1
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Olszta M, Hopkins D, Fiedler KR, Oostrom M, Akers S, Spurgeon SR. An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-11. [PMID: 35686442 DOI: 10.1017/s1431927622012065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Artificial intelligence (AI) promises to reshape scientific inquiry and enable breakthrough discoveries in areas such as energy storage, quantum computing, and biomedicine. Scanning transmission electron microscopy (STEM), a cornerstone of the study of chemical and materials systems, stands to benefit greatly from AI-driven automation. However, present barriers to low-level instrument control, as well as generalizable and interpretable feature detection, make truly automated microscopy impractical. Here, we discuss the design of a closed-loop instrument control platform guided by emerging sparse data analytics. We hypothesize that a centralized controller, informed by machine learning combining limited a priori knowledge and task-based discrimination, could drive on-the-fly experimental decision-making. This platform may unlock practical, automated analysis of a variety of material features, enabling new high-throughput and statistical studies.
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Affiliation(s)
- Matthew Olszta
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Derek Hopkins
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kevin R Fiedler
- College of Arts and Sciences, Washington State University - Tri-Cities, Richland, WA 99354, USA
| | - Marjolein Oostrom
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah Akers
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Steven R Spurgeon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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2
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Stepanov S, Kissick D, Makarov O, Hilgart M, Becker M, Venugopalan N, Xu S, Smith JL, Fischetti RF. Fast automated energy changes at synchrotron radiation beamlines equipped with transfocator or focusing mirrors. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:393-399. [PMID: 35254302 PMCID: PMC8900858 DOI: 10.1107/s1600577522001084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Algorithms and procedures to fully automate retuning of synchrotron radiation beamlines over wide energy ranges are discussed. The discussion is based on the implementation at the National Institute of General Medical Sciences and the National Cancer Institute Structural Biology Facility at the Advanced Photon Source. When a user selects a new beamline energy, software synchronously controls the beamline monochromator and undulator to maintain the X-ray beam flux after the monochromator, preserves beam attenuation by determining a new set of attenuator foils, changes, as needed, mirror reflecting stripes and the undulator harmonic, preserves beam focal distance of compound refractive lens focusing by changing the In/Out combination of lenses in the transfocator, and, finally, restores beam position at the sample by on-the-fly scanning of either the Kirkpatrick-Baez mirror angles or the transfocator up/down and inboard/outboard positions. The sample is protected from radiation damage by automatically moving it out of the beam during the energy change and optimization.
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Affiliation(s)
- Sergey Stepanov
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - Oleg Makarov
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - Mark Hilgart
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - Michael Becker
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - Nagarajan Venugopalan
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - Shenglan Xu
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439, USA
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3
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Atakisi H, Conger L, Moreau DW, Thorne RE. Resolution and dose dependence of radiation damage in biomolecular systems. IUCRJ 2019; 6:1040-1053. [PMID: 31709060 PMCID: PMC6830208 DOI: 10.1107/s2052252519008777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/19/2019] [Indexed: 05/30/2023]
Abstract
The local Fourier-space relation between diffracted intensity I, diffraction wavevector q and dose D, , is key to probing and understanding radiation damage by X-rays and energetic particles in both diffraction and imaging experiments. The models used in protein crystallography for the last 50 years provide good fits to experimental I(q) versus nominal dose data, but have unclear physical significance. More recently, a fit to diffraction and imaging experiments suggested that the maximum tolerable dose varies as q -1 or linearly with resolution. Here, it is shown that crystallographic data have been strongly perturbed by the effects of spatially nonuniform crystal irradiation and diffraction during data collection. Reanalysis shows that these data are consistent with a purely exponential local dose dependence, = I 0(q)exp[-D/D e(q)], where D e(q) ∝ q α with α ≃ 1.7. A physics-based model for radiation damage, in which damage events occurring at random locations within a sample each cause energy deposition and blurring of the electron density within a small volume, predicts this exponential variation with dose for all q values and a decay exponent α ≃ 2 in two and three dimensions, roughly consistent with both diffraction and imaging experiments over more than two orders of magnitude in resolution. The B-factor model used to account for radiation damage in crystallographic scaling programs is consistent with α = 2, but may not accurately capture the dose dependencies of structure factors under typical nonuniform illumination conditions. The strong q dependence of radiation-induced diffraction decays implies that the previously proposed 20-30 MGy dose limit for protein crystallography should be replaced by a resolution-dependent dose limit that, for atomic resolution data sets, will be much smaller. The results suggest that the physics underlying basic experimental trends in radiation damage at T ≃ 100 K is straightforward and universal. Deviations of the local I(q, D) from strictly exponential behavior may provide mechanistic insights, especially into the radiation-damage processes responsible for the greatly increased radiation sensitivity observed at T ≃ 300 K.
