The magic triangle goes MAD: experimental phasing with a bromine derivative

5-Amino-2,4,6-tribromoisophthalic acid is used as a phasing tool for protein structure determination by MAD phasing. It is the second representative of a novel class of compounds for heavy-atom derivatization that combine heavy atoms with amino and carboxyl groups for binding to proteins

Geometric properties of nucleic acids with potential for autobuilding

Algorithms and geometrical properties are described for the automated building of nucleic acids in experimental electron density

iGentifier: indexing and large-scale profiling of unknown transcriptomes

Development and refinement of methods to analyse differential gene expression has been essential in the progress of molecular biology. A novel approach called iGentifier is presented for profiling known and unknown transcriptomes, thus bypassing a major limitation in microarray analysis. The iGentifier technology combines elements of fragment display (e.g. Differential Display or RMDD) and tag sequencing (e.g. SAGE, MPSS) and allows for analysis of samples in high throughput using current capillary electrophoresis equipment. Application to epidermal tissue of wild-type and mlo5 barley (Hordeum vulgare) plants, infected with powdery mildew [Blumeria graminis (DC.) E.O. Speer f.sp.hordei], led to the identification of several 100 genes induced or repressed upon infection with many well known for their response to fungal pathogens or other stressors. Ten of these genes are suggested to be classified as marker genes for durable resistance mediated by the mlo5 resistance gene

<i>mrtailor</i>: a tool for PDB-file preparation for the generation of external restraints

Model building starting from, for example, a molecular-replacement solution with low sequence similarity introduces model bias, which can be difficult to detect, especially at low resolution. The program mrtailor removes low-similarity regions from a template PDB file according to sequence similarity between the target sequence and the template sequence and maps the target sequence onto the PDB file. The modified PDB file can be used to generate external restraints for low-resolution refinement with reduced model bias and can be used as a starting point for model building and refinement. The program can call ProSMART [Nicholls et al. (2012), Acta Cryst. D68, 404-417] directly in order to create external restraints suitable for REFMAC5 [Murshudov et al. (2011), Acta Cryst. D67, 355-367]. Both a command-line version and a GUI exist.Volkswagen Stiftung via the Niedersachsen-professu

New method to compute <i>R</i> _complete enables maximum likelihood refinement for small datasets

Significance Modern crystallographic structure determination uses maximum likelihood methods. They rely on error estimates between the work model and the unknown target based on a small fraction of the data. This can introduce a large uncertainty and, even worse, restricts the method to projects where sufficient data are available. We investigate the R complete method. It enables the use of all data for error estimation. It reduces the uncertainty associated with the conventional R free approach for small datasets. We show that our approach reduces the effect of overfitting. This enables maximum likelihood methods to be extended to a much wider field of applications, including free electron laser experiments, high-pressure crystallography, and low-resolution structures. </jats:p