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  1. 2nd International BioXFEL Conference Detailed Agenda

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    05 Dec 2014 | Downloads | Contributor(s): Tom Grant

    This is a detailed agenda for the 2nd International BioXFEL Conference to be held in Ponce, Puerto Rico in January 2015. For more details about the event and to register, visit https://www.bioxfel.org/events/details/6

  2. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

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    04 Dec 2014 | BioXFEL Publications | Contributor(s): Jason Tenboer, Shibom Basu, Nadia Zatsepin, Kanupriya Pande, Despina Milathianaki, Matthias Frank, Mark S. Hunter, Sébastien Boutet, Garth J. Williams, Jason E. Koglin, Dominik Oberthuer, Michael Heymann, Christopher Kupitz, Chelsie E Conrad, Jesse David Coe, Shatabdi Roy-Chowdhury, Uwe Weierstall, Daniel James, Dingjie Wang, Thomas Grant, Anton Barty, Oleksandr Yefanov, Jennifer Scales, Cornelius Gati, Carolin Seuring, Vukica Srajer, Robert Henning, Peter Schwander, Raimund Fromme, Abbas Ourmazd, Keith Moffat, Jasper J. Van Thor, John Spence, Petra Fromme, Henry Chapman, Marius Schmidt

    http://dx.doi.org/10.1126/science.1259357 Jason Tenboer and Shibom Basu and Nadia Zatsepin and Kanupriya Pande and Despina Milathianaki and Matthias Frank and Mark Hunter and Sébastien Boutet and Garth J. Williams and Jason E. Koglin and Dominik Oberthuer and Michael Heymann and Christopher …

  3. Trajectories of the ribosome as a Brownian nanomachine

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    24 Nov 2014 | BioXFEL Publications | Contributor(s): Ali Dashti, Peter Schwander, Robert Langlois, Russell Fung, Wen Li, Ahmad Hosseinizadeh, Hstau Y. Liao, Jesper Pallesen, Gyanesh Sharma, Vera A. Stupina, Anne E. Simon, Jonathan D. Dinman, Joachim Frank, Abbas Ourmazd

    http://dx.doi.org/10.1073/pnas.1419276111 Ali Dashti and Peter Schwander and Robert Langlois and Russell Fung and Wen Li and Ahmad Hosseinizadeh and Hstau Y. Liao and Jesper Pallesen and Gyanesh Sharma and Vera A. Stupina and Anne E. Simon and Jonathan D. Dinman and Joachim Frank and Abbas Ourmazd …

  4. Measuring the temporal structure of few-femtosecond free-electron laser X-ray pulses directly in the time domain

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    24 Nov 2014 | BioXFEL Publications | Contributor(s): W. Helml, A. R. Maier, W. Schweinberger, I. Grguraš, P. Radcliffe, G. Doumy, C. Roedig, J. Gagnon, M. Messerschmidt, S. Schorb, C. Bostedt, F. Grüner, L. F. DiMauro, D. Cubaynes, J. D. Bozek, Th. Tschentscher, J. T. Costello, M. Meyer, R. Coffee, S. Düsterer, A. L. Cavalieri, R. Kienberger

    http://dx.doi.org/10.1038/nphoton.2014.278 journal-article Helml, W. et al., 2014. Measuring the temporal structure of few-femtosecond free-electron laser X-ray pulses directly in the time domain. Nature Photonics, 8(12), pp.950–957. Available at: http://dx.doi.org/10.1038/nphoton.2014.278. W. …

  5. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions

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    17 Nov 2014 | BioXFEL Publications | Contributor(s): Yahli Lorch, Barbara Maier-Davis, Roger Kornberg

    journal-article http://dx.doi.org/10.1101/gad.250704.114 Lorch, Y., Maier-Davis, B. & Kornberg, R.D., 2014. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions. Genes & Development, 28(22), pp.2492–2497. Available at: …