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Affiliation(s)
- Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | | | - David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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4
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Oscarsson M, Beteva A, Flot D, Gordon E, Guijarro M, Leonard G, McSweeney S, Monaco S, Mueller-Dieckmann C, Nanao M, Nurizzo D, Popov AN, von Stetten D, Svensson O, Rey-Bakaikoa V, Chado I, Chavas LMG, Gadea L, Gourhant P, Isabet T, Legrand P, Savko M, Sirigu S, Shepard W, Thompson A, Mueller U, Nan J, Eguiraun M, Bolmsten F, Nardella A, Milàn-Otero A, Thunnissen M, Hellmig M, Kastner A, Schmuckermaier L, Gerlach M, Feiler C, Weiss MS, Bowler MW, Gobbo A, Papp G, Sinoir J, McCarthy AA, Karpics I, Nikolova M, Bourenkov G, Schneider T, Andreu J, Cuní G, Juanhuix J, Boer R, Fogh R, Keller P, Flensburg C, Paciorek W, Vonrhein C, Bricogne G, de Sanctis D. MXCuBE2: the dawn of MXCuBE Collaboration. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:393-405. [PMID: 30855248 PMCID: PMC6412183 DOI: 10.1107/s1600577519001267] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/23/2019] [Indexed: 05/22/2023]
Abstract
MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF - the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.
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Affiliation(s)
- Marcus Oscarsson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonia Beteva
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David Flot
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elspeth Gordon
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matias Guijarro
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon Leonard
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Stephanie Monaco
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Max Nanao
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Didier Nurizzo
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Alexander N. Popov
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David von Stetten
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | | | | | - Laurent Gadea
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | | | - Martin Savko
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | - Serena Sirigu
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | - Uwe Mueller
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | | | | | | | | | - Michael Hellmig
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Alexandra Kastner
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Lukas Schmuckermaier
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Martin Gerlach
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Christian Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ivars Karpics
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Marina Nikolova
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Gleb Bourenkov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Jordi Andreu
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Guifré Cuní
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Judith Juanhuix
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Roeland Boer
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Rasmus Fogh
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Peter Keller
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Claus Flensburg
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Wlodek Paciorek
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Clemens Vonrhein
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Gerard Bricogne
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Daniele de Sanctis
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
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5
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McCarthy AA, Barrett R, Beteva A, Caserotto H, Dobias F, Felisaz F, Giraud T, Guijarro M, Janocha R, Khadrouche A, Lentini M, Leonard GA, Lopez Marrero M, Malbet-Monaco S, McSweeney S, Nurizzo D, Papp G, Rossi C, Sinoir J, Sorez C, Surr J, Svensson O, Zander U, Cipriani F, Theveneau P, Mueller-Dieckmann C. ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1249-1260. [PMID: 29979188 PMCID: PMC6038607 DOI: 10.1107/s1600577518007166] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/13/2018] [Indexed: 05/05/2023]
Abstract
ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).
