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Schönherr R, Boger J, Lahey-Rudolph JM, Harms M, Kaiser J, Nachtschatt S, Wobbe M, Duden R, König P, Bourenkov G, Schneider TR, Redecke L. A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun 2024; 15:1709. [PMID: 38402242 PMCID: PMC10894269 DOI: 10.1038/s41467-024-45985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024] Open
Abstract
With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - J Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Hamburg, Germany
- X-ray technology lab, TH Lübeck - University of Applied Sciences Lübeck, Lübeck, Germany
| | - Mareike Harms
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | | | | | - Marla Wobbe
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Rainer Duden
- Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Peter König
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), University of Lübeck, German Center for Lung Research (DZL), Lübeck, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany.
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
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2
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Zhao FZ, Wang ZJ, Xiao QJ, Yu L, Sun B, Hou Q, Chen LL, Liang H, Wu H, Guo WH, He JH, Wang QS, Yin DC. Microfluidic rotating-target device capable of three-degrees-of-freedom motion for efficient in situ serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:347-358. [PMID: 36891848 PMCID: PMC10000801 DOI: 10.1107/s1600577523000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
There is an increasing demand for simple and efficient sample delivery technology to match the rapid development of serial crystallography and its wide application in analyzing the structural dynamics of biological macromolecules. Here, a microfluidic rotating-target device is presented, capable of three-degrees-of-freedom motion, including two rotational degrees of freedom and one translational degree of freedom, for sample delivery. Lysozyme crystals were used as a test model with this device to collect serial synchrotron crystallography data and the device was found to be convenient and useful. This device enables in situ diffraction from crystals in a microfluidic channel without the need for crystal harvesting. The circular motion ensures that the delivery speed can be adjusted over a wide range, showing its good compatibility with different light sources. Moreover, the three-degrees-of-freedom motion guarantees the full utilization of crystals. Hence, sample consumption is greatly reduced, and only 0.1 mg of protein is consumed in collecting a complete dataset.
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Affiliation(s)
- Feng-Zhu Zhao
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
- School of NCO, Army Medical University, Shijiazhuang 050081, People’s Republic of China
| | - Zhi-Jun Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Qing-Jie Xiao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Qian Hou
- School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Liang-Liang Chen
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Huan Liang
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Hai Wu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Wei-Hong Guo
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Jian-Hua He
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Qi-Sheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Da-Chuan Yin
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
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3
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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4
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Karasawa A, Andi B, Fuchs MR, Shi W, McSweeney S, Hendrickson WA, Liu Q. Multi-crystal native-SAD phasing at 5 keV with a helium environment. IUCRJ 2022; 9:768-777. [PMID: 36381147 PMCID: PMC9634608 DOI: 10.1107/s205225252200971x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
De novo structure determination from single-wavelength anomalous diffraction using native sulfur or phospho-rus in biomolecules (native-SAD) is an appealing method to mitigate the labor-intensive production of heavy-atom derivatives and seleno-methio-nyl substitutions. The native-SAD method is particularly attractive for membrane proteins, which are difficult to produce and often recalcitrant to grow into decent-sized crystals. Native-SAD uses lower-energy X-rays to enhance anomalous signals from sulfur or phospho-rus. However, at lower energies, the scattering and absorption of air contribute to the background noise, reduce the signals and are thus adverse to native-SAD phasing. We have previously demonstrated native-SAD phasing at an energy of 5 keV in air at the NSLS-II FMX beamline. Here, the use of a helium path developed to reduce both the noise from background scattering and the air absorption of the diffracted X-ray beam are described. The helium path was used for collection of anomalous diffraction data at 5 keV for two proteins: thaumatin and the membrane protein TehA. Although anomalous signals from each individual crystal are very weak, robust anomalous signals are obtained from data assembled from micrometre-sized crystals. The thaumatin structure was determined from 15 microcrystals and the TehA structure from 18 microcrystals. These results demonstrate the usefulness of a helium environment in support of native-SAD phasing at 5 keV.