  6. Trace phase detection and strain characterization from serial X-ray free-electron laser crystallography of a Pr0.5Ca0.5MnO3 powder

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    17 Nov 2014 | BioXFEL Publications | Contributor(s): Kenneth R. Beyerlein, Christian Jooss, Anton Barty, Richard Bean, Sébastien Boutet, Sarnjeet S. Dhesi, R. Bruce Doak, Michael Först, Lorenzo Galli, Richard Kirian, Joseph Kozak, Michael Lang, Roman Mankowsky, Marc Messerschmidt, John Spence, Dingjie Wang, Uwe Weierstall, Thomas A. White, Garth J. Williams, Oleksandr Yefanov, Nadia Zatsepin, Andrea Cavalleri, Henry Chapman

    http://dx.doi.org/10.1017/s0885715614001171 We report on the analysis of virtual powder-diffraction patterns from serial femtosecond crystallography (SFX) data collected at an X-ray free-electron laser. Different approaches to binning and normalizing these patterns are discussed with respect to the …

  7. Production and Properties of XFEL Radiation

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    13 Nov 2014 | Teaching Materials

    Dr. Pietro Musumeci (UCLA) discusses an introduction to the physics and characteristics of X-ray free electron lasers.

  8. BioXFEL Lecture Series

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    13 Nov 2014 | Courses

    The BioXFEL Lecture Series is an online colloquium featuring lectures on various topics related to XFEL science in biology. Prominent experts in their respective fields, lecturers will present a broad range of materials from an introduction to XFEL radiation to more advanced topics of time-resolved …

  9. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta

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    12 Nov 2014 | BioXFEL Publications | Contributor(s): Paolo Rossi, Lei Shi, Gaohua Liu, Christopher M. Barbieri, Hsiau-Wei Lee, Thomas D. Grant, Joseph Luft, Rong Xiao, Thomas B. Acton, Edward Snell, Gaetano T. Montelione, David Baker, Oliver F. Lange, Nikolaos G. Sgourakis

    http://dx.doi.org/10.1002/prot.24719 journal-article Rossi, P. et al., 2014. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins: Structure, Function, and Bioinformatics, 83(2), pp.309–317. Available at: …

  10. Insulator-based dielectrophoresis with β-galactosidase in nanostructured devices

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    12 Nov 2014 | BioXFEL Publications | Contributor(s): Asuka Nakano, Fernanda Camacho-Alanis, Alexandra Ros

    http://dx.doi.org/10.1039/c4an01503g Asuka Nakano and Fernanda Camacho-Alanis and Alexandra Ros Nakano, A., Camacho-Alanis, F. & Ros, A., 2015. Insulator-based dielectrophoresis with β-galactosidase in nanostructured devices. Analyst, 140(3), pp.860–868. Available at: …

  11. Goniometer-based femtosecond crystallography with X-ray free electron lasers

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    01 Nov 2014 | BioXFEL Publications | Contributor(s): Aina E. Cohen, S. Michael Soltis, Ana González, Laura Aguila, Roberto Alonso-Mori, Christopher Barnes, Elizabeth L. Baxter, Winnie Brehmer, Aaron S. Brewster, Axel T. Brunger, Guillermo Calero, Joseph F. Chang, Matthieu Chollet, Paul Ehrensberger, Thomas L. Eriksson, Yiping Feng, Johan Hattne, Britt Hedman, Michael Hollenbeck, James Holton, Stephen Keable, Brian K. Kobilka, Elena G. Kovaleva, Andrew C. Kruse, Henrik T. Lemke, Guowu Lin, Artem Y. Lyubimov, Aashish Manglik, Irimpan I. Mathews, Scott E. McPhillips, Silke Nelson, John W. Peters, Nicholas K. Sauter, Clyde A. Smith, Jinhu Song, Hilary P. Stevenson, Yingssu Tsai, Monarin Uervirojnangkoorn, Vladimir Vinetsky, Soichi Wakatsuki, William I. Weis, Oleg A. Zadvornyy, Oliver B. Zeldin, Diling Zhu, Keith O. Hodgson

    journal-article http://dx.doi.org/10.1073/pnas.1418733111 Cohen, A.E. et al., 2014. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proceedings of the National Academy of Sciences, 111(48), pp.17122–17127. Available at: http://dx.doi.org/10.1073/pnas.1418733111. …