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Affiliation(s)
- Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Akim Khadrouche
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Marcos Lopez Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | | | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Christopher Rossi
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
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6
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From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library. J Biotechnol 2017; 261:207-214. [DOI: 10.1016/j.jbiotec.2017.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 02/06/2023]
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7
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Bowler MW, Svensson O, Nurizzo D. Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data. CRYSTALLOGR REV 2016. [DOI: 10.1080/0889311x.2016.1155050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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8
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de Sanctis D, Oscarsson M, Popov A, Svensson O, Leonard G. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines. Acta Crystallogr D Struct Biol 2016; 72:413-20. [PMID: 26960128 PMCID: PMC4784672 DOI: 10.1107/s2059798316001042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/18/2016] [Indexed: 11/10/2022] Open
Abstract
The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated.
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Affiliation(s)
- Daniele de Sanctis
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Marcus Oscarsson
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Alexander Popov
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon Leonard
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
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9
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Abstract
In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.
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10
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Svensson O, Malbet-Monaco S, Popov A, Nurizzo D, Bowler MW. Fully automatic characterization and data collection from crystals of biological macromolecules. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1757-67. [PMID: 26249356 PMCID: PMC4528805 DOI: 10.1107/s1399004715011918] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/22/2015] [Indexed: 11/24/2022]
Abstract
Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Stéphanie Malbet-Monaco
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Alexander Popov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit for Virus–Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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11
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Xi S, Borgna LS, Du Y. General method for automatic on-line beamline optimization based on genetic algorithm. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:661-665. [PMID: 25931082 DOI: 10.1107/s1600577515001861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/28/2015] [Indexed: 06/04/2023]
Abstract
It is essential but inconvenient to perform high-quality on-line optimization for synchrotron radiation beamlines. Usually, synchrotron radiation beamlines are optimized manually, which is time-consuming and difficult to obtain global optimization for all optical elements of the beamline. In this contribution a general method based on the genetic algorithm for automatic beamline optimization is introduced. This method can optimize all optical components of any beamline simultaneously and efficiently. To test this method, a program developed using LabVIEW is examined at the XAFCA beamline of the Singapore Synchrotron Light Source to optimize the beam flux at the sample position. The results demonstrate that the beamline can be optimized within 17 generations even when the initial flux is as low as 4% of its maximum value.
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Affiliation(s)
- Shibo Xi
- Institute of Chemical and Engineering Sciences, A*STAR, 1 Pesek Road, Jurong Island, Singapore 627833
| | - Lucas Santiago Borgna
- Institute of Chemical and Engineering Sciences, A*STAR, 1 Pesek Road, Jurong Island, Singapore 627833
| | - Yonghua Du
- Institute of Chemical and Engineering Sciences, A*STAR, 1 Pesek Road, Jurong Island, Singapore 627833
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12
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De Maria Antolinos A, Pernot P, Brennich ME, Kieffer J, Bowler MW, Delageniere S, Ohlsson S, Malbet Monaco S, Ashton A, Franke D, Svergun D, McSweeney S, Gordon E, Round A. ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments. ACTA ACUST UNITED AC 2015; 71:76-85. [PMID: 25615862 PMCID: PMC4304688 DOI: 10.1107/s1399004714019609] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/29/2014] [Indexed: 11/15/2022]
Abstract
The ISPyB information-management system for crystallography has been adapted to include data from small-angle X-ray scattering of macromolecules in solution experiments. Logging experiments with the laboratory-information management system ISPyB (Information System for Protein crystallography Beamlines) enhances the automation of small-angle X-ray scattering of biological macromolecules in solution (BioSAXS) experiments. The ISPyB interface provides immediate user-oriented online feedback and enables data cross-checking and downstream analysis. To optimize data quality and completeness, ISPyBB (ISPyB for BioSAXS) makes it simple for users to compare the results from new measurements with previous acquisitions from the same day or earlier experiments in order to maximize the ability to collect all data required in a single synchrotron visit. The graphical user interface (GUI) of ISPyBB has been designed to guide users in the preparation of an experiment. The input of sample information and the ability to outline the experimental aims in advance provides feedback on the number of measurements required, calculation of expected sample volumes and time needed to collect the data: all of this information aids the users to better prepare for their trip to the synchrotron. A prototype version of the ISPyBB database is now available at the European Synchrotron Radiation Facility (ESRF) beamline BM29 and is already greatly appreciated by academic users and industrial clients. It will soon be available at the PETRA III beamline P12 and the Diamond Light Source beamlines I22 and B21.