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Affiliation(s)
- Akira Karasawa
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Babak Andi
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sean McSweeney
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Qun Liu
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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5
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Bazin D, Lucas IT, Rouzière S, Elkaim E, Mocuta C, Réguer S, Reid DG, Mathurin J, Dazzi A, Deniset-Besseau A, Petay M, Frochot V, Haymann JP, Letavernier E, Verpont MC, Foy E, Bouderlique E, Colboc H, Daudon M. Profile of an “at cutting edge” pathology laboratory for pathological human deposits: from nanometer to in vivo scale analysis on large scale facilities. CR CHIM 2022. [DOI: 10.5802/crchim.199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Martiel I, Beale JH, Karpik A, Huang CY, Vera L, Olieric N, Wranik M, Tsai CJ, Mühle J, Aurelius O, John J, Högbom M, Wang M, Marsh M, Padeste C. Versatile microporous polymer-based supports for serial macromolecular crystallography. Acta Crystallogr D Struct Biol 2021; 77:1153-1167. [PMID: 34473086 PMCID: PMC8411977 DOI: 10.1107/s2059798321007324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - John H. Beale
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, 5210 Windisch, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Laura Vera
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ching-Ju Tsai
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Jonas Mühle
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
- MAX IV Laboratory, Lund University, Fotongatan 2, 224 84 Lund, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - May Marsh
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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7
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Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
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8
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Illava G, Jayne R, Finke AD, Closs D, Zeng W, Milano SK, Huang Q, Kriksunov I, Sidorenko P, Wise FW, Zipfel WR, Apker BA, Thorne RE. Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2021; 77:628-644. [PMID: 33950019 PMCID: PMC8098472 DOI: 10.1107/s2059798321001868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Serial synchrotron crystallography (SSX) is enabling the efficient use of small crystals for structure-function studies of biomolecules and for drug discovery. An integrated SSX system has been developed comprising ultralow background-scatter sample holders suitable for room and cryogenic temperature crystallographic data collection, a sample-loading station and a humid `gloveless' glovebox. The sample holders incorporate thin-film supports with a variety of designs optimized for different crystal-loading challenges. These holders facilitate the dispersion of crystals and the removal of excess liquid, can be cooled at extremely high rates, generate little background scatter, allow data collection over >90° of oscillation without obstruction or the risk of generating saturating Bragg peaks, are compatible with existing infrastructure for high-throughput cryocrystallography and are reusable. The sample-loading station allows sample preparation and loading onto the support film, the application of time-varying suction for optimal removal of excess liquid, crystal repositioning and cryoprotection, and the application of sealing films for room-temperature data collection, all in a controlled-humidity environment. The humid glovebox allows microscope observation of the sample-loading station and crystallization trays while maintaining near-saturating humidities that further minimize the risks of sample dehydration and damage, and maximize working times. This integrated system addresses common problems in obtaining properly dispersed, properly hydrated and isomorphous microcrystals for fixed-orientation and oscillation data collection. Its ease of use, flexibility and optimized performance make it attractive not just for SSX but also for single-crystal and few-crystal data collection. Fundamental concepts that are important in achieving desired crystal distributions on a sample holder via time-varying suction-induced liquid flows are also discussed.
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Affiliation(s)
- Gabrielle Illava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - David Closs
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
| | - Wenjie Zeng
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Pavel Sidorenko
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Frank W. Wise
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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9
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Schneider DK, Shi W, Andi B, Jakoncic J, Gao Y, Bhogadi DK, Myers SF, Martins B, Skinner JM, Aishima J, Qian K, Bernstein HJ, Lazo EO, Langdon T, Lara J, Shea-McCarthy G, Idir M, Huang L, Chubar O, Sweet RM, Berman LE, McSweeney S, Fuchs MR. FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:650-665. [PMID: 33650577 PMCID: PMC7941291 DOI: 10.1107/s1600577520016173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5-30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s-1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s-1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods - serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362-1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238-246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.
