SPINE workshop on automated X-ray analysis: a progress report

Abstract

The Structural Proteomics In Europe (SPINE) consortium contained a workpackage to address the automated X-ray analysis of macromolecules. The aim of this workpackage was to increase the throughput of three-dimensional structures while maintaining the high quality of conventional analyses. SPINE was able to bring together developers of software with users from the partner laboratories. Here, the results of a workshop organized by the consortium to evaluate software developed in the member laboratories against a set of bacterial targets are described. The major emphasis was on molecular-replacement suites, where automation was most advanced. Data processing and analysis, use of experimental phases and model construction were also addressed, albeit at a lower level.

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

“…The R free and R work of the initial model were 39% and 34%, respectively. The model was further improved by iterative rounds of manual model building in COOT (46) and refinement in PHENIX (47). By using NCS restraints, TLS refinement, and SA the R free and R work could be improved to 22 and 28%, respectively.…”

Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine

“…Full data sets were collected to 1.35 Å (DH) and 2.1 Å resolution . Diffraction data of the DH complex were processed with the programs MOSFLM (19) and SCALA implemented in the program package CCP4i (20), whereas the data of the MSVIII-19 complex were processed with the program XIA using XDS (21). For crystal data and data collection statistics, see Table 1.…”

Structure of 5-formyltetrahydrofolate cyclo-ligase fromBacillus anthracis(BA4489)

“…Diffraction data were recorded (at the ESRF synchrotron, beamline ID14-EH1) in two passes: a high-resolution pass of 362 images was initially recorded using 0.5 oscillations, 6 s exposures and a crystal-to-detector distance of 114 mm, followed by a low-resolution pass of 113 images using 2 oscillations, 2 s (the first 21 images) or 1 s exposures and a crystal-to-detector distance of 286 mm. However, processing these images using either DENZO or MOSFLM was initially problematic owing to scaling problems that we attribute to a high mosaic spread (Bahar et al, 2006. In DENZO, refining the mosaicity proved unstable and the most plausible processing was obtained using a fixed mosaicity of 1.5 , while with MOSFLM the refined mosaicity varied between 1.2 and 4 . As part of a crystallographic workshop, the diffraction data were reprocessed using the program XDS (Kabsch, 1993), which yielded an improved data set with a mosaicity of 0.6 (using the XDS definition; see Table 1 and Bahar et al, 2006 for more details).…”