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Affiliation(s)
| | - Petra Pernot
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Martha E Brennich
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Jérôme Kieffer
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Solange Delageniere
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Staffan Ohlsson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Stephanie Malbet Monaco
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Alun Ashton
- DLS, Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Elspeth Gordon
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France
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Márquez JA, Cipriani F. CrystalDirect™: a novel approach for automated crystal harvesting based on photoablation of thin films. Methods Mol Biol 2014; 1091:197-203. [PMID: 24203334 DOI: 10.1007/978-1-62703-691-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The last years have seen a major development in automation for protein production, crystallization, and X-ray diffraction data collection, which has contributed to accelerate the pace of structure solution and to facilitate the study of ever more challenging targets through macromolecular crystallography. This has led to a considerable increase in the numbers of crystals produced and analyzed. However the process of recovering crystals from crystallization supports and mounting them in X-ray data collection pins remains a manual and delicate operation. Here we present a novel approach enabling full automation of the crystal mounting process and describe the operation of the first-automated CrystalDirect harvesting unit. Implications for crystallography applications and for the future operational integration of automated crystallization and data collection resources are discussed.
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Affiliation(s)
- José A Márquez
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
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14
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Webb B, Eswar N, Fan H, Khuri N, Pieper U, Dong G, Sali A. Comparative Modeling of Drug Target Proteins☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2014. [PMCID: PMC7157477 DOI: 10.1016/b978-0-12-409547-2.11133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this perspective, we begin by describing the comparative protein structure modeling technique and the accuracy of the corresponding models. We then discuss the significant role that comparative prediction plays in drug discovery. We focus on virtual ligand screening against comparative models and illustrate the state-of-the-art by a number of specific examples.
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15
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Malbet-Monaco S, Leonard GA, Mitchell EP, Gordon EJ. How the ESRF helps industry and how they help the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1289-96. [PMID: 23793155 PMCID: PMC3689532 DOI: 10.1107/s0907444913001108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 01/11/2013] [Indexed: 11/11/2022]
Abstract
The ESRF has worked with, and provided services for, the pharmaceutical industry since the construction of its first protein crystallography beamline in the mid-1990s. In more recent times, industrial clients have benefited from a portfolio of beamlines which offer a wide range of functionality and beam characteristics, including tunability, microfocus and micro-aperture. Included in this portfolio is a small-angle X-ray scattering beamline dedicated to the study of biological molecules in solution. The high demands on throughput and efficiency made by the ESRF's industrial clients have been a major driving force in the evolution of the ESRF's macromolecular crystallography resources, which now include remote access, the automation of crystal screening and data collection, and a beamline database allowing sample tracking, experiment reporting and real-time at-a-distance monitoring of experiments. This paper describes the key features of the functionality put in place on the ESRF structural biology beamlines and outlines the major advantages of the interaction of the ESRF with the pharmaceutical industry.
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Affiliation(s)
- Stéphanie Malbet-Monaco
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Edward P. Mitchell
- Business Development Office, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Elspeth J. Gordon
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
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16
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Monaco S, Gordon E, Bowler MW, Delagenière S, Guijarro M, Spruce D, Svensson O, McSweeney SM, McCarthy AA, Leonard G, Nanao MH. Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF. J Appl Crystallogr 2013; 46:804-810. [PMID: 23682196 PMCID: PMC3654316 DOI: 10.1107/s0021889813006195] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/04/2013] [Indexed: 12/02/2022] Open
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.
