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Suzuki R, Abe M, Kojima K, Tachibana M. Identification of grown-in dislocations in protein crystals by digital X-ray topography. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576720015356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
X-ray topography is a useful and nondestructive method for direct observation of crystal defects in nearly perfect single crystals. The grown-in dislocations from the cross-linked seed crystal in tetragonal hen egg-white lysozyme crystals were successfully characterized by digital X-ray topography. Digital X-ray topographs with various reflections were easily obtained by reconstruction of sequential rocking-curve images. The Burgers vector of the dislocation is different from those reported previously. Interestingly, one of the dislocations had a bent shape. The preferred direction of the dislocation line was analysed by the estimated dislocation energy based on the dislocation theory. The dislocation energy can be estimated by the dislocation theory even in protein crystals composed of macromolecules.
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Coughlan HD, Darmanin C, Kirkwood HJ, Phillips NW, Hoxley D, Clark JN, Vine DJ, Hofmann F, Harder RJ, Maxey E, Abbey B. Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:83-94. [PMID: 28009549 PMCID: PMC5182022 DOI: 10.1107/s1600577516017525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/01/2016] [Indexed: 05/09/2023]
Abstract
The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.
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Affiliation(s)
- H. D. Coughlan
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
- CSIRO Manufacturing Flagship, Parkville 3052, Australia
| | - C. Darmanin
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - H. J. Kirkwood
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - N. W. Phillips
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
- CSIRO Manufacturing Flagship, Parkville 3052, Australia
| | - D. Hoxley
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - J. N. Clark
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - D. J. Vine
- Advanced Light Source, Berkeley Lab, Berkeley, CA 94720, USA
| | - F. Hofmann
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - R. J. Harder
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - E. Maxey
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - B. Abbey
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
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Nave C, Sutton G, Evans G, Owen R, Rau C, Robinson I, Stuart DI. Imperfection and radiation damage in protein crystals studied with coherent radiation. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:228-37. [PMID: 26698068 PMCID: PMC4733927 DOI: 10.1107/s1600577515019700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/18/2015] [Indexed: 05/11/2023]
Abstract
Fringes and speckles occur within diffraction spots when a crystal is illuminated with coherent radiation during X-ray diffraction. The additional information in these features provides insight into the imperfections in the crystal at the sub-micrometre scale. In addition, these features can provide more accurate intensity measurements (e.g. by model-based profile fitting), detwinning (by distinguishing the various components), phasing (by exploiting sampling of the molecular transform) and refinement (by distinguishing regions with different unit-cell parameters). In order to exploit these potential benefits, the features due to coherent diffraction have to be recorded and any change due to radiation damage properly modelled. Initial results from recording coherent diffraction at cryotemperatures from polyhedrin crystals of approximately 2 µm in size are described. These measurements allowed information about the type of crystal imperfections to be obtained at the sub-micrometre level, together with the changes due to radiation damage.
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Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Geoff Sutton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robin Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Christoph Rau
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - David Ian Stuart
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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Coughlan HD, Darmanin C, Phillips NW, Hofmann F, Clark JN, Harder RJ, Vine DJ, Abbey B. Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041704. [PMID: 26798804 PMCID: PMC4711611 DOI: 10.1063/1.4919641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/22/2015] [Indexed: 05/11/2023]
Abstract
For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.
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Affiliation(s)
| | - C Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe University , Melbourne 3086, Australia
| | | | - F Hofmann
- Department of Engineering Science, University of Oxford , Oxford OX1 3PJ, United Kingdom
| | | | - R J Harder
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, USA
| | - D J Vine
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, USA
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van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber T. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein. Faraday Discuss 2014; 171:439-55. [PMID: 25415305 DOI: 10.1039/c4fd00011k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Femtosecond time resolved pump-probe protein X-ray crystallography requires highly accurate measurements of the photoinduced structure factor amplitude differences. In the case of femtosecond photolysis of single P63 crystals of the Photoactive Yellow Protein, it is shown that photochemical dynamics place a considerable restraint on the achievable time resolution due to the requirement to stretch and add second order dispersion in order to generate threshold concentration levels in the interaction region. Here, we report on using a 'quasi-cw' approach to use the rotation method with monochromatic radiation and 2 eV bandwidth at 9.465 keV at the Linac Coherent Light Source operated in SASE mode. A source of significant Bragg reflection intensity noise is identified from the combination of mode structure and jitter with very small mosaic spread of the crystals and very low convergence of the XFEL source. The accuracy with which the three dimensional reflection is approximated by the 'quasi-cw' rotation method with the pulsed source is modelled from the experimentally collected X-ray pulse intensities together with the measured rocking curves. This model is extended to predict merging statistics for recently demonstrated self seeded mode generated pulse train with improved stability, in addition to extrapolating to single crystal experiments with increased mosaic spread. The results show that the noise level can be adequately modelled in this manner, indicating that the large intensity fluctuations dominate the merged signal-to-noise (I/σI) value. Furthermore, these results predict that using the self seeded mode together with more mosaic crystals, sufficient accuracy may be obtained in order to resolve typical photoinduced structure factor amplitude differences, as taken from representative synchrotron results.
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Affiliation(s)
- Jasper J van Thor
- Imperial College London, Division of Molecular Biosciences, South Kensington Campus, London SW7 2AZ, UK.
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Koizumi H, Uda S, Fujiwara K, Tachibana M, Kojima K, Nozawa J. Improvement of crystal quality for tetragonal hen egg white lysozyme crystals under application of an external alternating current electric field. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889812048716] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
X-ray diffraction rocking-curve measurements were performed on tetragonal hen egg white lysozyme (HEWL) crystals grown with and without application of an external alternating current (AC) electric field, and then the crystal quality was assessed by the FWHMs of each rocking-curve profile. The FWHMs for HEWL crystals grown with an external electric field were smaller than those for crystals grown without. In particular, the average FWHM for the 12 12 0 reflection with an external electric field (0.0034°) was significantly smaller than that without (0.0061°). This indicates that the crystal quality of HEWL crystals was improved by application of the external AC electric field. This crystallization technique can be expected to enhance the resolution of protein molecule structure analysis by X-ray diffraction.
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