Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13

Perrakis, Anastassis; Cipriani, F.; Castagna, Jean-Charles; Claustre, L.; Burghammer, Manfred; Cusack, Stephen

doi:10.1107/s0907444999009348

Cited by 94 publications

(91 citation statements)

References 6 publications

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“…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. Examples of this include collection of 'helical' datasets in which the sample is translated with simultaneous oscillation ; the collection of multiple small datasets ('sub-datasets') from different positions on single crystals (Amunts, 2007); or the collection of sub-datasets from multiple crystals (Cockburn et al, 2004).…”

Section: Automatic Grouped Processingmentioning

confidence: 99%

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: Automatic Grouped Processingmentioning

confidence: 99%

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

et al. 2013

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“…Even for the Diamond beamlines, whose stability we are very familiar with, we set aside time at the start of each visit for a start-up routine to check some critical features together with the beamline scientists; if nothing else, this reminds us as users how to control the beamline and diagnose it once we are on our own during the rest of the visit. On-axis viewing systems (Perrakis et al, 1999) offer the extraordinary benefit that users are able to directly visualize the crystal-to-beam intersection. The beam position can easily be checked by mounting an X-ray sensitive screen to verify that the beam is actually at the position of the crystal, and many beamlines have motorized YAG screens that can be rapidly placed in the beam, even while the sample is on the goniometer.…”

Section: Mechanical Alignment Of the Beam With The Spindle Axismentioning

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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“…This approach was rejected because of the increase in divergence and concerns about the positional stability of the mini-focus beam. One straightforward path was to configure our goniometer as a mini-beam diffractometer (Perrakis et al, 1999) by installing a small aperture 30 mm upstream of the sample position. Overfilling this aperture would provide beam stability.…”

Section: Rationale For Pinhole Approach To Mini-beam Developmentmentioning

confidence: 99%

“…A pair of short Kirkpatrick-Baez mirrors placed close to the sample defines this mini-beam, at the cost of increased beam divergence owing to the high demagnification ratio. Most aperturedefined devices are based on a micrometer-sized shaping system that was developed several years ago at ESRF ID13 to produce clean beams down to 10 mm size from the 20 mm Â 40 mm focused beam size (Perrakis et al, 1999;Cipriani et al, 2007). This diffractometer, which features an air-bearing goniometer and microscope co-axial with the X-ray beam, is now available commercially (http://www.accel.de/News/ microdiffractometer.html).…”

Section: Introductionmentioning

confidence: 99%

Mini-beam collimator enables microcrystallography experiments on standard beamlines

Fischetti

Yoder

et al. 2009

J Synchrotron Radiat

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The high-brilliance X-ray beams from undulator sources at third-generation synchrotron facilities are excellent tools for solving crystal structures of important and challenging biological macromolecules and complexes. However, many of the most important structural targets yield crystals that are too small or too inhomogeneous for a 'standard' beam from an undulator source, $ 25-50 mm (FWHM) in the vertical and 50-100 mm in the horizontal direction. Although many synchrotron facilities have microfocus beamlines for other applications, this capability for macromolecular crystallography was pioneered at ID-13 of the ESRF. The National Institute of General Medical Sciences and National Cancer Institute Collaborative Access Team (GM/CA-CAT) dual canted undulator beamlines at the APS deliver high-intensity focused beams with a minimum focal size of 20 mm Â 65 mm at the sample position. To meet growing user demand for beams to study samples of 10 mm or less, a 'mini-beam' apparatus was developed that conditions the focused beam to either 5 mm or 10 mm (FWHM) diameter with high intensity. The mini-beam has a symmetric Gaussian shape in both the horizontal and vertical directions, and reduces the vertical divergence of the focused beam by 25%. Significant reduction in background was achieved by implementation of both forward-and back-scatter guards. A unique triple-collimator apparatus, which has been in routine use on both undulator beamlines since February 2008, allows users to rapidly interchange the focused beam and conditioned mini-beams of two sizes with a single mouse click. The device and the beam are stable over many hours of routine operation. The rapid-exchange capability has greatly facilitated sample screening and resulted in several structures that could not have been obtained with the larger focused beam.

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Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13

Cited by 94 publications

References 6 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

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

Mini-beam collimator enables microcrystallography experiments on standard beamlines

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