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Affiliation(s)
- Stéphanie Monaco
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Elspeth Gordon
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France
- Unit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Solange Delagenière
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Matias Guijarro
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Darren Spruce
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Olof Svensson
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Sean M. McSweeney
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France
- Unit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Max H. Nanao
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France
- Unit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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17
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18
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Cipriani F, Röwer M, Landret C, Zander U, Felisaz F, Márquez JA. CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1393-9. [DOI: 10.1107/s0907444912031459] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022]
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19
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Delagenière S, Brenchereau P, Launer L, Ashton AW, Leal R, Veyrier S, Gabadinho J, Gordon EJ, Jones SD, Levik KE, McSweeney SM, Monaco S, Nanao M, Spruce D, Svensson O, Walsh MA, Leonard GA. ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics 2011; 27:3186-92. [PMID: 21949273 DOI: 10.1093/bioinformatics/btr535] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. RESULTS ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.
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20
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Winter G, McAuley KE. Automated data collection for macromolecular crystallography. Methods 2011; 55:81-93. [DOI: 10.1016/j.ymeth.2011.06.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 06/29/2011] [Accepted: 06/30/2011] [Indexed: 10/18/2022] Open
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21
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Gabadinho J, Beteva A, Guijarro M, Rey-Bakaikoa V, Spruce D, Bowler MW, Brockhauser S, Flot D, Gordon EJ, Hall DR, Lavault B, McCarthy AA, McCarthy J, Mitchell E, Monaco S, Mueller-Dieckmann C, Nurizzo D, Ravelli RBG, Thibault X, Walsh MA, Leonard GA, McSweeney SM. MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments. JOURNAL OF SYNCHROTRON RADIATION 2010; 17:700-7. [PMID: 20724792 PMCID: PMC3025540 DOI: 10.1107/s0909049510020005] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 05/26/2010] [Indexed: 05/19/2023]
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.
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Affiliation(s)
- José Gabadinho
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Vicente Rey-Bakaikoa
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Darren Spruce
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Matthew W. Bowler
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Sandor Brockhauser
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Elspeth J. Gordon
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - David R. Hall
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Bernard Lavault
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble, France
| | - Joanne McCarthy
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Edward Mitchell
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Stéphanie Monaco
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | | | - Didier Nurizzo
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Raimond B. G. Ravelli
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble, France
| | - Xavier Thibault
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | | | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
- Correspondence e-mail: ,
| | - Sean M. McSweeney
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France
- Correspondence e-mail: ,
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22
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Bowler MW, Guijarro M, Petitdemange S, Baker I, Svensson O, Burghammer M, Mueller-Dieckmann C, Gordon EJ, Flot D, McSweeney SM, Leonard GA. Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:855-64. [PMID: 20693684 DOI: 10.1107/s0907444910019591] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 05/25/2010] [Indexed: 11/10/2022]
Abstract
Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRF's structural biology beamlines is also presented.
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Affiliation(s)
- Matthew W Bowler
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, F-38043 Grenoble, France.
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Giegé R, Sauter C. Biocrystallography: past, present, future. HFSP JOURNAL 2010; 4:109-21. [PMID: 21119764 PMCID: PMC2929629 DOI: 10.2976/1.3369281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/02/2010] [Indexed: 02/02/2023]
Abstract
The evolution of biocrystallography from the pioneers' time to the present era of global biology is presented in relation to the development of methodological and instrumental advances for molecular sample preparation and structure elucidation over the last 6 decades. The interdisciplinarity of the field that generated cross-fertilization between physics- and biology-focused themes is emphasized. In particular, strategies to circumvent the main bottlenecks of biocrystallography are discussed. They concern (i) the way macromolecular targets are selected, designed, and characterized, (ii) crystallogenesis and how to deal with physical and biological parameters that impact crystallization for growing and optimizing crystals, and (iii) the methods for crystal analysis and 3D structure determination. Milestones that have marked the history of biocrystallography illustrate the discussion. Finally, the future of the field is envisaged. Wide gaps of the structural space need to be filed and membrane proteins as well as intrinsically unstructured proteins still constitute challenging targets. Solving supramolecular assemblies of increasing complexity, developing a "4D biology" for decrypting the kinematic changes in macromolecular structures in action, integrating these structural data in the whole cell organization, and deciphering biomedical implications will represent the new frontiers.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