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Affiliation(s)
| | - Wuxian Shi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jean Jakoncic
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Stuart F. Myers
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bruno Martins
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, MI 48824, USA
| | - John M. Skinner
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jun Aishima
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kun Qian
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Herbert J. Bernstein
- Ronin Institute for Independent Scholarship, c/o NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Edwin O. Lazo
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Thomas Langdon
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John Lara
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Mourad Idir
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lei Huang
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleg Chubar
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Robert M. Sweet
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lonny E. Berman
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sean McSweeney
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
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10
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Blum TB, Housset D, Clabbers MTB, van Genderen E, Bacia-Verloop M, Zander U, McCarthy AA, Schoehn G, Ling WL, Abrahams JP. Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals. Acta Crystallogr D Struct Biol 2021; 77:75-85. [PMID: 33404527 PMCID: PMC7787111 DOI: 10.1107/s2059798320014540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/02/2020] [Indexed: 11/10/2022] Open
Abstract
Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, a low-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.
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Affiliation(s)
- Thorsten B. Blum
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Dominique Housset
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Eric van Genderen
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Maria Bacia-Verloop
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Wai Li Ling
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jan Pieter Abrahams
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
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11
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Martiel I, Huang CY, Villanueva-Perez P, Panepucci E, Basu S, Caffrey M, Pedrini B, Bunk O, Stampanoni M, Wang M. Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography. IUCRJ 2020; 7:1131-1141. [PMID: 33209324 PMCID: PMC7642777 DOI: 10.1107/s2052252520013238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Pablo Villanueva-Perez
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Synchrotron Radiation Research and NanoLund, Lund University, Box 118, Lund, 221 00, Sweden
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Shibom Basu
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- EMBL Grenoble, 71 avenue des Martyrs, Grenoble, 38042, France
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
| | - Bill Pedrini
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Oliver Bunk
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Marco Stampanoni
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Institute of Biomedical Engineering, University and ETH Zurich, Zurich, 8092, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
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12
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Yu J, Shinoda A, Kato K, Tanaka I, Yao M. A solution-free crystal-mounting platform for native SAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:938-945. [PMID: 33021495 DOI: 10.1107/s2059798320011584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/25/2020] [Indexed: 11/11/2022]
Abstract
The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.
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Affiliation(s)
- Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Akira Shinoda
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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13
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Pearson AR, Mehrabi P. Serial synchrotron crystallography for time-resolved structural biology. Curr Opin Struct Biol 2020; 65:168-174. [PMID: 32846363 DOI: 10.1016/j.sbi.2020.06.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based experiments. However, there is a large range of macromolecular systems where the biological interest is predominantly in the slower dynamics (μs-s), that produce well diffracting microcrystals, and for which synchrotron-based experiments are extremely well suited. The combination of microfocus X-ray beams and the development of a range of sample delivery platforms has now made routine millisecond time-resolved experiments at microfocus macromolecular crystallography beamlines a real possibility and is driving development of dedicated endstations for time-resolved serial synchrotron crystallography.
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Affiliation(s)
- Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany.
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany
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14
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Assmann GM, Wang M, Diederichs K. Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods. Acta Crystallogr D Struct Biol 2020; 76:636-652. [PMID: 32627737 PMCID: PMC7336379 DOI: 10.1107/s2059798320006348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Phasing by single-wavelength anomalous diffraction (SAD) from multiple crystallographic data sets can be particularly demanding because of the weak anomalous signal and possible non-isomorphism. The identification and exclusion of non-isomorphous data sets by suitable indicators is therefore indispensable. Here, simple and robust data-selection methods are described. A multi-dimensional scaling procedure is first used to identify data sets with large non-isomorphism relative to clusters of other data sets. Within each cluster that it identifies, further selection is based on the weighted ΔCC1/2, a quantity representing the influence of a set of reflections on the overall CC1/2 of the merged data. The anomalous signal is further improved by optimizing the scaling protocol. The success of iterating the selection and scaling steps was verified by substructure determination and subsequent structure solution. Three serial synchrotron crystallography (SSX) SAD test cases with hundreds of partial data sets and one test case with 62 complete data sets were analyzed. Structure solution was dramatically simplified with this procedure, and enabled solution of the structures after a few selection/scaling iterations. To explore the limits, the procedure was tested with much fewer data than originally required and could still solve the structure in several cases. In addition, an SSX data challenge, minimizing the number of (simulated) data sets necessary to solve the structure, was significantly underbid.
