Subscribe: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography
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Preview: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography

Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis
The type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities and has many potential applications in the industrial food processing sector. We report the crystal structure of TK-PUL which represents the first type III pullulan hydrolase to be solved, revealing N-terminal and C-terminal domains with significant differences from homologous structures.



IMAGINE: neutrons reveal enzyme chemistry
Capabilities of the IMAGINE neutron protein diffractometer at the Oak Ridge National Laboratory High Flux Isotope Reactor and highlights of the first 5 years of the scientific program are reviewed.



X-ray and UV radiation-damage phasing using synchrotron serial crystallography
Multi-crystal serial crystallography data can be used for UV and X-ray radiation-damage-induced phasing.



Exploiting distant homologues for phasing through generation of compact fragments, local fold refinement and partial solution combination
ARCIMBOLDO_SHREDDER solves structures with fragments from low-homology models. Search fragments are improved through refinement or trimming against the experimental data. Consistent solutions are combined.



Gyre and Gimble: a maximum-likelihood replacement for Patterson correlation refinement
Maximum-likelihood rigid-body refinement can be carried out to improve oriented models before the translation-function step of molecular replacement.



Overview of refinement procedures within REFMAC5: utilizing data from different sources
Here, a macromolecule-centred approach to three-dimensional structure determination as implemented in REFMAC5 is considered. The use of restraints to transfer chemical and structural information during macromolecular refinement, and how different sources of information can be combined in order to achieve models that are more consistent with data derived from a variety of experimental techniques, including macromolecular crystallography, cryo-EM and NMR spectroscopy, are discussed.



ARCIMBOLDO on coiled coils
The ARCIMBOLDO method of phasing through the location of small fragments combined with density modification and autotracing is particularly suited to helical structures, but coiled coils remain challenging. Features designed for solving coiled coils at resolutions of up to 3 Å were tested on a pool of 150 structures.



DIALS: implementation and evaluation of a new integration package
A new X-ray diffraction data-analysis package is presented with a description of the algorithms and examples of its application to biological and chemical crystallography.



Where is crystallography going?
Macromolecular crystallography has provided results that underpin much biological discovery and there is still scope for further development; however, a revolution in electron imaging now means that it can also routinely provide detailed atomic-level descriptions. This article attempts to tease out where crystallography is going and consider what its place might be in the new landscape.



CCP4i2: the new graphical user interface to the CCP4 program suite
CCP4i2 is a graphical user interface to the CCP4 (Collaborative Computational Project, Number 4) software suite and a Python language framework for software automation.



An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features
Experimental phasing of macromolecular crystals is described and explained, with the emphasis on its implementation in the programs SHELXC, SHELXD and SHELXE, which are also used in a number of macromolecular structure-solution pipelines.



Distributed computing for macromolecular crystallography
The paper describes recent CCP4 initiatives and projects aimed at bringing software and data services which utilize distributed computational resources to users.



Substructure determination using phase-retrieval techniques
The relaxed averaged alternating reflections (RAAR) phase-retrieval method has been applied to crystallography for the first time and has been shown to outperform charge flipping in anomalous substructure determination.



Macromolecular refinement by model morphing using non-atomic parameterizations
A method is described for the refinement of an electron-density model against a set of structure-factor observations which does not rely on atomic parameters. The effective level of detail in the parameterization can be varied to ensure that the refinement is well determined at any resolution supported by the data.



Maximum-likelihood determination of anomalous substructures
Likelihood-based SAD substructure determination can be initiated using a fast translation-search algorithm based on a linear approximation to the SAD likelihood target, followed by log-likelihood-gradient map completion.



Model validation: local diagnosis, correction and when to quit
An overview is provided of current crystallographic model validation of proteins and RNA, both foundations and criteria, at all resolution ranges, together with advice on how to correct specific types of problems and when you should not try so hard that you are overfitting.