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Paithankar KS, Garman EF. Know your dose: RADDOSE. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:381-8. [PMID: 20382991 PMCID: PMC2852302 DOI: 10.1107/s0907444910006724] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 02/22/2010] [Indexed: 11/10/2022]
Abstract
The program RADDOSE is widely used to compute the dose absorbed by a macromolecular crystal during an X-ray diffraction experiment. A number of factors affect the absorbed dose, including the incident X-ray flux density, the photon energy and the composition of the macromolecule and of the buffer in the crystal. An experimental dose limit for macromolecular crystallography (MX) of 30 MGy at 100 K has been reported, beyond which the biological information obtained may be compromised. Thus, for the planning of an optimized diffraction experiment the estimation of dose has become an additional tool. A number of approximations were made in the original version of RADDOSE. Recently, the code has been modified in order to take into account fluorescent X-ray escape from the crystal (version 2) and the inclusion of incoherent (Compton) scattering into the dose calculation is now reported (version 3). The Compton cross-section, although negligible at the energies currently commonly used in MX, should be considered in dose calculations for incident energies above 20 keV. Calculations using version 3 of RADDOSE reinforce previous studies that predict a reduction in the absorbed dose when data are collected at higher energies compared with data collected at 12.4 keV. Hence, a longer irradiation lifetime for the sample can be achieved at these higher energies but this is at the cost of lower diffraction intensities. The parameter 'diffraction-dose efficiency', which is the diffracted intensity per absorbed dose, is revisited in an attempt to investigate the benefits and pitfalls of data collection using higher and lower energy radiation, particularly for thin crystals.
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Affiliation(s)
- Karthik S Paithankar
- Department of Biochemistry, Laboratory of Molecular Biophysics, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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25
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Flot D, Mairs T, Giraud T, Guijarro M, Lesourd M, Rey V, van Brussel D, Morawe C, Borel C, Hignette O, Chavanne J, Nurizzo D, McSweeney S, Mitchell E. The ID23-2 structural biology microfocus beamline at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2010; 17:107-18. [PMID: 20029119 PMCID: PMC3025444 DOI: 10.1107/s0909049509041168] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 10/08/2009] [Indexed: 05/20/2023]
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.
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Affiliation(s)
- David Flot
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble, France.
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26
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Round AR, Franke D, Moritz S, Huchler R, Fritsche M, Malthan D, Klaering R, Svergun DI, Roessle M. Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J Appl Crystallogr 2008; 41:913-917. [PMID: 25484841 PMCID: PMC4233401 DOI: 10.1107/s0021889808021018] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 07/07/2008] [Indexed: 11/10/2022] Open
Abstract
An automated sample changer for small-angle X-ray scattering (SAXS) on protein in solution is reported. The technical implementation and integration to a synchrotron-based SAXS beamline is described. There is a rapidly increasing interest in the use of synchrotron small-angle X-ray scattering (SAXS) for large-scale studies of biological macromolecules in solution, and this requires an adequate means of automating the experiment. A prototype has been developed of an automated sample changer for solution SAXS, where the solutions are kept in thermostatically controlled well plates allowing for operation with up to 192 samples. The measuring protocol involves controlled loading of protein solutions and matching buffers, followed by cleaning and drying of the cell between measurements. The system was installed and tested at the X33 beamline of the EMBL, at the storage ring DORIS-III (DESY, Hamburg), where it was used by over 50 external groups during 2007. At X33, a throughput of approximately 12 samples per hour, with a failure rate of sample loading of less than 0.5%, was observed. The feedback from users indicates that the ease of use and reliability of the user operation at the beamline were greatly improved compared with the manual filling mode. The changer is controlled by a client–server-based network protocol, locally and remotely. During the testing phase, the changer was operated in an attended mode to assess its reliability and convenience. Full integration with the beamline control software, allowing for automated data collection of all samples loaded into the machine with remote control from the user, is presently being implemented. The approach reported is not limited to synchrotron-based SAXS but can also be used on laboratory and neutron sources.