  12. Crystal Structure of Human Protein N-Terminal Glutamine Amidohydrolase, an Initial Component of the N-End Rule Pathway

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    30 Oct 2014 | BioXFEL Publications | Contributor(s): Mi Seul Park, Eduard Bitto, Kyung Rok Kim, Craig A. Bingman, Mitchell Miller, Hyun-Jung Kim, Byung Woo Han, George Phillips

    http://dx.doi.org/10.1371/journal.pone.0111142 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Park, M.S. et al., 2014. Crystal Structure of Human Protein N-Terminal Glutamine Amidohydrolase, an Initial Component of the N-End Rule Pathway T. J. Boggon, ed. PLoS ONE, 9(10), …

  13. Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution

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    30 Oct 2014 | BioXFEL Publications | Contributor(s): R. Sophia Weerth, Karolina Michalska, Craig A. Bingman, Ragothaman M. Yennamalli, Hui Li, Robert Jedrzejczak, Fengbin Wang, Gyorgy Babnigg, Andrzej Joachimiak, Michael G. Thomas, George Phillips

    http://dx.doi.org/10.1002/prot.24705 journal-article Weerth, R.S. et al., 2014. Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution. Proteins: Structure, Function, and Bioinformatics, 83(2), pp.383–388. Available at: …

  14. Tabletop source for intense hard X-rays: toward a compact XFEL

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    28 Oct 2014 | Seminars

    Dr. William Graves ASU Biophysics Seminar Series Today x-ray science is pursued either at major facilities housed in national labs, where the large synchrotrons and x-ray free-electron lasers (XFELs) produce an x-ray brilliance of at least 1020 photons/(sec mm2 mrad2 0.1%), or else it is pursued …

  15. European XFEL Users Meeting

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    28 Oct 2014 | Downloads

  16. Crystallographic Methods - Crystallographic Symmetry - Part III

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    22 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  17. Crystallographic Methods - Crystallographic Symmetry - Part II

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    20 Oct 2014 | Teaching Materials

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  18. Crystallographic Methods - Crystallographic Symmetry - Part I

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    20 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  19. XRayView

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    09 Oct 2014 | Downloads | Contributor(s): George Phillips

    XRayView : A Virtual X-Ray Crystallography Laboratory This software uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, …

  20. Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts

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    07 Oct 2014 | BioXFEL Publications | Contributor(s): GANESH SUBRAMANIAN, Shibom Basu, Haiguang Liu, Jian-Min Zuo, John Spence

    http://dx.doi.org/10.1016/j.ultramic.2014.08.013 Ganesh Subramanian and Shibom Basu and Haiguang Liu and Jian-Min Zuo and John C.H. Spence Subramanian, G. et al., 2015. Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts. Ultramicroscopy, 148, pp.87–93. Available …

  21. Double-focusing mixing jet for XFEL study of chemical kinetics

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    06 Oct 2014 | BioXFEL Publications | Contributor(s): Dingjie Wang, Uwe Weierstall, Lois Pollack, John Spence

    Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

  22. Probing the Nature of Charge Transfer at Nano–Bio Interfaces: Peptides on Metal Oxide Nanoparticles

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    03 Oct 2014 | BioXFEL Publications | Contributor(s): Pilarisetty Tarakeshwar, Julio L. Palma, Gregory P. Holland, Petra Fromme, Jeffery L. Yarger, Vladimiro Mujica

    journal-article http://dx.doi.org/10.1021/jz501854x Tarakeshwar, P. et al., 2014. Probing the Nature of Charge Transfer at Nano–Bio Interfaces: Peptides on Metal Oxide Nanoparticles. The Journal of Physical Chemistry Letters, 5(20), pp.3555–3559. Available at: …

