Version 1.2 of the Crystallography and NMR system

Version 1.2 of the software system, termed Crystallography and NMR system (CNS), for crystallographic and NMR structure determination has been released. Since its first release, the goals of CNS have been (i) to create a flexible computational framework for exploration of new approaches to structure determination, (ii) to provide tools for structure solution of difficult or large structures, (iii) to develop models for analyzing structural and dynamical properties of macromolecules and (iv) to integrate all sources of information into all stages of the structure determination process. Version 1.2 includes an improved model for the treatment of disordered solvent for crystallographic refinement that employs a combined grid search and least-squares optimization of the bulk solvent model parameters. The method is more robust than previous implementations, especially at lower resolution, generally resulting in lower R values. Other advances include the ability to apply thermal factor sharpening to electron density maps. Consistent with the modular design of CNS, these additions and changes were implemented in the high-level computing language of CNS.

[1]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[2]  S. Phillips,et al.  Structure and refinement of oxymyoglobin at 1.6 A resolution. , 1980, Journal of molecular biology.

[3]  F. M. Richards,et al.  Calculation of molecular volumes and areas for structures of known geometry. , 1985, Methods in enzymology.

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

[5]  G. Stubbs,et al.  Molecular dynamics in refinement against fiber diffraction data. , 1993, Acta crystallographica. Section A, Foundations of crystallography.

[6]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[7]  G. Phillips,et al.  Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[8]  A T Brünger,et al.  Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. , 1994, Journal of molecular biology.

[9]  V. N. Molchanov,et al.  Superconducting Single Crystals of Tl2Ba2CaCu2O8 and YBa2Cu4O8: Crystal Structures in the Vicinity of Tc , 1998 .

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

[11]  Shankar Subramaniam,et al.  Protein structure determination using a database of interatomic distance probabilities , 1999, Protein science : a publication of the Protein Society.

[12]  Paul D. Adams,et al.  On the handling of atomic anisotropic displacement parameters , 2002 .

[13]  Pavel Strop,et al.  Crystal Structure of Escherichia coli MscS, a Voltage-Modulated and Mechanosensitive Channel , 2002, Science.

[14]  John D Westbrook,et al.  The PDB format, mmCIF, and other data formats. , 2003, Methods of biochemical analysis.

[15]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

[16]  Kristina Downing,et al.  Faculty Opinions recommendation of HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003 .

[17]  Michael Nilges,et al.  ARIA: automated NOE assignment and NMR structure calculation , 2003, Bioinform..

[18]  Charles D Schwieters,et al.  The Xplor-NIH NMR molecular structure determination package. , 2003, Journal of magnetic resonance.

[19]  B. Delabarre,et al.  Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains , 2003, Nature Structural Biology.

[20]  Thomas Simonson,et al.  Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum. , 2003, Acta crystallographica. Section D, Biological crystallography.

[21]  Axel T Brunger,et al.  Nucleotide dependent motion and mechanism of action of p97/VCP. , 2005, Journal of molecular biology.

[22]  P. Adams,et al.  Electronic Reprint Biological Crystallography a Robust Bulk-solvent Correction and Anisotropic Scaling Procedure Afonine Et Al. ¯ Bulk-solvent Correction and Anisotropic Scaling Biological Crystallography a Robust Bulk-solvent Correction and Anisotropic Scaling Procedure , 2004 .

[23]  Axel T Brunger,et al.  Considerations for the refinement of low-resolution crystal structures. , 2006, Acta crystallographica. Section D, Biological crystallography.