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Affiliation(s)
- Greta M. Assmann
- Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany
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15
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Takemaru L, Guo G, Zhu P, Hendrickson WA, McSweeney S, Liu Q. PyMDA: microcrystal data assembly using Python. J Appl Crystallogr 2020; 53:277-281. [PMID: 32047415 PMCID: PMC6998775 DOI: 10.1107/s160057671901673x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/13/2019] [Indexed: 11/15/2022] Open
Abstract
The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation damaged with incomplete data per microcrystal and with unit-cell variations. A multi-stage data assembly method has previously been designed for microcrystal synchrotron crystallography. Here the strategy has been implemented as a Python program for microcrystal data assembly (PyMDA). PyMDA optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, PyMDA may be applicable for assembling data sets from larger crystals for improved data quality.
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Affiliation(s)
- Lina Takemaru
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Gongrui Guo
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Sciences Division, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ping Zhu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sean McSweeney
- Photon Sciences Division, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Sciences Division, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
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16
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Allen AJ. Recent trends in crystallography - a current IUCr journals perspective. IUCRJ 2019; 6:984-987. [PMID: 31709052 PMCID: PMC6830219 DOI: 10.1107/s2052252519014507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This Editorial considers the impact of recent work published in IUCrJ and other IUCr journals, as well as the relationship between IUCrJ and the other journals, in terms of where the most cited recent papers are used.
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Affiliation(s)
- Andrew J. Allen
- Materials Measurement Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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17
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Guo G, Zhu P, Fuchs MR, Shi W, Andi B, Gao Y, Hendrickson WA, McSweeney S, Liu Q. Synchrotron microcrystal native-SAD phasing at a low energy. IUCRJ 2019; 6:532-542. [PMID: 31316798 PMCID: PMC6608635 DOI: 10.1107/s2052252519004536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/03/2019] [Indexed: 05/31/2023]
Abstract
De novo structural evaluation of native biomolecules from single-wavelength anomalous diffraction (SAD) is a challenge because of the weakness of the anomalous scattering. The anomalous scattering from relevant native elements - primarily sulfur in proteins and phospho-rus in nucleic acids - increases as the X-ray energy decreases toward their K-edge transitions. Thus, measurements at a lowered X-ray energy are promising for making native SAD routine and robust. For microcrystals with sizes less than 10 µm, native-SAD phasing at synchrotron microdiffraction beamlines is even more challenging because of difficulties in sample manipulation, diffraction data collection and data analysis. Native-SAD analysis from microcrystals by using X-ray free-electron lasers has been demonstrated but has required use of thousands of thousands of microcrystals to achieve the necessary accuracy. Here it is shown that by exploitation of anomalous microdiffraction signals obtained at 5 keV, by the use of polyimide wellmounts, and by an iterative crystal and frame-rejection method, microcrystal native-SAD phasing is possible from as few as about 1 200 crystals. Our results show the utility of low-energy native-SAD phasing with microcrystals at synchrotron microdiffraction beamlines.
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Affiliation(s)
- Gongrui Guo
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ping Zhu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sean McSweeney
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
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18
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Dauter Z. Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays. IUCRJ 2019; 6:503-504. [PMID: 31316793 PMCID: PMC6608617 DOI: 10.1107/s2052252519008698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
A practical approach for obtaining S-SAD data from native protein microcrystals with low-wavelength synchrotron radiation [Guo et al. (2019), IUCrJ, 6, 532-542] is presented in this issue of IUCrJ.
