issue contents

Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047

April 2011 issue

From crystal to structure with CCP4

Proceedings of the CCP4 study weekend

Highlighted illustration

Cover illustration: Human Thr160-phospho-CDK2-cyclin A complexed with a bis-anilino-pyrimidine inhibitor, PDB entry 2iw6. Drawn using CCP4mg (p. 386).



research papers



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Protein surface engineering is increasingly used as a routine tool to enhance the crystallization propensity of proteins. Future possibilities include the use of multi-site protein variants, rational modulation of solubility and the development of strategies to tackle membrane proteins.


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Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented.

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A new graphical user interface to the MOSFLM program has been developed to simplify the processing of macromolecular diffraction data. The interface, iMOSFLM, allows data processing via a series of clearly defined tasks and provides visual feedback on the progress of each stage.


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Typical topics and problems encountered during data processing of diffraction experiments are discussed and the tools provided in the autoPROC software are described.

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The molecular-replacement model-improvement program Sculptor is described, with an analysis of the algorithms used.

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The automated pipelines for molecular replacement MrBUMP and BALBES are reviewed, with an emphasis on understanding their output. Conclusions are drawn from their performance in extensive trials.

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Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described.

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Recent developments in the CRANK software suite for experimental phasing have led to many more structures being built automatically.

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SAD data can be used in Phaser to solve novel structures, supplement molecular-replacement phase information or identify anomalous scatterers from a final refined model.

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A cross-validation-based method for bias reduction in `classical' iterative density modification of experimental X-ray crystallography maps provides significantly more accurate phase-quality estimates and leads to improved automated model building.

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The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.

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The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures.

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Methods for the analysis of the relationship between macromolecular complexes and interactions and their manifestation in crystal packing are described and discussed.

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The CCP4 molecular-graphics program now uses the Qt framework to provide a modern look and feel. There are many new features including rendering for publication-quality images and sequence alignment.
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