  23. Crystallographic Methods - X-ray Diffraction Physics - Part IX

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    03 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  24. Crystallographic Methods - X-ray Diffraction Physics - Part VIII

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    01 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  25. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

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    29 Sep 2014 | BioXFEL Publications | Contributor(s): Hung T. Nguyen, Suzette A. Pabit, Steve P. Meisburger, Lois Pollack, David Case

    http://dx.doi.org/10.1063/1.4896220 journal-article Nguyen, H.T. et al., 2014. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. The Journal of Chemical Physics, 141(22), p.22D508. Available at: http://dx.doi.org/10.1063/1.4896220. Hung T. …

  26. Crystallographic Methods - X-ray Diffraction Physics - Part VII

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    28 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  27. Crystallographic Methods - X-ray Diffraction Physics - Part VI

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    25 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  28. Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine

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    25 Sep 2014 | BioXFEL Publications | Contributor(s): Brianna B. Williams, Andrew H. Van Benschoten, Peter Cimermancic, Mohamed S. Donia, Michael Zimmermann, Mao Taketani, Atsushi Ishihara, Purna C. Kashyap, James S. Fraser, Michael A. Fischbach

    http://dx.doi.org/10.1016/j.chom.2014.09.001 journal-article Williams, B.B. et al., 2014. Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine. Cell Host & Microbe, 16(4), pp.495–503. Available at: …

  29. Microfluidic Platforms for Bimolecular and Nanocrystal Separation

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    23 Sep 2014 | Seminars | Contributor(s): Alexandra Ros

    Dr. Alexandra Ros Analytical and bioanalytical applications of microfluidic devices or so called Lab-on-a-Chip Systems have been an extensive field of research over the past two decades. In many instances, integration of (bio)chemical analyses onto microfluidic platforms has been inspired by …

  30. The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm

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    23 Sep 2014 | BioXFEL Publications | Contributor(s): Haiguang Liu, John Spence

    Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will …

  31. Crystallographic Methods - X-ray Diffraction Physics - Part V

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    22 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  32. Crystallographic Methods - Geometrical Crystallography - Part I

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    19 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

  33. Crystallographic Methods - X-ray Diffraction Physics - Part IV

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    18 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  34. Structure and Function of REP34 Implicates Carboxypeptidase Activity inFrancisella tularensisHost Cell Invasion

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    18 Sep 2014 | BioXFEL Publications | Contributor(s): Geoffrey K. Feld, Sahar El-Etr, Michele H. Corzett, Mark S. Hunter, Kamila Belhocine, Denise M. Monack, Matthias Frank, Brent W. Segelke, Amy Rasley

    http://dx.doi.org/10.1074/jbc.m114.599381 journal-article Feld, G.K. et al., 2014. Structure and Function of REP34 Implicates Carboxypeptidase Activity inFrancisella tularensisHost Cell Invasion. Journal of Biological Chemistry, 289(44), pp.30668–30679. Available at: …

  35. Crystallographic Methods - X-ray Diffraction Physics - Part III

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    15 Sep 2014 | Teaching Materials

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  36. Crystallographic Methods - X-ray Diffraction Physics - Part II

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    11 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  37. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

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    11 Sep 2014 | Publications

    Authors: Kupitz, C., Basu, S., Grotjohann, I., Fromme, R., Zatsepin, N. A., Rendek, K. N., Hunter, M. S., Shoeman, R. L., White, T. A., Wang, D., James, D., Yang, J. H., Cobb, D. E., Reeder, B., Sierra, R. G., Liu, H., Barty, A., Aquila, A. L., Deponte, D., Kirian, R. A., Bari, S., Bergkamp, J. J., …

