Data acquisition
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Open Access
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 .
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Aug 2014
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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
Open Access
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.
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Feb 2015
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I24-Microfocus Macromolecular Crystallography
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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
Open Access
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.
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Mar 2015
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Open Access
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.
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Jun 2015
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Open Access
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.
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Apr 2016
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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
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.
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Nov 2016
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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
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.
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Feb 2017
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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
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.
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Jun 2017
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I19-Small Molecule Single Crystal Diffraction
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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
Open Access
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.
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Feb 2018
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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
Open Access
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.
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Feb 2018
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