CCP 4 Version 4 0 The

CCP 4 Version 4. 0. . . The most recent version of the CCP 4 suite is 4. 0, which was released in January 2000, with a minor patch release shortly after. Below are some of the highlights in this latest version of the Suite. Data harvesting molrep Alexei Vagin’s automated program for molecular replacement. Data harvesting means that the software used in structure solution outputs details of the method used and the results obtained (for example, the heavy atom sites used in phasing). The information is stored in deposition files (also called harvest files) - by the time the user is ready to deposit the model coordinates there should be a collection of such files holding details of how the model was obtained. These can be sent directly to the deposition centre - thereby by-passing much of the manual processing required by Auto. Dep. Within CCP 4 4. 0 the programs SCALA, TRUNCATE, MLPHARE, REFMAC and RESTRAIN have been upgraded to produce harvest files. For more information on Data Harvesting see CCP 4 Newsletters 37 (October 1999) and 35 (July 1998). The program utilises new approaches in data processing and rotational and translation searching to give improved molecular replacement solutions. Left: The enzyme D-alanine-D-lactate ligase (Van. A) from Enterococcus faecium BM 4147 is directly responsible for the biosynthesis of alternate cell wall precursors in clinically prevalent Enterococcal species which are resistant to the glycopeptide antiobiotic Vancomycin. The structure of Van. A was determined from data extending to 2. 5Å with the aid of MOLREP. The structure of the active site was found to differ significantly from the model previously assumed (from the functionally related D-Alanyl-D-Alanine ligase from E. coli), leading to a revised understanding of the mechanism for Vancomycin resistance. Reference: Roper, D. I. , Huyton T. , Veguine A. , & Dodson G. (2000) “The Molecular Basis of Vancomycin Resistance in Clinically Relevant Enterococci. Crystal Structure of D-alanyl-D-lactate ligase (Van. A)” PNAS (in press) sc Right: Surface complementarity between influzena virus tern N 9 neuraminidase (right) and the NC 10 single-chain antibody variable domain (left), based on the coordinates of the PDB entry 1 A 14. The interface is shown opened out in book-like fashion, with Sc values coloured from white (Sc = 0. 0) to blue (Sc=1. 0). Regions shown in red have Sc<0. 0, or lie outside of the buried area considered for the calculation of Sc. Mike Lawrence’s program for determining the shape complementarity statistic Sc of two interacting molecular surfaces. The picture was generated using the program SC , and displayed using GRASP (Nichols, A. J. , (1993) Biophys. J. 64, A 116. ) ccp 4 i: CCP 4 graphical interface CCP 4 i provides a simple graphical user interface for running the CCP 4 programs, plus a set of utilities for easy viewing of standard CCP 4 -format files, a database facility to assist with project management, and an integrated help system. CCP 4 i version 1. 1. 1 is now officially part of the main suite and is no longer distributed separately. Reference: Lawrence, M. C. & Coleman, P. M. (1993) “Shape complementarity at protein/protein interfaces” J. Mol. Biol. 234, 946 -950. oasis Program using direct methods to break the intrinsic phase ambiguity in OAS and SIR problems (Q. Hao, Y. X. Gu, C. D. Zheng & H. F. Fan). Direct Methods on their own require high resolution - OASIS however has been successful at moderate resolution (1. 4 - 2. 5Å). Left: Rusticyanin is a type-1 blue copper protein (17 k. Da) and is thought to be a principal component in the iron respiratory electron transport chain of Thiobacillus ferrooxidans. The structure of rusticyanin was solved with the aid of the OASIS program using one wavelength anomalous scattering data at 2. 1Å resolution collected near the copper absorption edge. Updated programs • DM 2. 0. 5 - density modification package. • SCALA 2. 7. 2 - scale together multiple observations of reflections. • TOPP 6. 5 - automatic topological and atomic comparison program. • AMORE - a major new version of Jorge Navaza’s molecular replacement package. • RASMOL 2. 7. 1 - updated version of the molecular visualisation program. • SFCHECK 5. 3. 4 - program for assessing agreement between atomic model and X-ray data. • ARP_WARP 5. 0 - popular automated refinement program. Plus: updated versions of AREAIMOL, DETWIN, SCALEIT, TRUNCATE and others Reference: Harvey, I. , Hao, Q. , Duke, E. M. H. , Ingledew, W. J. & Hasnain, S. S. (1998) Acta. Cryst. D 54 629 -635 “Structure Determination of a 16. 8 k. Da Copper Protein at 2. 1Å Resolution Using Anomalous Scattering Data with Direct Methods. ” Future developments CCP 4 NT : a preliminary version is now available which allows the CCP 4 suite to run under Microsoft NT REFMAC : the current β-release of Refmac includes: refinement of TLS parameters; bulk solvent correction; new dictionary. It also dispences with the need to run PROTIN. MAPSLICE : viewing contoured sections through maps (replacement for NPO) CCP 4 4. 1 : the next release will include D*TREK 2 MTZ, CAVENV, ROTGEN, FFFEAR, MOSFLM and others