<i>MxCuBE</i>: a synchrotron beamline control environment customized for macromolecular crystallography experiments

Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren; Bowler, Matthew W.; Brockhauser, Sándor; Flot, David; Gordón, E.; Hall, David R.; Lavault, Bernard; McCarthy, A.A.; McCarthy, Joanne; Mitchell, Edward P.; Monaco, S.; Mueller-Dieckmann, Christoph; Nurizzo, Didier; Ravelli, R.B.G.; Thibault, X.; Walsh, Martin A.; Leonard, Gordon A.; McSweeney, Seán

doi:10.1107/s0909049510020005

Cited by 205 publications

(172 citation statements)

References 26 publications

(30 reference statements)

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“…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). The process of automatic data reduction begins when the user initiates a data collection in MxCuBE and has enabled the 'Process and Analyze Data' check box (activated by default).…”

Section: Mxcube and The Autoprocessing Servermentioning

confidence: 99%

“…Several programming languages and protocols have been employed to integrate the disparate technologies involved. The ESRF MX beamline control graphical user interface (GUI) MxCuBE (Gabadinho et al, 2010) and the autoprocessing server are written in Python. Perl is used as a 'glue code' to pipeline XDS (Kabsch, 2010), XSCALE (Kabsch, 2010), SCALEPACK2MTZ (Winn et al, 2011), SCALA (Evans, 2011), POINTLESS (Evans, 2011), TRUNCATE (Winn et al, 2011) and SHELXC/D/E (Sheldrick, 2010).…”

Section: Architecturementioning

confidence: 99%

“…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 now 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). In many cases, complete diffraction datasets can be collected in under one minute (Hü lsen et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

et al. 2013

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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.

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Section: Mxcube and The Autoprocessing Servermentioning

confidence: 99%

Section: Architecturementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

et al. 2013

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“…Diffraction data of native and derivative crystals at the peak edge of tantalum were collected at beamline 14-4, European Synchrotron Radiation Facility (ESRF), Grenoble. Optimal diffraction volumes were defined by diffraction cartography (38) as implemented in the workflow interface of the beamline control GUI MXCuBE (39,40). Integration, scaling, and merging of intensities were carried out using Mosflm and Scala from the CCP4 program suite (41).…”

Section: Methodsmentioning

confidence: 99%

QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing

Fan

Dong

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Significance Quorum sensing is a bacterial cell–cell communication system that is activated when the concentration of quorum sensing signal (autoinducer) reaches a threshold. In Pseudomonas aeruginosa , an opportunistic human pathogen, the quorum sensing threshold and response are defined by a novel antiactivator, QslA, which binds to the transcription factor LasR and prevents it from binding to its target DNA. However, how QslA binds to LasR and negatively regulates quorum sensing is poorly understood. Here we show that QsIA binds LasR to disrupt its dimerization, thereby inhibiting the DNA binding of LasR and shutting down transcription. Our findings reveal the molecular basis of a unique QsIA-mediated LasR inactivation and add an example to understand the antiactivation mechanism in bacterial quorum sensing.

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“…Protein crystallography is now a mainstream research technique and the rate of structure deposition in the Protein Data Bank keeps increasing (AbadZapatero, 2012). Nevertheless, despite much automation, data collection remains a nontrivial experiment that requires diligent planning and careful checks, while the brightness and brilliance of third-generation synchrotrons pose a whole additional set of challenges (Chavas et al, 2012;Dauter et al, 2010;Fodje et al, 2012;Gabadinho et al, 2010;Gonzá lez et al, 2008;McCarthy et al, 2009). The availability of ever smaller and brighter beams has boosted the field on the one hand, but it has also increased the requirement of the experimenter to make the correct choices at the beamline.…”

Section: Introductionmentioning

confidence: 99%

Squeezing the most from every crystal: the fine details of data collection

Krojer¹,

Pike²,

Delft³

2013

Acta Crystallogr D Biol Cryst

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Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice.

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MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

Cited by 205 publications

References 26 publications

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing

Squeezing the most from every crystal: the fine details of data collection

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