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Affiliation(s)
- Zbigniew Dauter
- National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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19
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Basu S, Finke A, Vera L, Wang M, Olieric V. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source. Acta Crystallogr D Struct Biol 2019; 75:262-271. [PMID: 30950397 PMCID: PMC6450063 DOI: 10.1107/s2059798319003103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/01/2019] [Indexed: 01/19/2023] Open
Abstract
Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 µm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Aaron Finke
- MacCHESS, Cornell University, Ithaca, New York, USA
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
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20
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Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II. Molecules 2019; 24:molecules24030496. [PMID: 30704096 PMCID: PMC6384729 DOI: 10.3390/molecules24030496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/17/2022] Open
Abstract
Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II-AMX and FMX-deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins-Akt1, PI3Kα, and CDP-Chase-to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or "raster-collect", a more automated approach for a larger number of crystals (using CDP-Chase as an example).
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21
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Basu S, Kaminski JW, Panepucci E, Huang CY, Warshamanage R, Wang M, Wojdyla JA. Automated data collection and real-time data analysis suite for serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:244-252. [PMID: 30655492 PMCID: PMC6337882 DOI: 10.1107/s1600577518016570] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/21/2018] [Indexed: 05/03/2023]
Abstract
At the Swiss Light Source macromolecular crystallography (MX) beamlines the collection of serial synchrotron crystallography (SSX) diffraction data is facilitated by the recent DA+ data acquisition and analysis software developments. The SSX suite allows easy, efficient and high-throughput measurements on a large number of crystals. The fast continuous diffraction-based two-dimensional grid scan method allows initial location of microcrystals. The CY+ GUI utility enables efficient assessment of a grid scan's analysis output and subsequent collection of multiple wedges of data (so-called minisets) from automatically selected positions in a serial and automated way. The automated data processing (adp) routines adapted to the SSX data collection mode provide near real time analysis for data in both CBF and HDF5 formats. The automatic data merging (adm) is the latest extension of the DA+ data analysis software routines. It utilizes the sxdm (SSX data merging) package, which provides automatic online scaling and merging of minisets and allows identification of a minisets subset resulting in the best quality of the final merged data. The results of both adp and adm are sent to the MX MongoDB database and displayed in the web-based tracker, which provides the user with on-the-fly feedback about the experiment.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jakub W. Kaminski
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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22
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Doak RB, Nass Kovacs G, Gorel A, Foucar L, Barends TRM, Grünbein ML, Hilpert M, Kloos M, Roome CM, Shoeman RL, Stricker M, Tono K, You D, Ueda K, Sherrell DA, Owen RL, Schlichting I. Crystallography on a chip - without the chip: sheet-on-sheet sandwich. Acta Crystallogr D Struct Biol 2018; 74:1000-1007. [PMID: 30289410 PMCID: PMC6173051 DOI: 10.1107/s2059798318011634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/16/2018] [Indexed: 11/29/2022] Open
Abstract
Crystallography chips are fixed-target supports consisting of a film (for example Kapton) or wafer (for example silicon) that is processed using semiconductor-microfabrication techniques to yield an array of wells or through-holes in which single microcrystals can be lodged for raster-scan probing. Although relatively expensive to fabricate, chips offer an efficient means of high-throughput sample presentation for serial diffraction data collection at synchrotron or X-ray free-electron laser (XFEL) sources. Truly efficient loading of a chip (one microcrystal per well and no wastage during loading) is nonetheless challenging. The wells or holes must match the microcrystal size of interest, requiring that a large stock of chips be maintained. Raster scanning requires special mechanical drives to step the chip rapidly and with micrometre precision from well to well. Here, a `chip-less' adaptation is described that essentially eliminates the challenges of loading and precision scanning, albeit with increased, yet still relatively frugal, sample usage. The device consists simply of two sheets of Mylar with the crystal solution sandwiched between them. This sheet-on-sheet (SOS) sandwich structure has been employed for serial femtosecond crystallography data collection with micrometre-sized crystals at an XFEL. The approach is also well suited to time-resolved pump-probe experiments, in particular for long time delays. The SOS sandwich enables measurements under XFEL beam conditions that would damage conventional chips, as documented here. The SOS sheets hermetically seal the sample, avoiding desiccation of the sample provided that the X-ray beam does not puncture the sheets. This is the case with a synchrotron beam but not with an XFEL beam. In the latter case, desiccation, setting radially outwards from each punched hole, sets lower limits on the speed and line spacing of the raster scan. It is shown that these constraints are easily accommodated.
