issue contents

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983

April 2012 issue

Model building, refinement and validation

Proceedings of the CCP4 study weekend edited by Roberto A. Steiner, Bernhard Rupp and Charles Ballard

Highlighted illustration

Cover illustration: Speakers at the 2011 CCP4 Study Weekend.



research papers


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Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules.

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ARCIMBOLDO combines the location of small fragments with Phaser and density modification with SHELXE of all possible Phaser solutions. Its uses are explained and illustrated through practical test cases.

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Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described.

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phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

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Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled.

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Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.

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DEN refinement and automated model building with AutoBuild were used to determine the structure of a putative succinyl-diaminopimelate desuccinylase from C. glutamicum. This difficult case of molecular-replacement phasing shows that the synergism between DEN refinement and AutoBuild outperforms standard refinement protocols.

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Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening.

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A review of published tetartohedrally twinned macromolecular structures is presented, together with details of the recent structure determination of triclinic tetartohedrally twinned crystals of human complement factor I.

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Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models. The current state of ligand tools is presented.

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The CCP4 template-restraint library defines restraints for biopolymers, their modifications and ligands that are used in macromolecular structure refinement. JLigand is a graphical editor for generating descriptions of new ligands and covalent linkages.

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The challenges that arise in nucleic acid model building as a consequence of their simpler and more symmetric super-secondary structures are addressed.

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Noncrystallographic symmetry is automatically detected and used to achieve higher completeness and greater accuracy of automatically built protein structures at resolutions of 2.3 Å or poorer.

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A likelihood-based metric for scoring the local agreement of a structure model with the observed electron density is described.

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A simple rule of thumb based on resolution is not adequate to identify the best treatment of atomic displacements in macromolecular structural models. The choice to use isotropic B factors, anisotropic B factors, TLS models or some combination of the three should be validated through statistical analysis of the model refinement.

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The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described.

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The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.
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