ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography

An automated data-collection system named ZOO has been developed. This system enabled faster data collection, facilitated advanced data-collection and data-processing techniques, and permitted the collection of higher quality data.

[1]  Mark A Hill,et al.  Will reduced radiation damage occur with very small crystals? , 2005, Journal of synchrotron radiation.

[2]  A. N. Popov,et al.  MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines , 2015, Acta crystallographica. Section D, Biological crystallography.

[3]  Masaki Yamamoto,et al.  Remote access and automation of SPring-8 MX beamlines , 2016 .

[4]  Nicholas K. Sauter,et al.  New Python-based methods for data processing , 2013, Acta crystallographica. Section D, Biological crystallography.

[5]  Elspeth F. Garman,et al.  RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography , 2013 .

[6]  Masaki Yamamoto,et al.  Micro-crystallography comes of age. , 2012, Current opinion in structural biology.

[7]  Michael Becker,et al.  Automated sample-scanning methods for radiation damage mitigation and diffraction-based centering of macromolecular crystals. , 2011, Journal of synchrotron radiation.

[8]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[9]  George M. Sheldrick,et al.  Experimental phasing with SHELXC/D/E: combining chain tracing with density modification , 2010, Acta crystallographica. Section D, Biological crystallography.

[10]  K. Hasegawa,et al.  Protein microcrystallography using synchrotron radiation , 2017, IUCrJ.

[11]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[12]  Nicholas K Sauter,et al.  High-speed fixed-target serial virus crystallography , 2017, Nature Methods.

[13]  Cheng Zhang,et al.  Structure and Function of an Irreversible Agonist-β2 Adrenoceptor complex , 2010, Nature.

[14]  Anton Barty,et al.  Recent developments in CrystFEL 1 , 2016, Journal of applied crystallography.

[15]  K. Hirata,et al.  KAMO: towards automated data processing for microcrystals , 2018, Acta crystallographica. Section D, Structural biology.

[16]  Yoshiki Tanaka,et al.  Structural basis of Sec-independent membrane protein insertion by YidC , 2014, Nature.

[17]  M. Liang,et al.  Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons , 2017, Nature Communications.

[18]  J. Berger,et al.  A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions , 2015, Acta crystallographica. Section D, Biological crystallography.

[19]  Anton Barty,et al.  Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data , 2014, Journal of applied crystallography.

[20]  Y. Sugita,et al.  Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT , 2013, Proceedings of the National Academy of Sciences.

[21]  Alexander Popov,et al.  Hierarchical clustering for multiple-crystal macromolecular crystallography experiments: the ccCluster program , 2017, Journal of applied crystallography.

[22]  W. Kabsch Processing of X-ray snapshots from crystals in random orientations , 2014, Acta crystallographica. Section D, Biological crystallography.

[23]  Kevin Cowtan,et al.  The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.

[24]  K. Hasegawa,et al.  Structural Biology with Microfocus Beamlines , 2016 .

[25]  Wolfgang Kabsch,et al.  Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants , 1993 .

[26]  Anton Barty,et al.  Room-temperature macromolecular serial crystallography using synchrotron radiation , 2014, IUCrJ.

[27]  Ezequiel Panepucci,et al.  Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. , 2015, Acta crystallographica. Section D, Biological crystallography.

[28]  Graeme Winter,et al.  xia2: an expert system for macromolecular crystallography data reduction , 2010 .

[29]  O. Nureki,et al.  X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog , 2017, Nature Structural &Molecular Biology.

[30]  K. Hirata,et al.  Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells. , 2017, ACS nano.

[31]  Aaron S. Brewster,et al.  Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams , 2015, Acta crystallographica. Section D, Biological crystallography.

[32]  Henry N. Chapman,et al.  Serial crystallography on in vivo grown microcrystals using synchrotron radiation , 2014, IUCrJ.

[33]  Anton Barty,et al.  Crystallographic data processing for free-electron laser sources , 2013, Acta crystallographica. Section D, Biological crystallography.

[34]  G. Bourenkov,et al.  The complex analysis of X-ray mesh scans for macromolecular crystallography , 2018, Acta crystallographica. Section D, Structural biology.

[35]  K. Hasegawa,et al.  Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography , 2017, Journal of synchrotron radiation.

[36]  Hideaki E. Kato,et al.  Crystal structure of the channelrhodopsin light-gated cation channel , 2012, Nature.

[37]  S. Iwata,et al.  Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography , 2012, Acta crystallographica. Section D, Biological crystallography.

[38]  Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor , 2018 .

[39]  Kunio Hirata,et al.  Achievement of protein micro-crystallography at SPring-8 beamline BL32XU , 2013 .

[40]  R. Stevens,et al.  High-Resolution Crystal Structure of an Engineered Human β2-Adrenergic G Protein–Coupled Receptor , 2007, Science.

[41]  Georg Weidenspointner,et al.  Femtosecond X-ray protein nanocrystallography , 2011, Nature.

[42]  Ilme Schlichting,et al.  Serial femtosecond crystallography: the first five years , 2015, IUCrJ.

[43]  Wolfgang Kabsch,et al.  Integration, scaling, space-group assignment and post-refinement , 2010, Acta crystallographica. Section D, Biological crystallography.

[44]  Gwyndaf Evans,et al.  DIALS: implementation and evaluation of a new integration package , 2018, Acta crystallographica. Section D, Structural biology.

[45]  O. Bunk,et al.  Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystals , 2016, Journal of applied crystallography.

[46]  Owen Johnson,et al.  iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM , 2011, Acta crystallographica. Section D, Biological crystallography.

[47]  Takashi Kumasaka,et al.  Upgrade of automated sample exchanger SPACE , 2012 .

[48]  R. Stevens,et al.  Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 µm size X-ray synchrotron beam , 2009, Journal of The Royal Society Interface.

[49]  Yoshiki Tanaka,et al.  Structural basis for the drug extrusion mechanism by a MATE multidrug transporter , 2013, Nature.

[50]  Takashi Kumasaka,et al.  Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8. , 2005, Journal of synchrotron radiation.

[51]  A. N. Popov,et al.  The application of hierarchical cluster analysis to the selection of isomorphous crystals. , 2012, Acta Crystallographica Section D: Biological Crystallography.

[52]  Olof Svensson,et al.  Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF , 2013, Journal of applied crystallography.

[53]  S. Rasmussen,et al.  Structure of a nanobody-stabilized active state of the β2 adrenoceptor , 2010, Nature.

[54]  T. Hatsui,et al.  Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. , 2018, Structure.

[55]  Elspeth F. Garman,et al.  Know your dose : RADDOSE , 2010 .

[56]  Christian Morawe,et al.  The ID23-2 structural biology microfocus beamline at the ESRF , 2009, Journal of synchrotron radiation.

[57]  Stephen Corcoran,et al.  Radiation damage in protein crystals is reduced with a micron-sized X-ray beam , 2011, Proceedings of the National Academy of Sciences.

[58]  Nicholas K. Sauter,et al.  The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework , 2002 .