  38. Crystallographic Methods - X-ray Diffraction Physics - Part I

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    08 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  39. Silicon single crystal as back-reflector for high-intensity hard x-rays

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    05 Sep 2014 | BioXFEL Publications | Contributor(s): Tom Pardini, Sébastien Boutet, Joseph Bradley, Tilo Doeppner, Luke B. Fletcher, Dennis F. Gardner, Randy M. Hill, Mark S. Hunter, Jacek Krzywinski, Marc Messerschmidt, Arthur E. Pak, Florian Quirin, Klaus Sokolowski-Tinten, Garth J. Williams, Stefan Hau-Riege

    http://dx.doi.org/10.1117/12.2061087 proceedings-article Pardini, T. et al., 2014. Silicon single crystal as back-reflector for high-intensity hard x-rays S. P. Hau-Riege, S. P. Moeller, & M. Yabashi, eds. X-Ray Free-Electron Lasers: Beam Diagnostics, Beamline Instrumentation, and Applications …

  40. Crystallographic Methods - Geometrical Crystallography - Part II

    0.0 out of 5 stars 

    04 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

  41. Psana Tutorial

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    03 Sep 2014 | Teaching Materials

    Chris O'Grady (SLAC) Psana is the main analysis tool developed by LCLS, upon which some other tools are based. It uses a combination of C++ and python. I will discuss recent psana developments and future plans. Recent developments include the ability to express complex analysis ideas with simple …

  42. Cheetah Tutorial

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    03 Sep 2014 | Teaching Materials

    Anton Barty (CFEL)

  43. CASS and SFX SAD Tutorial

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    03 Sep 2014 | Teaching Materials

    Karol Nass (MPI) Extraction of diffraction images of the lysozyme Gadolinium derivative (Barends et al. Science 2013) from the raw LCLS format to HDF5 format. Integration of CrystFEL analysis with CASS start-up scripts. Ab initio SAD phasing of SFX data.

  44. CrystFEL Tutorial

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    03 Sep 2014 | Teaching Materials

    Tom White (CFEL)

  45. cctbx.xfel Tutorial

    0.0 out of 5 stars 

    03 Sep 2014 | Teaching Materials

    Nick Sauter (LBNL) Aaron Brewster (LBNL) Oliver Zeldin (Stanford)

  46. Data Analysis and Sample Delivery

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    John Spence (ASU/LBNL) How XFEL MX differs from MX and why we do it.

  47. Free Electron Lasers and Crystallography

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Paul Adams (LBNL) BioXFEL in the greater context of crystallography

  48. SFX Data Reduction and Preprocessing

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Anton Barty (CFEL) Photons, detectors and data streams: how to get at the data and what it records. Data reduction and pre-processing: how it works and how to optimize it.

  49. Rapid Data Quality Feedback and Online Monitoring using CASS

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    29 Aug 2014 | Teaching Materials

    Karol Nass (MPI) Description of the layout of CASS software suite and its functionality on the LCLS online and offline data streams. Real time monitoring of the SFX experiment: hit rate, resolution, pixel saturation, 2D powder pattern. Rapid offline processing of the raw LCLS data: crystal hit …

  50. Introduction to CrystFEL

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    29 Aug 2014 | Teaching Materials

    Tom White (CFEL) CrystFEL is a suite of programs that deal with viewing, indexing, integrating and merging serial crystallography data, evaluating its quality and simulating patterns. At the core of CrystFEL is an automated, high throughput processing pipeline which indexes and integrates each …

  51. How good are my data?

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    29 Aug 2014 | Teaching Materials

    Nick Sauter (LBNL) A design goal of the data reduction package cctbx.xfel is to discover and apply the numerous systematic corrections necessary to correctly model XFEL diffraction images. Numerous challenges must be addressed to interpret serial femtosecond diffraction, including an inaccurate …

  52. Practical considerations during processing of serial crystallographic XFEL data

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    29 Aug 2014 | Teaching Materials

