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  1. Article ; Online: Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis.

    Hough, Michael A / Owen, Robin L

    Current opinion in structural biology

    2021  Volume 71, Page(s) 232–238

    Abstract: An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are ... ...

    Abstract An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.
    MeSH term(s) Catalysis ; Crystallography, X-Ray ; Metalloproteins ; Spectrum Analysis ; Synchrotrons
    Chemical Substances Metalloproteins
    Language English
    Publishing date 2021-08-26
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2021.07.007
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  2. Article: Experimental evidence for the benefits of higher X-ray energies for macromolecular crystallography.

    Storm, Selina L S / Axford, Danny / Owen, Robin L

    IUCrJ

    2021  Volume 8, Issue Pt 6, Page(s) 896–904

    Abstract: X-ray-induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete data sets for the structure solution of challenging samples. Increasing the X-ray energy beyond ...

    Abstract X-ray-induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete data sets for the structure solution of challenging samples. Increasing the X-ray energy beyond the typical 10-15 keV range promises to provide an extension of crystal lifetime via an increase in diffraction efficiency. To date, however, hardware limitations have negated any possible gains. Through the first use of a cadmium telluride EIGER2 detector and a beamline optimized for high-energy data collection, it is shown that at higher energies fewer crystals will be required to obtain complete data, as the diffracted intensity per unit dose increases by a factor of more than two between 12.4 and 25 keV. Additionally, these higher energy data can provide more information, as shown by a systematic increase in the high-resolution cutoff of the data collected. Taken together, these gains point to a high-energy future for synchrotron-based macromolecular crystallography.
    Language English
    Publishing date 2021-09-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252521008423
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  3. Article ; Online: A standard descriptor for fixed-target serial crystallography.

    Owen, Robin L / de Sanctis, Daniele / Pearson, Arwen R / Beale, John H

    Acta crystallographica. Section D, Structural biology

    2023  Volume 79, Issue Pt 8, Page(s) 668–672

    Abstract: Fixed-target crystallography has become a widely used approach for serial crystallography at both synchrotron and X-ray free-electron laser (XFEL) sources. A plethora of fixed targets have been developed at different facilities and by various ... ...

    Abstract Fixed-target crystallography has become a widely used approach for serial crystallography at both synchrotron and X-ray free-electron laser (XFEL) sources. A plethora of fixed targets have been developed at different facilities and by various manufacturers, with different characteristics and dimensions and with little or no emphasis on standardization. These many fixed targets have good reasons for their design, shapes, fabrication materials and the presence or absence of apertures and fiducials, reflecting the diversity of serial experiments. Given this, it would be a Sisyphean task to design and manufacture a new standard fixed target that would satisfy all possible experimental configurations. Therefore, a simple standardized descriptor to fully describe fixed targets is proposed rather than a standardized device. This descriptor is a dictionary that could be read by fixed-target beamline software and straightforwardly allow data collection from fixed targets new to that beamline. The descriptor would therefore allow a much easier exchange of fixed targets between sources and facilitate the uptake of new fixed targets, benefiting beamlines, users and manufacturers. This descriptor was first presented at, and was developed following, a meeting of representatives from multiple synchrotron and XFEL sources in Hamburg in January 2023.
    MeSH term(s) Crystallography, X-Ray ; Synchrotrons ; Software ; Data Collection ; Lasers
    Language English
    Publishing date 2023-07-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798323005429
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  4. Article ; Online: An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin.

    Hill, Jake A / Nyathi, Yvonne / Horrell, Sam / von Stetten, David / Axford, Danny / Owen, Robin L / Beddard, Godfrey S / Pearson, Arwen R / Ginn, Helen M / Yorke, Briony A

    Communications chemistry

    2024  Volume 7, Issue 1, Page(s) 81

    Abstract: Human gamma-D crystallin (HGD) is a major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. ...

