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



 



Estimation of the protein–ligand interaction energy for model building and validation
The use of the protein–ligand interaction energy as an additional parameter for the automated identification of crystallographic ligands and its applicability to structure validation are described.



Proper modelling of ligand binding requires an ensemble of bound and unbound states
The importance of modelling the superpositions of ligand-bound and unbound states that commonly occur in crystallographic data sets is emphasized and demonstrated. The generation of an ensemble that models not only the state of interest is important for the high-quality refinement of low-occupancy ligands, as well as to explain the observed density more completely.



Tools for ligand validation in Coot
The current tools for ligand validation and comparison in Coot are presented. The user-selected ligand is assessed by ligand-distortion, map-correlation and temperature-factor metrics and compared with those of ligands from the wwPDB to create a percentile rank.



Gentle, fast and effective crystal soaking by acoustic dispensing
A high-throughput method is described for crystal soaking using acoustic droplet ejection, and its effectiveness is demonstrated.



The Dynamo package for tomography and subtomogram averaging: components for Matlab, GPU computing and EC2 Amazon Web Services
A technical description of the Dynamo software package for subtomogram averaging is provided. Details are given on advanced Matlab libraries, parallelization strategies, the use of GPU and accessibility though the Amazon cloud computing services.



Low-dose fixed-target serial synchrotron crystallography
A time- and sample-efficient approach for the serial collection of room-temperature diffraction data using a fixed target at a synchrotron is demonstrated.



Crystal structures of Hsp104 N-terminal domains from Saccharomyces cerevisiae and Candida albicans suggest the mechanism for the function of Hsp104 in dissolving prions
The crystal structures of Hsp104 N-terminal domains from S. cerevisiae (ScHsp104NTD) and C. albicans (CaHsp104NTD) were determined to high resolution. The structures of ScHsp104NTD and CaHsp104NTD reveal that the yeast Hsp104 N-terminal domain may utilize a conserved putative peptide-binding groove to interact with misfolded polypeptides.



1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF
The crystal structure of the carbapenem-resistance protein CarF has been determined at 1.8 Å resolution. CarF confers partial intrinsic resistance to the naturally occurring antibiotic 1-carbapen-2-em-3-carboxylic acid.



`Atomic resolution': a badly abused term in structural biology
The term `atomic resolution' is very often abused in presenting macromolecular structures.



Is dimerization a common feature in thioredoxins?: the case of thioredoxin from Litopenaeus vannamei
This study of shrimp thioredoxin sheds new light on the existence of monomeric and dimeric populations in solution. It is demonstrated that the Cys73 residue is essential for dimer formation and that the Cys73Ser mutant has the same activity as the wild type.



Crystal structures of human 3-hydroxyanthranilate 3,4-dioxygenase with native and non-native metals bound in the active site
Two structures of human 3-hydroxyanthranilate 3,4-dioxygenase, one with iron bound at the active site and one with zinc bound at the active site, are reported.



CheckMyMetal: a macromolecular metal-binding validation tool
The metal-site validation tool CheckMyMetal is described, with examples to follow.



The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery
Small-molecule crystal structures are of tremendous value in understanding protein–ligand complexes, both individually and as a collection.



Dissecting random and systematic differences between noisy composite data sets
A multidimensional scaling analysis of pairwise correlation coefficients is presented which positions data sets in a sphere with unit radius of an abstract, low-dimensional space at radii inversely proportional to their levels of random error and at spherical angles related to their mutual systematic differences. This reduction in dimensionality can not only be used for classification purposes, but also to derive data-set relations on a continuous scale.



Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography
Using all available metal-containing organic compound structures in the Cambridge Structural Database, a novel data-driven method to derive bond-valence R0 parameters was developed. While confirming almost all reference literature values, we observe two distinct populations of FeII—N and FeIII—N bonds, which are interpreted as low-spin and high-spin states of the coordinating iron. Based on the R0 parameters derived here, guidelines for the modeling of iron–ligand distances in macromolecular structures are suggested.



Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode
The structure of an Hfq homolog from the deep-branching thermophilic bacterium A. aeolicus, determined to 1.5 Å resolution both in the apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer.



The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination
XChemExplorer is a graphical workflow and data-management tool for the parallel determination of protein–ligand complexes. Its implementation, usage and application are described here.



A pipeline approach to single-particle processing in RELION
The formal description of a workflow to cryo-EM structure determination in the RELION program allows standardization of procedures and on-the-fly image processing during data acquisition.