    Aaron Brewster (LBNL) Fundamental differences exist between processing rotational data collected at a synchrotron source and data collected during a serial crystallographic XFEL experiment. Practical techniques will be described to enable the user to get the most out of their data using the …

  53. From cctbx to cctbx.xfel and beyond

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    29 Aug 2014 | Teaching Materials

    Johan Hattne (HHMI) Algorithms to process X-ray diffraction images into accurate atomic models of macromolecules have undergone steady refinement over the past decades. As methods by which crystallographic diffraction patters are obtained are further developed, these techniques continue to provide …

  54. Handling sample heterogeneity in serial crystallography

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    29 Aug 2014 | Teaching Materials

    Oliver Zeldin (Stanford) Serial crystallography data is made up of images obtained from a population of slightly in-homogenous crystals. We will discuss clustering and filtering approaches to (1) characterizing sample heterogeneity in unmerged data, and (2) identifying optimal sub-sets of images …

  55. Winning the Battle of Signal vs. Noise

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    29 Aug 2014 | Teaching Materials

    James Holton (UCSF/LBNL) I will review the major sources of error that contribute to macromolecular crystallography (MX) data with a particular focus on MX data from X-ray Free Electron Lasers. The absolute limits will be defined, and the potential of new and future technologies for overcoming …

  56. Clustering and main sources of variance of SFX data

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    29 Aug 2014 | Teaching Materials

    Wolfgang Brehm (University of Konstanz) Clustering approaches and variance analysis are explained using the example of the indexing ambiguity in serial crystallography. Recently published algorithms for detwinning and advancements thereof will be shown. Variance analysis can lead to a more …

  57. BioXFEL Expert Panel Discussion

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    29 Aug 2014 | Teaching Materials

    Expert Panel Discussion including: Anton Barty, Michael Rossman, James Holton, Tom White, Wolfgang Brehm, Oliver Zeldin, John Spence, Karol Nass, Nick Sauter, Aaron Brewster, Johan Hattne

  58. Spectral encoding method for measuring the relative arrival time between x-ray/optical pulses

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    28 Aug 2014 | BioXFEL Publications | Contributor(s): M. R. Bionta, N. Hartmann, M. Weaver, D. French, D. J. Nicholson, J. P. Cryan, J. M. Glownia, K. Baker, C. Bostedt, M. Chollet, Y. Ding, D. M. Fritz, A. R. Fry, D. J. Kane, J. Krzywinski, H. T. Lemke, M. Messerschmidt, S. Schorb, D. Zhu, W. E. White, R. N. Coffee

    journal-article http://dx.doi.org/10.1063/1.4893657 Bionta, M.R. et al., 2014. Spectral encoding method for measuring the relative arrival time between x-ray/optical pulses. Review of Scientific Instruments, 85(8), p.083116. Available at: http://dx.doi.org/10.1063/1.4893657. M. R. Bionta and N. …

  59. Biochemical Characterization and Crystal Structures of a Fungal Family 3  -Glucosidase, Cel3A from Hypocrea jecorina

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    27 Aug 2014 | BioXFEL Publications | Contributor(s): Saeid Karkehabadi, Kate E. Helmich, Thijs Kaper, Henrik Hansson, Nils-Egil Mikkelsen, Mikael Gudmundsson, Kathleen Piens, Meredith Fujdala, Goutami Banerjee, John S. Scott-Craig, Jonathan D. Walton, George Phillips, Mats Sandgren

    http://dx.doi.org/10.1074/jbc.m114.587766 journal-article Karkehabadi, S. et al., 2014. Biochemical Characterization and Crystal Structures of a Fungal Family 3  -Glucosidase, Cel3A from Hypocrea jecorina. Journal of Biological Chemistry, 289(45), pp.31624–31637. Available at: …