    Abstract Human gamma-D crystallin (HGD) is a major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. One outstanding question is the structural basis of this longevity despite oxidative aging and environmental stressors including ultraviolet radiation (UV). Here we present crystallographic structures evidencing a UV-induced crystallin redox switch mechanism. The room-temperature serial synchrotron crystallographic (SSX) structure of freshly prepared crystallin mutant (R36S) shows no post-translational modifications. After aging for nine months in the absence of light, a thiol-adduct (dithiothreitol) modifying surface cysteines is observed by low-dose SSX. This is shown to be UV-labile in an acutely light-exposed structure. This suggests a mechanism by which a major source of crystallin damage, UV, may also act as a rescuing factor in a finely balanced redox system.
    Language English
    Publishing date 2024-04-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2929562-2
    ISSN 2399-3669 ; 2399-3669
    ISSN (online) 2399-3669
    ISSN 2399-3669
    DOI 10.1038/s42004-024-01163-w
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  5. Article ; Online: Experimental evidence for the benefits of higher X-ray energies for macromolecular crystallography

    Selina L. S. Storm / Danny Axford / Robin L. Owen

    IUCrJ, Vol 8, Iss 6, Pp 896-

    2021  Volume 904

    Abstract: X-ray-induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete data sets for the structure solution of challenging samples. Increasing the X-ray energy beyond ...

    Abstract X-ray-induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete data sets for the structure solution of challenging samples. Increasing the X-ray energy beyond the typical 10–15 keV range promises to provide an extension of crystal lifetime via an increase in diffraction efficiency. To date, however, hardware limitations have negated any possible gains. Through the first use of a cadmium telluride EIGER2 detector and a beamline optimized for high-energy data collection, it is shown that at higher energies fewer crystals will be required to obtain complete data, as the diffracted intensity per unit dose increases by a factor of more than two between 12.4 and 25 keV. Additionally, these higher energy data can provide more information, as shown by a systematic increase in the high-resolution cutoff of the data collected. Taken together, these gains point to a high-energy future for synchrotron-based macromolecular crystallography.
    Keywords high-energy x-rays ; macromolecular crystallography ; x-ray radiation damage ; Science ; Q
    Subject code 500
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher International Union of Crystallography
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Direct measurement of X-ray-induced heating of microcrystals.

    Warren, Anna J / Axford, Danny / Owen, Robin L

    Journal of synchrotron radiation

    2019  Volume 26, Issue Pt 4, Page(s) 991–997

    Abstract: Temperature control is a key aspect of macromolecular crystallography, with the technique of cryocooling routinely being used to mitigate X-ray-induced damage. Beam-induced heating could cause the temperature of crystals to rise above the glass ... ...

    Abstract Temperature control is a key aspect of macromolecular crystallography, with the technique of cryocooling routinely being used to mitigate X-ray-induced damage. Beam-induced heating could cause the temperature of crystals to rise above the glass transition temperature, greatly increasing the rate of damage. X-ray-induced heating of ruby crystals of 20-40 µm in size has been quantified non-invasively by monitoring the emission wavelengths of X-ray-induced fluorescence during exposure to the X-ray beam. For the beam sizes and dose rates typically used in macromolecular crystallography, the temperature rises are of the order of 20 K. The temperature changes observed are compared with models in the literature and can be used as a validation tool for future models.
    MeSH term(s) Crystallization ; Crystallography, X-Ray/methods ; Heating ; X-Rays
    Language English
    Publishing date 2019-05-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2021413-3
    ISSN 1600-5775 ; 0909-0495
    ISSN (online) 1600-5775
    ISSN 0909-0495
    DOI 10.1107/S1600577519003849
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  7. Book ; Online: Can Euclidean Symmetry be Leveraged in Reinforcement Learning and Planning?

    Zhao, Linfeng / Howell, Owen / Park, Jung Yeon / Zhu, Xupeng / Walters, Robin / Wong, Lawson L. S.

    2023  

    Abstract: In robotic tasks, changes in reference frames typically do not influence the underlying physical properties of the system, which has been known as invariance of physical laws.These changes, which preserve distance, encompass isometric transformations ... ...

