M D Winn | PubMed Health

PubMed2002

An overview of the CCP4 project in protein crystallography: an example of a collaborative project.

The Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. CCP4 now distributes a large software suite and is active in developing new software. Equally importantly, CCP4 provides a focus for the whole protein crystallography community via meetings, workshops, email lists and various publications. In this Article, an overview is given of CCP4 activities and their administration. The emphasis is on generic features of the collaboration rather than details specific to protein crystallography. The CCP4 model has inspired similar developments in NMR, and it is hoped that the biological XAS community may pursue similar collaboration.

Crystallography, X-Ray↗

PubMed2002

Ongoing developments in CCP4 for high-throughput structure determination.

Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. From these beginnings, CCP4 now distributes a large software suite and is active in developing new software. In this article, an overview is given of recent and ongoing developments in the CCP4 software suite, in particular as they pertain to high-throughput studies. Developments in individual programs are discussed first, although these are covered in more detail elsewhere. The bulk of the article focuses on the infrastructure of the software suite which allows the user to move effortlessly between different programs or to create automated schemas. Major changes to the software library at the heart of the CCP4 suite, developments in the CCP4 graphical user interface, and data management within CCP4 are discussed. The latter is crucial to high-throughput studies, where a large number of data are imported, created and finally archived.

Crystallography, X-Ray↗

PubMed2001

Use of TLS parameters to model anisotropic displacements in macromolecular refinement.

An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.

Glyceraldehyde-3-Phosphate Dehydrogenases↗