Journal ArticleDOI
Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL
Kunio Hirata,Kyoko Shinzawa-Itoh,Naomine Yano,Shuhei Takemura,Koji Kato,Koji Kato,Miki Hatanaka,Kazumasa Muramoto,Takako Kawahara,Tomitake Tsukihara,Tomitake Tsukihara,Eiki Yamashita,Kensuke Tono,Go Ueno,Takaaki Hikima,Hironori Murakami,Yuichi Inubushi,Makina Yabashi,Tetsuya Ishikawa,Masaki Yamamoto,Takashi Ogura,Hiroshi Sugimoto,Jian Ren Shen,Shinya Yoshikawa,Hideo Ago +24 more
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TLDR
The performance of the femtosecond crystallography method is demonstrated by determining a 1.9-Å radiation damage–free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.Abstract:
By combining the use of relatively large crystals and an X-ray free-electron laser, a radiation damage–free three-dimensional structure of a radiation-sensitive protein (bovine cytochrome oxidase) was solved at 1.9-A resolution. We report a method of femtosecond crystallography for solving radiation damage–free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-A radiation damage–free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.read more
Citations
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Journal ArticleDOI
Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.
Michihiro Suga,Fusamichi Akita,Kunio Hirata,Go Ueno,Hironori Murakami,Yoshiki Nakajima,Tetsuya Shimizu,Keitaro Yamashita,Masaki Yamamoto,Hideo Ago,Jian Ren Shen +10 more
TL;DR: A ‘radiation-damage-free’ structure of PSII from Thermosynechococcus vulcanus in the S1 state is reported, and it is expected that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.
Journal ArticleDOI
A three-dimensional movie of structural changes in bacteriorhodopsin
Eriko Nango,Antoine Royant,Antoine Royant,Minoru Kubo,Takanori Nakane,Cecilia Wickstrand,Tetsunari Kimura,Tomoyuki Tanaka,Kensuke Tono,Changyong Song,Rie Tanaka,Toshi Arima,Ayumi Yamashita,Jun Kobayashi,Toshiaki Hosaka,Eiichi Mizohata,Przemyslaw Nogly,Michihiro Sugahara,Daewoong Nam,Takashi Nomura,Tatsuro Shimamura,Dohyun Im,Takaaki Fujiwara,Yasuaki Yamanaka,Byeonghyun Jeon,Tomohiro Nishizawa,Tomohiro Nishizawa,Kazumasa Oda,Masahiro Fukuda,Rebecka Andersson,Petra Båth,Robert Dods,Jan Davidsson,Shigeru Matsuoka,Satoshi Kawatake,Michio Murata,Osamu Nureki,Shigeki Owada,Takashi Kameshima,Takaki Hatsui,Yasumasa Joti,Gebhard F. X. Schertler,Gebhard F. X. Schertler,Makina Yabashi,Ana-Nicoleta Bondar,Jörg Standfuss,Richard Neutze,So Iwata +47 more
TL;DR: Time-resolved serial femtosecond crystallography at an x-ray free electron laser shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.
Journal ArticleDOI
SwissFEL: The Swiss X-ray Free Electron Laser
Christopher J. Milne,Thomas Schietinger,M. Aiba,Arturo Alarcon,J. Alex,Alexander Anghel,Vladimir Arsov,Carl Beard,Paul Beaud,Simona Bettoni,M. Bopp,H. Brands,Manuel Brönnimann,Ingo Brunnenkant,Marco Calvi,A. Citterio,Paolo Craievich,Marta Csatari Divall,Mark Dällenbach,Michael D’Amico,Andreas Dax,Yunpei Deng,Alexander Dietrich,Roberto Dinapoli,Edwin Divall,Sladana Dordevic,Simon Ebner,Christian Erny,Hansrudolf Fitze,Uwe Flechsig,Rolf Follath,F. Frei,Florian Gärtner,Romain Ganter,Terence Garvey,Zheqiao Geng,I. Gorgisyan,C. Gough,A. Hauff,Christoph P. Hauri,Nicole Hiller,Tadej Humar,Stephan Hunziker,Gerhard Ingold,Rasmus Ischebeck,Markus Janousch,Pavle Juranić,M. Jurcevic,Maik Kaiser,Babak Kalantari,Roger Kalt,B. Keil,Christoph Kittel,Gregor Knopp,W. Koprek,Henrik T. Lemke,Thomas Lippuner,Daniel Llorente Sancho,Florian Löhl,C. Lopez-Cuenca,Fabian Märki,F. Marcellini,G. Marinkovic,Isabelle Martiel,Ralf Menzel,Aldo Mozzanica,Karol Nass,Gian Luca Orlandi,Cigdem Ozkan Loch,Ezequiel Panepucci,Martin Paraliev,Bruce D. Patterson,Bill Pedrini,Marco Pedrozzi,Patrick Pollet,Claude Pradervand,Eduard Prat,Peter Radi,Jean-Yves Raguin,S. Redford,Jens Rehanek,Julien Réhault,Sven Reiche,Matthias Ringele,J. Rittmann,Leonid Rivkin,Albert Romann,Marie Ruat,C. Ruder,Leonardo Sala,Lionel Schebacher,T. Schilcher,Volker Schlott,Thomas J. Schmidt,Bernd Schmitt,Xintian Shi,M. Stadler,L. Stingelin,Werner Sturzenegger,Jakub Szlachetko,D. Thattil,D. Treyer,A. Trisorio,Wolfgang Tron,S. Vetter,Carlo Vicario,Didier Voulot,Meitian Wang,Thierry Zamofing,Christof Zellweger,R. Zennaro,Elke Zimoch,Rafael Abela,Luc Patthey,Hans-Heinrich Braun +114 more
TL;DR: The SwissFEL X-ray Free Electron Laser (XFEL) facility as discussed by the authors started construction at the Paul Scherrer Institute (Villigen, Switzerland) in 2013 and will be ready to accept its first users in 2018 on the Aramis hard Xray branch.
Journal ArticleDOI
Serial femtosecond crystallography: the first five years
TL;DR: The advent of hard X-ray free-electron lasers has opened a new chapter in macromolecular crystallography and the prospects of serial femtosecond crystallography are described.
Journal ArticleDOI
Oxygen Activation and Energy Conservation by Cytochrome c Oxidase
TL;DR: This review focuses on the type A cytochrome c oxidases (CcO), which are found in all mitochondria and also in several aerobic bacteria, and describes the states of the catalytic cycle and points out the few remaining uncertainties.
References
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Book ChapterDOI
Processing of X-ray diffraction data collected in oscillation mode
Zbyszek Otwinowski,Wladek Minor +1 more
TL;DR: The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
REFMAC5 for the refinement of macromolecular crystal structures
Garib N. Murshudov,Pavol Skubák,Andrey Lebedev,Navraj S. Pannu,Roberto A. Steiner,Robert A. Nicholls,Winn,Fei Long,Alexei A. Vagin +8 more
TL;DR: The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.
Journal ArticleDOI
Scaling and assessment of data quality
TL;DR: The various physical factors affecting measured diffraction intensities are discussed, as are the scaling models which may be used to put the data on a consistent scale and algorithms used by the CCP4 scaling program SCALA.
Journal ArticleDOI
How good are my data and what is the resolution
TL;DR: The new scaling program AIMLESS is described and tests of refinements at different resolutions are compared with analyses from the scaling step.
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