    Abstract In robotic tasks, changes in reference frames typically do not influence the underlying physical properties of the system, which has been known as invariance of physical laws.These changes, which preserve distance, encompass isometric transformations such as translations, rotations, and reflections, collectively known as the Euclidean group. In this work, we delve into the design of improved learning algorithms for reinforcement learning and planning tasks that possess Euclidean group symmetry. We put forth a theory on that unify prior work on discrete and continuous symmetry in reinforcement learning, planning, and optimal control. Algorithm side, we further extend the 2D path planning with value-based planning to continuous MDPs and propose a pipeline for constructing equivariant sampling-based planning algorithms. Our work is substantiated with empirical evidence and illustrated through examples that explain the benefits of equivariance to Euclidean symmetry in tackling natural control problems.

    Comment: Preprint. Website: http://lfzhao.com/SymCtrl
    Keywords Computer Science - Machine Learning ; Computer Science - Robotics
    Subject code 629
    Publishing date 2023-07-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Radiation damage and derivatization in macromolecular crystallography: a structure factor's perspective.

    Owen, Robin L / Sherrell, Darren A

    Acta crystallographica. Section D, Structural biology

    2016  Volume 72, Issue Pt 3, Page(s) 388–394

    Abstract: During, or even after, data collection the presence and effects of radiation damage in macromolecular crystallography may not always be immediately obvious. Despite this, radiation damage is almost always present, with site-specific damage occurring on ... ...

    Abstract During, or even after, data collection the presence and effects of radiation damage in macromolecular crystallography may not always be immediately obvious. Despite this, radiation damage is almost always present, with site-specific damage occurring on very short time (dose) scales well before global damage becomes apparent. A result of both site-specific radiation damage and derivatization is a change in the relative intensity of reflections. The size and approximate rate of onset of X-ray-induced transformations is compared with the changes expected from derivatization, and strategies for minimizing radiation damage are discussed.
    MeSH term(s) Animals ; Crystallography, X-Ray/methods ; Dose-Response Relationship, Radiation ; Humans ; Macromolecular Substances/chemistry ; Models, Molecular ; Protein Conformation/radiation effects ; Receptors, IgG/chemistry ; X-Rays
    Chemical Substances Macromolecular Substances ; Receptors, IgG
    Language English
    Publishing date 2016-03-01
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798315021555
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  9. Article ; Online: Variability in X-ray induced effects in [Rh(COD)Cl]

    Fernando, Nathalie K / Boström, Hanna L B / Murray, Claire A / Owen, Robin L / Thompson, Amber L / Dickerson, Joshua L / Garman, Elspeth F / Cairns, Andrew B / Regoutz, Anna

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 46, Page(s) 28444–28456

    Abstract: X-ray characterisation methods have undoubtedly enabled cutting-edge advances in all aspects of materials research. Despite the enormous breadth of information that can be extracted from these techniques, the challenge of radiation-induced sample change ... ...

    Abstract X-ray characterisation methods have undoubtedly enabled cutting-edge advances in all aspects of materials research. Despite the enormous breadth of information that can be extracted from these techniques, the challenge of radiation-induced sample change and damage remains prevalent. This is largely due to the emergence of modern, high-intensity X-ray source technologies and the growing potential to carry out more complex, longer duration
    MeSH term(s) X-Rays ; Synchrotrons ; Crystallography ; X-Ray Diffraction ; Photons
    Language English
    Publishing date 2022-11-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d2cp03928a
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  10. Article ; Online: xia2.multiplex: a multi-crystal data-analysis pipeline.

    Gildea, Richard J / Beilsten-Edmands, James / Axford, Danny / Horrell, Sam / Aller, Pierre / Sandy, James / Sanchez-Weatherby, Juan / Owen, C David / Lukacik, Petra / Strain-Damerell, Claire / Owen, Robin L / Walsh, Martin A / Winter, Graeme

    Acta crystallographica. Section D, Structural biology

    2022  Volume 78, Issue Pt 6, Page(s) 752–769

    Abstract: In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in ... ...

    Abstract In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
    MeSH term(s) COVID-19 ; Crystallography, X-Ray ; Data Analysis ; Humans ; Macromolecular Substances/chemistry ; SARS-CoV-2
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2022-05-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798322004399
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