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Affiliation(s)
- A R Round
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
| | - D Franke
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
| | - S Moritz
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - R Huchler
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - M Fritsche
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - D Malthan
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - R Klaering
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
| | - D I Svergun
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany ; Institute of Crystallography, Russian Academy of Sciences, Leninsky prospekt 59, 117333 Moscow, Russian Federation
| | - M Roessle
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
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Jhoti H, Cleasby A, Verdonk M, Williams G. Fragment-based screening using X-ray crystallography and NMR spectroscopy. Curr Opin Chem Biol 2007; 11:485-93. [PMID: 17851109 DOI: 10.1016/j.cbpa.2007.07.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 07/25/2007] [Accepted: 07/27/2007] [Indexed: 11/17/2022]
Abstract
Approaches which start from a study of the interaction of very simple molecules (fragments) with the protein target are proving to be valuable additions to drug design. Fragment-based screening allows the complementarity between a protein active site and drug-like molecules to be rapidly and effectively explored, using structural methods. Recent improvements in the intensities of laboratory X-ray sources permits the collection of greater amounts of high-quality diffraction data and have been matched by developments in automation, crystallisation and data analysis. Developments in NMR screening, including the use of cryogenically cooled NMR probes and (19)F-containing reporter molecules have expanded the scope of this technique, while increasing the availability of binding site and quantitative affinity data for the fragments. Application of these methods has led to a greater knowledge of the chemical variety, structural features and energetics of protein-fragment interactions. While fragment-based screening has already been shown to reduce the timescales of the drug discovery process, a more detailed characterisation of fragment screening hits can reveal unexpected similarities between fragment chemotypes and protein active sites leading to improved understanding of the pharmacophores and the re-use of this information against other protein targets.
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Affiliation(s)
- Harren Jhoti
- Astex Therapeutics, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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28
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Jenney FE, Adams MWW. The impact of extremophiles on structural genomics (and vice versa). Extremophiles 2007; 12:39-50. [PMID: 17563834 DOI: 10.1007/s00792-007-0087-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 04/19/2007] [Indexed: 11/24/2022]
Abstract
The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure. Thus, in the late 1990s, an international effort known as structural genomics (SG) was initiated, its primary goal to "fill sequence-structure space" by determining the 3D structures of representatives of all known protein families. This was to be achieved mainly by X-ray crystallography and it was estimated that at least 5,000 new structures would be required. While the proteins (genes) for SG have subsequently been derived from hundreds of different organisms, extremophiles and particularly thermophiles have been specifically targeted due to the increased stability and ease of handling of their proteins, relative to those from mesophiles. This review summarizes the significant impact that extremophiles and proteins derived from them have had on SG projects worldwide. To what extent SG has influenced the field of extremophile research is also discussed.
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Affiliation(s)
- Francis E Jenney
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, GA 30602-7229, USA
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29
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Abstract
In this perspective, we begin by describing the comparative protein structure modeling technique and the accuracy of the corresponding models. We then discuss the significant role that comparative prediction plays in drug discovery. We focus on virtual ligand screening against comparative models and illustrate the state of the art by a number of specific examples.
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30
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Sorensen TLM, McAuley KE, Flaig R, Duke EMH. New light for science: synchrotron radiation in structural medicine. Trends Biotechnol 2006; 24:500-8. [PMID: 17005277 DOI: 10.1016/j.tibtech.2006.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2006] [Revised: 08/03/2006] [Accepted: 09/14/2006] [Indexed: 10/24/2022]
Abstract
Macromolecular crystallography (MX) is a powerful method for obtaining detailed three-dimensional structural information about macromolecules. MX using synchrotron X-rays has contributed, significantly, to both fundamental and applied research, including the structure-based design of drugs to combat important diseases. New third-generation synchrotrons offer substantial improvements in terms of quality and brightness of the X-ray beams they produce. Important classes of macromolecules, such as membrane proteins (including many receptors) and macromolecular complexes, are difficult to obtain in quantity and to crystallise, which has hampered analysis by MX. Intensely bright X-rays from the latest synchrotrons will enable the use of extremely small crystals, and should usher in a period of rapid progress in resolving these previously refractory structures.
