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16 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2 [Next/Last]

Instruments / Technical Area	Publication Details	Published
Data acquisition	dxtbx: the diffraction experiment toolbox James Parkhurst , Aaron S. Brewster , Luis Fuentes-montero , David G Waterman , Johan Hattne , Alun Ashton , Nathaniel Echols , Gwyndaf Evans , Nicholas K. Sauter , Graeme Winter Journal Of Applied Crystallography 47, 1459 - 1465 DOI: 10.1107/S1600576714011996 PMID: 25242914 Open Access Show Abstract ▼ Abstract: Data formats for recording X-ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from single-crystal X-ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open-source licence at http://cctbx.sourceforge.net .	Aug 2014
	The NeXus data format Mark Könnecke , Frederick A. Akeroyd , Herbert J. Bernstein , Aaron S. Brewster , Stuart Campbell , Björn Clausen , Stephen Cottrell , Jens Uwe Hoffmann , Pete R. Jemian , David Männicke , Raymond Osborn , Peter F. Peterson , Tobias Richter , Jiro Suzuki , Benjamin Watts , Eugen Wintersberger , Joachim Wuttke Journal Of Applied Crystallography 48 (1), 301 - 305 DOI: 10.1107/S1600576714027575 PMID: 26089752 Open Access Show Abstract ▼ Abstract: NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.	Feb 2015
I24-Microfocus Macromolecular Crystallography	Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data Helen M Ginn , Marc Messerschmidt , Xiaoyun Ji , Hanwen Zhang , Danny Axford , Richard J Gildea , Graeme Winter , Aaron S. Brewster , Johan Hattne , Armin Wagner , Jonathan M Grimes , Gwyndaf Evans , Nicholas K. Sauter , Geoff Sutton , David I Stuart Nature Communications 6 DOI: 10.1038/ncomms7435 PMID: 25751308 Open Access Show Abstract ▼ Abstract: The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.	Mar 2015
	A revised partiality model and post-refinement algorithm for X-ray free-electron laser data Helen Ginn , Aaron S. Brewster , Johan Hattne , Gwyndaf Evans , Armin Wagner , Jonathan Grimes , Nicholas K. Sauter , Geoff Sutton , Dave Stuart Acta Crystallographica Section D Biological Crystallography 71, 1400 - 1410 DOI: 10.1107/S1399004715006902 PMID: 26057680 Open Access Show Abstract ▼ Abstract: Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the Rsplit value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.	Jun 2015
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Diffraction-geometry refinement in the DIALS framework David G. Waterman , Graeme Winter , Richard J. Gildea , James M. Parkhurst , Aaron S. Brewster , Nicholas K. Sauter , Gwyndaf Evans Acta Crystallographica Section D Structural Biology 72 (4), 558 - 575 DOI: 10.1107/S2059798316002187 Open Access Show Abstract ▼ Abstract: Rapid data collection and modern computing resources provide the opportunity to revisit the task of optimizing the model of diffraction geometry prior to integration. A comprehensive description is given of new software that builds upon established methods by performing a single global refinement procedure, utilizing a smoothly varying model of the crystal lattice where appropriate. This global refinement technique extends to multiple data sets, providing useful constraints to handle the problem of correlated parameters, particularly for small wedges of data. Examples of advanced uses of the software are given and the design is explained in detail, with particular emphasis on the flexibility and extensibility it entails.	Apr 2016
	Structure of photosystem II and substrate binding at room temperature Iris D. Young , Mohamed Ibrahim , Ruchira Chatterjee , Sheraz Gul , Franklin D. Fuller , Sergey Koroidov , Aaron S. Brewster , Rosalie Tran , Roberto Alonso-mori , Thomas Kroll , Tara Michels-clark , Hartawan Laksmono , Raymond G. Sierra , Claudiu A. Stan , Rana Hussein , Miao Zhang , Lacey Douthit , Markus Kubin , Casper De Lichtenberg , Long Vo Pham , Håkan Nilsson , Mun Hon Cheah , Dmitriy Shevela , Claudio Saracini , Mackenzie A. Bean , Ina Seuffert , Dimosthenis Sokaras , Tsu-chien Weng , Ernest Pastor , Clemens Weninger , Thomas Fransson , Louise Lassalle , Philipp Bräuer , Pierre Aller , Peter T. Docker , Babak Andi , Allen M. Orville , James M. Glownia , Silke Nelson , Marcin Sikorski , Diling Zhu , Mark S. Hunter , Thomas J. Lane , Andy Aquila , Jason E. Koglin , Joseph Robinson , Mengning Liang , Sébastien Boutet , Artem Y. Lyubimov , Monarin Uervirojnangkoorn , Nigel W. Moriarty , Dorothee Liebschner , Pavel V. Afonine , David G. Waterman , Gwyndaf Evans , Philippe Wernet , Holger Dobbek , William I. Weis , Axel T. Brunger , Petrus H. Zwart , Paul D. Adams , Athina Zouni , Johannes Messinger , Uwe Bergmann , Nicholas K. Sauter , Jan Kern , Vittal K. Yachandra , Junko Yano Nature DOI: 10.1038/nature20161 Show Abstract ▼ Abstract: Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2, 3. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site4, 5, 6. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8, 9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10, 11, 12, 13. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.	Nov 2016
	Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Franklin D Fuller , Sheraz Gul , Ruchira Chatterjee , E. Sethe Burgie , Iris D. Young , Hugo Lebrette , Vivek Srinivas , Aaron Brewster , Tara Michels-clark , Jonathan A Clinger , Babak Andi , Mohamed Ibrahim , Ernest Pastor , Casper De Lichtenberg , Rana Hussein , Christopher J Pollock , Miao Zhang , Claudiu A Stan , Thomas Kroll , Thomas Fransson , Clemens Weninger , Markus Kubin , Pierre Aller , Louise Lassalle , Philipp Braeuer , Mitchell D. Miller , Muhamed Amin , Sergey Koroidov , Christian G. Roessler , Marc Allaire , Raymond G Sierra , Peter T. Docker , James M. Glownia , Silke Nelson , Jason E Koglin , Diling Zhu , Matthieu Chollet , Sanghoon Song , Henrik Lemke , Mengning Liang , Dimosthenis Sokaras , Roberto Alonso-mori , Athina Zouni , Johannes Messinger , Uwe Bergmann , Amie K. Boal , J. Martin Bollinger , Carsten Krebs , Martin Högbom , George N. Phillips , Richard D. Vierstra , Nicholas K Sauter , Allen M. Orville , Jan Kern , Vittal K Yachandra , Junko Yano Nature Methods 5 DOI: 10.1038/nmeth.4195 Show Abstract ▼ Abstract: X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.	Feb 2017
	High-speed fixed-target serial virus crystallography Philip Roedig , Helen M. Ginn , Tim Pakendorf , Geoff Sutton , Karl Harlos , Thomas S. Walter , Jan Meyer , Pontus Fischer , Ramona Duman , Ismo Vartiainen , Bernd Reime , Martin Warmer , Aaron S. Brewster , Iris D. Young , Tara Michels-clark , Nicholas K. Sauter , Abhay Kotecha , James Kelly , David J. Rowlands , Marcin Sikorsky , Silke Nelson , Daniel S. Damiani , Roberto Alonso-mori , Jingshan Ren , Elizabeth E. Fry , Christian David , David I. Stuart Stuart , Armin Wagner , Alke Meents Nature Methods 8 DOI: 10.1038/nmeth.4335 Show Abstract ▼ Abstract: We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.	Jun 2017
I19-Small Molecule Single Crystal Diffraction	DIALS : implementation and evaluation of a new integration package Graeme Winter , David G. Waterman , James M. Parkhurst , Aaron S. Brewster , Richard J. Gildea , Markus Gerstel , Luis Fuentes-montero , Melanie Vollmar , Tara Michels-clark , Iris D. Young , Nicholas K. Sauter , Gwyndaf Evans Acta Crystallographica Section D Structural Biology 74, 85 - 97 DOI: 10.1107/S2059798317017235 Open Access Show Abstract ▼ Abstract: The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.	Feb 2018
	Towards in cellulo virus crystallography Helen M. E. Duyvesteyn , Helen M. Ginn , Maija K. Pietila , Armin Wagner , Johan Hattne , Jonathan M. Grimes , Elina Hirvonen , Gwyndaf Evans , Marie-laure Parsy , Nicholas K. Sauter , Aaron S. Brewster , Juha Huiskonen , David I. Stuart , Geoff Sutton , Dennis H. Bamford Scientific Reports 8 DOI: 10.1038/s41598-018-21693-3 Open Access Show Abstract ▼ Abstract: Viruses are a significant threat to both human health and the economy, and there is an urgent need for novel anti-viral drugs and vaccines. High-resolution viral structures inform our understanding of the virosphere, and inspire novel therapies. Here we present a method of obtaining such structural information that avoids potentially disruptive handling, by collecting diffraction data from intact infected cells. We identify a suitable combination of cell type and virus to accumulate particles in the cells, establish a suitable time point where most cells contain virus condensates and use electron microscopy to demonstrate that these are ordered crystalline arrays of empty capsids. We then use an X-ray free electron laser to provide extremely bright illumination of sub-micron intracellular condensates of bacteriophage phiX174 inside living Escherichia coli at room temperature. We have been able to collect low resolution diffraction data. Despite the limited resolution and completeness of these initial data, due to a far from optimal experimental setup, we have used novel methodology to determine a putative space group, unit cell dimensions, particle packing and likely maturation state of the particles.	Feb 2018

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