OVIONE: a new vector-search rotation-function program for macromolecular crystallography

A computer program (OVIONE) that uses a new vector-search rotation function for crystal-structure determination by the molecular-replacement method has been developed. Image-seeking functions have proved to be useful rotation functions in macromolecular crystallography, provided that some conditions on the statistical parameters of both the crystal and the model Patterson maps are fulfilled. An appropriate selection of the vectors involved in the calculation of the image-seeking functions is crucial for the success of the proposed procedure. This selection relies on certain parameters, a careful analysis of which has been performed in order to establish optimal ranges in which the discrimination of the rotation function is enhanced. Finally, the refinement of the highest peaks of the rotation function is carried out by making use of a simple and quick minimization algorithm.

[1]  S. H. YÜ,et al.  Determination of Absolute from Relative X-Ray Intensity Data , 1942, Nature.

[2]  Steven Sheriff,et al.  Implementation of a six-dimensional search using the AMoRe translation function for difficult molecular-replacement problems , 1999 .

[3]  C. Nordman.  An application of vector space search methods to the Patterson function of myoglobin , 1972 .

[4]  J. Darnell,et al.  Structure of the amino-terminal protein interaction domain of STAT-4. , 1998, Science.

[5]  T. Eyck,et al.  Efficient structure-factor calculation for large molecules by the fast Fourier transform , 1977 .

[6]  D. Blow,et al.  The detection of sub‐units within the crystallographic asymmetric unit , 1962 .

[7]  J. Hartsuck,et al.  Rotation‐function space groups , 1980 .

[8]  L. Delbaere,et al.  The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination. , 1994, The Journal of biological chemistry.

[9]  R. C. Agarwal.  A new least‐squares refinement technique based on the fast Fourier transform algorithm: erratum , 1978 .

[10]  Robert E. Lynch,et al.  Molecular replacement real‐space averaging , 1992 .

[11]  George M. Sheldrick,et al.  Crystallographic Computing 3: Data Collection, Structure Determination, Proteins and Databases , 1985 .

[12]  Randy J. Read,et al.  Experiences with a new translation-function program , 1987 .

[13]  H. Hauptman.  Solution of the phase problem , 1953 .

[14]  T O Yeates,et al.  Intensity-based domain refinement of oriented but unpositioned molecular replacement models. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[15]  Glaucius Oliva,et al.  Fast Rigid-Body Refinement for Molecular-Replacement Techniques , 1992 .

[16]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[17]  M. Buerger.  Vector space : and its application in crystal-structure investigation , 1959 .

[18]  F. Winkler,et al.  Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution. , 1995, Biochemistry.

[19]  C. Nordman.  Procedures for Detection and Idealization of Non-crystallographic Symmetry with Application to Phase Refinement of the Satellite Tobacco Necrosis Virus Structure , 1980 .

[20]  D. Rabinovich,et al.  A new approach to structure determination of large molecules by multi-dimensional search methods , 1984 .

[21]  Jorge Navaza,et al.  [33] AMoRe: An automated molecular replacement program package. , 1997, Methods in enzymology.

[22]  M G Rossmann,et al.  The molecular replacement method. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[23]  L. M. Urzhumtseva,et al.  Tcl/Tk-based programs. II. CONVROT: a program to recalculate different rotation descriptions , 1997 .

[24]  Axel T. Brunger,et al.  X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .

[25]  L. Delbaere,et al.  Mutation of serine-46 to aspartate in the histidine-containing protein of Escherichia coli mimics the inactivation by phosphorylation of serine-46 in HPrs from gram-positive bacteria. , 1996, Biochemistry.

[26]  C. E. Nordman.  A generalized Patterson-search method , 1994 .

[27]  Axel T. Brunger,et al.  Extension of molecular replacement: a new search strategy based on Patterson correlation refinement , 1990 .

[28]  Alfonso Mondragón,et al.  Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I , 1994, Nature.

[29]  G. Sheldrick,et al.  Search for a fragment of known geometry by integrated Patterson and direct methods , 1984 .

[30]  R. Sessions,et al.  Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group. , 1999, Nucleic acids research.

[31]  K. Nakatsu,et al.  Interpretation of the Patterson Function of Crystals Containing a Known Molecular Fragment. the Structure of an Alstonia Alkaloid , 1963 .