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MESH Headings
- Antitubercular Agents/chemistry
- Crystallography, X-Ray
- Drug Design
- Fusion Proteins, bcr-abl
- Humans
- Hypoglycemic Agents/chemistry
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Membrane Proteins/chemistry
- Models, Molecular
- Multiprotein Complexes/chemistry
- Protein Conformation
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Synchrotrons
- Tuberculosis, Pulmonary/drug therapy
- X-Rays
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Affiliation(s)
- Thomas L-M Sorensen
- Macromolecular Crystallography Group, Diamond Light Source Limited, Chilton, Didcot, Oxfordshire OX11 0DE, UK.
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31
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Nanao MH, Ravelli RBG. Phasing macromolecular structures with UV-induced structural changes. Structure 2006; 14:791-800. [PMID: 16615919 DOI: 10.1016/j.str.2006.02.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 01/29/2006] [Accepted: 02/14/2006] [Indexed: 10/24/2022]
Abstract
Experimental phasing of macromolecular crystal structures relies on the accurate measurement of two or more sets of reflections from isomorphous crystals, where the scattering power of a few atoms is different for each set. Recently, it was demonstrated that X-ray-induced intensity differences can also contain phasing information, exploiting specific structural changes characteristic of X-ray damage. This method (radiation damage-induced phasing; RIP) has the advantage that it can be performed on a single crystal of the native macromolecule. However, a drawback is that X-rays introduce many small changes to both solvent and macromolecule. In this study, ultraviolet (UV) radiation has been used to induce specific changes in the macromolecule alone, leading to a larger contrast between radiation-susceptible and nonsusceptible sites. Unlike X-ray RIP, UV RIP does not require the use of a synchrotron. The method has been demonstrated for a series of macromolecules.
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Affiliation(s)
- Max H Nanao
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, B.P. 181, 38042 Grenoble Cedex 9, France
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32
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Owen RL, Rudiño-Piñera E, Garman EF. Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc Natl Acad Sci U S A 2006; 103:4912-7. [PMID: 16549763 PMCID: PMC1458769 DOI: 10.1073/pnas.0600973103] [Citation(s) in RCA: 290] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Radiation damage to cryocooled protein crystals during x-ray structure determination has become an inherent part of macromolecular diffraction data collection at third-generation synchrotrons. Generally, radiation damage is an undesirable component of the experiment and can result in erroneous structural detail in the final model. The characterization of radiation damage thus has become an important area for structural biologists. The calculated dose limit of 2 x 10(7) Gy for the diffracting power of cryocooled protein crystals to drop by half has been experimentally evaluated at a third-generation synchrotron source. Successive data sets were collected from four holoferritin and three apoferritin crystals. The absorbed dose for each crystal was calculated by using the program raddose after measurement of the incident photon flux and determination of the elemental crystal composition by micro-particle-induced x-ray emission. Degradation in diffraction quality and specific structural changes induced by synchrotron radiation then could be compared directly with absorbed dose for different dose/dose rate regimes: a 10% lifetime decrease for a 10-fold dose rate increase was observed. Remarkable agreement both between different crystals of the same type and between apoferritin and holoferritin was observed for the dose required to reduce the diffracted intensity by half (D(1/2)). From these measurements, a dose limit of D(1/2) = 4.3 (+/-0.3) x10(7) Gy was obtained. However, by considering other data quality indicators, an intensity reduction to I(ln2) = ln2 x I(0), corresponding to an absorbed dose of 3.0 x 10(7) Gy, is recommended as an appropriate dose limit for typical macromolecular crystallography experiments.
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Affiliation(s)
- Robin Leslie Owen
- *Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom; and
| | - Enrique Rudiño-Piñera
- Instituto de Biotecnologia, Universidad Nacional Autonoma De Mexico, Cuernavaca, Morelos, C.P. 62271, Mexico
| | - Elspeth F. Garman
- *Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom; and
- To whom correspondence should be addressed at:
Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, Rex Richards Building, South Parks Road, Oxford OX1 3QU, United Kingdom. E-mail:
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