial phase set greatly influences the power of ARP. Applied to the refinement of a medium-size structure at 1.0 A resolution and starting from one heavy-atom position, ARP determined the complete structure in a fully automated manner. ARP uses atomicity as the main property of the structure and differs completely from, for example, direct methods that are based on atomicity through statistical relationships between amplitudes of structure factors.

[1]  V. Luzzati,et al.  Resolution d'un structure cristalline lorsque les positions d'une partie des atoms sont connues: traitement statistique , 1953 .

[2]  L. H. Jensen,et al.  X-Ray Structure Determination: A Practical Guide , 1989 .

[3]  M Zwick,et al.  Improving crystallographic macromolecular images: the real-space approach. , 1987, Annual Review of Biophysics and Biophysical Chemistry.

[4]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[5]  Peter Main,et al.  Histogram matching as a new density modification technique for phase refinement and extension of protein molecules , 1990 .

[6]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[7]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[8]  Wayne A. Hendrickson,et al.  A restrained-parameter thermal-factor refinement procedure , 1980 .

[9]  K S Wilson,et al.  Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin. , 1995, Structure.

[10]  Peter Main.  A formula for electron density histograms for equal-atom structures , 1990 .

[11]  R. Read.  Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .

[12]  G. Sheldrick.  Phase annealing in SHELX-90: direct methods for larger structures , 1990 .

[13]  Alexandre Urzhumtsev,et al.  Phase Improvement in Protein Crystallography Using a Mixed Electron Density Model , 1985 .

[14]  D. Sayre,et al.  On least-squares refinement of the phases of crystallographic structure factors , 1972 .

[15]  Zbigniew Dauter,et al.  Crystal structure of a dUTPase , 1992, Nature.