Abstract
The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.
Highlights
The European Synchrotron Radiation Facility (ESRF) MX beamline control graphical user interface (GUI) MxCuBE (Gabadinho et al, 2010) and the autoprocessing server are written in Python
MxCuBE is the generic beamline control GUI used on all the Joint Structural Biology Group (JSBG) MX beamlines at the ESRF (Gabadinho et al, 2010)
An increasingly common strategy for obtaining a higher-quality dataset than would otherwise be possible by collecting from a single position in a crystal is through the exploitation of small X-ray beams and high-precision goniometers (Perrakis et al, 1999; Hilgart et al, 2011), where radiation damage is limited by exposing fresh crystal volumes
Summary
The combination of highly intense focused X-ray beams, automatic sample changers, automated beam delivery, online data analysis and fast readout detectors at synchrotron macromolecular crystallography (MX) beamlines allows for the collection of hundreds of datasets during each assigned experimental session (Arzt et al, 2005; Beteva et al, 2006; Bourenkov & Popov, 2010; Bowler et al, 2010; Cherezov et al, 2009; Cipriani et al, 2006; de Sanctis et al, 2012; Flot et al, 2010; Gabadinho et al, 2010; Incardona et al, 2009; Jacquamet et al, 2009; Leslie et al, 2002; McCarthy et al, 2009; McPhillips et al, 2002; Nurizzo et al, 2006; Soltis et al, 2008). The first and most benign effect is a vast increase in the amount of work and book-keeping necessary if all datasets are to be processed and analysed In such situations it can be difficult even to identify the best dataset [for example, highest overall resolution, best overall hI/(I )i] from a particular project or experimental session. No existing solution could offer the level of integration that we needed; we created an in-house automatic data processing system that relies heavily on the built-in automation of the XDS processing package (Kabsch, 2010) We describe this simple and fast system, which processes diffraction data collected at the ESRF MX beamlines and presents the results and data to users
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