CRANK: new methods for automated macromolecular crystal structure solution.

CRANK is a novel suite for automated macromolecular structure solution and uses recently developed programs for substructure detection, refinement, and phasing. CRANK utilizes methods for substructure detection and phasing and combines them with existing crystallographic programs for density modification and automated model building in a convenient and easy-to-use CCP4i graphical interface. The data model used conforms to the XML eXtensible Markup Language specification and works as a common language to communicate data between many different applications inside and outside of the suite. The application of CRANK on various test cases has yielded promising results: with minimal user input, CRANK can produce better quality solutions over currently available programs.

[1]  G. Bricogne,et al.  [27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. , 1997, Methods in enzymology.

[2]  Z Dauter,et al.  Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A. , 2000, Structure.

[3]  Russ Miller,et al.  The design and implementation of SnB version 2.0 , 1999 .

[4]  J P Abrahams,et al.  Matrix methods for solving protein substructures of chlorine and sulfur from anomalous data. , 2001, Acta crystallographica. Section D, Biological crystallography.

[5]  Thomas C. Terwilliger,et al.  Automated MAD and MIR structure solution , 1999, Acta crystallographica. Section D, Biological crystallography.

[6]  Didier Nurizzo,et al.  Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27. , 2003, Structure.

[7]  A Wlodawer,et al.  Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics. , 2001, Acta crystallographica. Section D, Biological crystallography.

[8]  Zbigniew Dauter,et al.  Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme , 2000, Nature Structural Biology.

[9]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[10]  Nobutoshi Ito,et al.  Development of PDBj-ML , 2002 .

[11]  K S Wilson,et al.  Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein. , 1997, Biochemistry.

[12]  Robert H. Blessing,et al.  Towards automated protein structure determination: BnP, the SnB-PHASES interface , 2002 .

[13]  Maria Cristina Burla,et al.  SAD or MAD phasing: location of the anomalous scatterers. , 2003, Acta crystallographica. Section D, Biological crystallography.

[14]  P Murray-Rust,et al.  The globalization of crystallographic knowledge. , 1998, Acta crystallographica. Section D, Biological crystallography.

[15]  Randy J Read,et al.  The application of multivariate statistical techniques improves single-wavelength anomalous diffraction phasing. , 2004, Acta crystallographica. Section D, Biological crystallography.

[16]  P J Briggs,et al.  Ongoing developments in CCP4 for high-throughput structure determination. , 2002, Acta crystallographica. Section D, Biological crystallography.

[17]  Randy J Read,et al.  Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing. , 2003, Acta crystallographica. Section D, Biological crystallography.

[18]  Robert H. Blessing,et al.  Difference structure‐factor normalization for heavy‐atom or anomalous‐scattering substructure determinations , 1999 .

[19]  Tom Alber,et al.  Automated protein crystal structure determination using ELVES. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D Spruce,et al.  Automation of the collection and processing of X-ray diffraction data -- a generic approach. , 2002, Acta crystallographica. Section D, Biological crystallography.

[21]  P. Adams,et al.  Substructure search procedures for macromolecular structures. , 2003, Acta crystallographica. Section D, Biological crystallography.

[22]  Zbigniew Dauter,et al.  Jolly SAD. , 2003, Acta crystallographica. Section D, Biological crystallography.

[23]  Peter Briggs,et al.  A graphical user interface to the CCP4 program suite. , 2003, Acta crystallographica. Section D, Biological crystallography.

[24]  Manfred S. Weiss,et al.  Global indicators of X-ray data quality , 2001 .

[25]  G. D. Smith,et al.  Matching selenium-atom peak positions with a different hand or origin , 2002 .

[26]  K S Wilson,et al.  Crystallization and preliminary X-ray diffraction studies of an alkaline protease from Bacillus lentus. , 1988, Journal of molecular biology.

[27]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[28]  Thomas R. Schneider,et al.  HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs , 2004 .

[29]  Zhong Ren,et al.  Automated crystallographic system for high-throughput protein structure determination. , 2003, Acta crystallographica. Section D, Biological crystallography.

[30]  Anastassis Perrakis,et al.  The crystal structure of DNA mismatch repair protein MutS binding to a G·T mismatch , 2000, Nature.

[31]  G Bricogne,et al.  Can anomalous signal of sulfur become a tool for solving protein crystal structures? , 1999, Journal of molecular biology.

[32]  Z Dauter,et al.  Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy. , 2001, Acta crystallographica. Section D, Biological crystallography.