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ABSTRACT: Introduction: X-ray crystallography is the main tool for macromolecular structure solution at atomic resolution. It provides key information for the understanding of protein function, opening opportunities for the modulation of enzymatic mechanisms, and protein-ligand interactions. As a consequence, macromolecular crystallography plays an essential role in drug design, as well as in the a posteriori validation of drug mechanisms. Areas covered: The demand for method developments and also tools for macromolecular crystallography has significantly increased over the past 10 years. As a consequence, access to the facilities required for these investigations, such as synchrotron beamlines, became more difficult and significant efforts were dedicated to the automation of the experimental setup in laboratories. In this article, the authors describe how this was accomplished and how robot-based systems contribute to the enhancement of the macromolecular structure solution pipeline. Expert opinion: The evolution in robot technology, together with progress in X-ray beam performance and software developments, contributes to a new era in macromolecular X-ray crystallography. Highly integrated experimental environments open new possibilities for crystallography experiments. It is likely that it will also change the way this technique will be used in the future, opening the field to a larger community.
Expert Opinion on Drug Discovery 05/2013; · 2.12 Impact Factor
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José Gabadinho,
Antonia Beteva,
Matias Guijarro,
Vicente Rey-Bakaikoa,
Darren Spruce,
Matthew W Bowler,
Sandor Brockhauser,
David Flot,
Elspeth J Gordon,
David R Hall, [......],
Joanne McCarthy,
Edward Mitchell,
Stéphanie Monaco,
Christoph Mueller-Dieckmann, Didier Nurizzo,
Raimond B G Ravelli,
Xavier Thibault,
Martin A Walsh,
Gordon A Leonard,
Sean M McSweeney
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ABSTRACT: The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1.
Journal of Synchrotron Radiation 09/2010; 17(5):700-7. · 2.73 Impact Factor
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David Flot,
Trevor Mairs,
Thierry Giraud,
Matias Guijarro,
Marc Lesourd,
Vicente Rey,
Denis van Brussel,
Christian Morawe,
Christine Borel,
Olivier Hignette,
Joel Chavanne, Didier Nurizzo,
Sean McSweeney,
Edward Mitchell
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ABSTRACT: The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick-Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.
Journal of Synchrotron Radiation 01/2010; 17(1):107-18. · 2.73 Impact Factor
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ABSTRACT: ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade.
Journal of Synchrotron Radiation 11/2009; 16(Pt 6):803-12. · 2.73 Impact Factor
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ABSTRACT: During the last twenty years macromolecular crystallography (MX) has become the predominant tool for the investigation of structure/function relationships in biology. This is due to many technological advances and, in particular, improved access to synchrotron radiation (SR) sources, data from which has lead to 80% of the macromolecular crystal structures currently being deposited in the Protein Data Bank (PDB) (Figure 1, http://www.rcsb.org). The demand for synchrotron beam-time is also being fuelled by the funding of a number of structural genomics programmes [11.
Norvell , J.C. and Zapp Machalek , A. 2000 . Nature Structural Biology , 7 : 921 – 931 . [CrossRef]View all references], which, following an initial investment in protein production technology, have now contributed 1000 new structures to the PDB.
Synchrotron Radiation News 05/2007; 20(3):18-24.
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ABSTRACT: The demand for access to macromolecular crystallography synchrotron beam time continues to increase. To meet this demand the ESRF has constructed a dual station beamline using a canted undulator system as the X-ray source. The first phase of the beamline to be constructed is ID23-1, a tunable MAD-capable station with a mini-focus X-ray beam. The beamline makes use of well characterized optical elements: a channel-cut monochromator with a high-precision toroidal mirror to focus the X-ray beam. The beamline has been conceived with the aim of providing high levels of automation to create an industrial-like environment for protein crystallography. A new software suite has been developed to permit reliable easy operation for the beamline users and beamline staff. High levels of diagnostics are built in to allow rapid trouble-shooting. These developments are now being exported to the ESRF macromolecular crystallography beamline complex and have been made in a modular fashion to facilitate transportability to other synchrotrons.
Journal of Synchrotron Radiation 06/2006; 13(Pt 3):227-38. · 2.73 Impact Factor
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ABSTRACT: Structural proteomics has promoted the rapid development of automated protein structure determination using X-ray crystallography. Robotics are now routinely used along the pipeline from genes to protein structures. However, a bottleneck still remains. At synchrotron beamlines, the success rate of automated sample alignment along the X-ray beam is limited by difficulties in visualization of protein crystals, especially when they are small and embedded in mother liquor. Despite considerable improvement in optical microscopes, the use of visible light transmitted or reflected by the sample may result in poor or misleading contrast. Here, the endogenous fluorescence from aromatic amino acids has been used to identify even tiny or weakly fluorescent crystals with a high success rate. The use of a compact laser at 266 nm in combination with non-fluorescent sample holders provides an efficient solution to collect high-contrast fluorescence images in a few milliseconds and using standard camera optics. The best image quality was obtained with direct illumination through a viewing system coaxial with the UV beam. Crystallographic data suggest that the employed UV exposures do not generate detectable structural damage.
Acta Crystallographica Section D Biological Crystallography 04/2006; 62(Pt 3):253-61. · 12.62 Impact Factor
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Steffi Arzt,
Antonia Beteva,
Florent Cipriani,
Solange Delageniere,
Franck Felisaz,
Gabriele Förstner,
Elspeth Gordon,
Ludovic Launer,
Bernard Lavault,
Gordon Leonard, [......],
Jens Meyer,
Edward Mitchell,
Stephanie Monaco, Didier Nurizzo,
Raimond Ravelli,
Vicente Rey,
William Shepard,
Darren Spruce,
Olof Svensson,
Pascal Theveneau
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ABSTRACT: The production of three-dimensional crystallographic structural information of macromolecules can now be thought of as a pipeline which is being streamlined at every stage from protein cloning, expression and purification, through crystallisation to data collection and structure solution. Synchrotron X-ray beamlines are a key section of this pipeline as it is at these that the X-ray diffraction data that ultimately leads to the elucidation of macromolecular structures are collected. The burgeoning number of macromolecular crystallography (MX) beamlines available worldwide may be enhanced significantly with the automation of both their operation and of the experiments carried out on them. This paper reviews the current situation and provides a glimpse of how a MX beamline may look in the not too distant future.
Progress in Biophysics and Molecular Biology 11/2005; 89(2):124-52. · 3.20 Impact Factor