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Affiliation(s)
- R. Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Mario Hilpert
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marco Kloos
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Christopher M. Roome
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Miriam Stricker
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, England
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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23
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Nazaretski E, Xu W, Yan H, Huang X, Coburn DS, Ge M, Lee WK, Gao Y, Xu W, Fuchs M, Chu YS. Microscopy Instrumentation and Nanopositioning at NSLS-II: Current Status and Future Directions. SYNCHROTRON RADIATION NEWS 2018; 31:3-8. [PMID: 31467463 PMCID: PMC6714041 DOI: 10.1080/08940886.2018.1506233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- E Nazaretski
- Brookhaven National Laboratory, Upton, New York, USA
| | - W Xu
- Brookhaven National Laboratory, Upton, New York, USA
| | - H Yan
- Brookhaven National Laboratory, Upton, New York, USA
| | - X Huang
- Brookhaven National Laboratory, Upton, New York, USA
| | - D S Coburn
- Brookhaven National Laboratory, Upton, New York, USA
| | - M Ge
- Brookhaven National Laboratory, Upton, New York, USA
| | - W-K Lee
- Brookhaven National Laboratory, Upton, New York, USA
| | - Y Gao
- Brookhaven National Laboratory, Upton, New York, USA
| | - W Xu
- Brookhaven National Laboratory, Upton, New York, USA
| | - M Fuchs
- Brookhaven National Laboratory, Upton, New York, USA
| | - Y S Chu
- Brookhaven National Laboratory, Upton, New York, USA
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24
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Gao Y, Xu W, Shi W, Soares A, Jakoncic J, Myers S, Martins B, Skinner J, Liu Q, Bernstein H, McSweeney S, Nazaretski E, Fuchs MR. High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1362-1370. [PMID: 30179174 PMCID: PMC6140394 DOI: 10.1107/s1600577518010354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/18/2018] [Indexed: 05/06/2023]
Abstract
The Frontier Microfocus Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II with its 1 µm beam size and photon flux of 3 × 1012 photons s-1 at a photon energy of 12.66 keV has reached unprecedented dose rates for a structural biology beamline. The high dose rate presents a great advantage for serial microcrystallography in cutting measurement time from hours to minutes. To provide the instrumentation basis for such measurements at the full flux of the FMX beamline, a high-speed, high-precision goniometer based on a unique XYZ piezo positioner has been designed and constructed. The piezo-based goniometer is able to achieve sub-100 nm raster-scanning precision at over 10 grid-linepairs s-1 frequency for fly scans of a 200 µm-wide raster. The performance of the scanner in both laboratory and serial crystallography measurements up to the maximum frame rate of 750 Hz of the Eiger 16M's 4M region-of-interest mode has been verified in this work. This unprecedented experimental speed significantly reduces serial-crystallography data collection time at synchrotrons, allowing utilization of the full brightness of the emerging synchrotron radiation facilities.
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Affiliation(s)
- Yuan Gao
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Weihe Xu
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
- Case Center for Synchrotron Biosciences, Case Western Reserve University, OH 44106, USA
| | - Alexei Soares
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jean Jakoncic
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Stuart Myers
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bruno Martins
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John Skinner
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Herbert Bernstein
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
- School of Chemistry and Materials Science, Rochester Institute of Technology, NY 14623, USA
| | - Sean McSweeney
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Evgeny Nazaretski
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
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25
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Huang CY, Olieric V, Howe N, Warshamanage R, Weinert T, Panepucci E, Vogeley L, Basu S, Diederichs K, Caffrey M, Wang M. In situ serial crystallography for rapid de novo membrane protein structure determination. Commun Biol 2018; 1:124. [PMID: 30272004 PMCID: PMC6123769 DOI: 10.1038/s42003-018-0123-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022] Open
Abstract
De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Nicole Howe
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Lutz Vogeley
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, M647, D-78457, Konstanz, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland.
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