  60. Structure of RNA 3′-phosphate cyclase bound to substrate RNA

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    27 Aug 2014 | BioXFEL Publications | Contributor(s): Kevin K. Desai, Craig A. Bingman, Chin L. Cheng, George Phillips, Ronald T. Raines

    http://dx.doi.org/10.1261/rna.045823.114 journal-article Desai, K.K. et al., 2014. Structure of RNA 3′-phosphate cyclase bound to substrate RNA. RNA, 20(10), pp.1560–1566. Available at: http://dx.doi.org/10.1261/rna.045823.114. Kevin K. Desai and Craig A. Bingman and Chin L. Cheng and George …

  61. 2014 Data Analysis Workshop

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    26 Aug 2014 | Workshops | Contributor(s): Tom Grant, Nadia Zatsepin

    Video and interactive web presentations with PDF slides available for download. Description Serial crystallography is a rapidly growing field with a correspondingly rapidly growing user base. One of the main bottlenecks in serial crystallography is the ability to efficiently filter and analyze …

  62. Crystallographic Methods - Introduction and Overview

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    25 Aug 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Introduction     Protein structural elements: 1° aa sequence,  2° α-helix, β strand, β sheet, loop, 3° domain fold,  4° domain assembly; Overview of biomacromolecular crystallography

  63. Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source

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    25 Aug 2014 | BioXFEL Publications | Contributor(s): K. Tiedtke, A. A. Sorokin, U. Jastrow, P. Juranić, S. Kreis, N. Gerken, M. Richter, U. Arp, Y. Feng, D. Nordlund, R. Soufli, M. Fernández-Perea, L. Juha, P. Heimann, B. Nagler, H. J. Lee, S. Mack, M. Cammarata, O. Krupin, M. Messerschmidt, M. Holmes, M. Rowen, W. Schlotter, S. Moeller, J. J. Turner

    journal-article http://dx.doi.org/10.1364/oe.22.021214 Tiedtke, K. et al., 2014. Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source. Optics Express, 22(18), p.21214. Available at: http://dx.doi.org/10.1364/oe.22.021214. K. Tiedtke and A. A. Sorokin and U. Jastrow …

  64. Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41

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    23 Aug 2014 | BioXFEL Publications | Contributor(s): Zhen Gong, Sarah A. Kessans, Lusheng Song, Katerina Dörner, Ho-Hsien Lee, Lydia R Meador, Joshua LaBaer, Brenda Hogue, Tsafrir S. Mor, Petra Fromme

    http://dx.doi.org/10.1002/pro.2540 journal-article Gong, Z. et al., 2014. Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41. Protein Science, 23(11), pp.1607–1618. Available at: …

  65. Electron microscopy of gold nanoparticles at atomic resolution

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    21 Aug 2014 | BioXFEL Publications | Contributor(s): M. Azubel, J. Koivisto, S. Malola, D. Bushnell, G. L. Hura, A. L. Koh, H. Tsunoyama, T. Tsukuda, M. Pettersson, H. Hakkinen, R. D. Kornberg

    http://dx.doi.org/10.1126/science.1251959 journal-article Azubel, M. et al., 2014. Electron microscopy of gold nanoparticles at atomic resolution. Science, 345(6199), pp.909–912. Available at: http://dx.doi.org/10.1126/science.1251959. M. Azubel and J. Koivisto and S. Malola and D. Bushnell …

  66. Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

    0.0 out of 5 stars 

    19 Aug 2014 | BioXFEL Publications | Contributor(s): Ho-Hsien Lee, Irene Cherni, HongQi Yu, Raimund Fromme, Jeffrey D. Doran, Ingo Grotjohann, Michele Mittman, Shibom Basu, Arpan Deb, Katerina Dörner, Andrew Aquila, Anton Barty, Sébastien Boutet, Henry Chapman, R. Bruce Doak, Mark S. Hunter, Daniel James, Richard Kirian, Christopher Kupitz, Robert M Lawrence, Haiguang Liu, Karol Nass, Ilme Schlichting, Kevin E. Schmidt, M. Marvin Seibert, Robert L. Shoeman, John Spence, Francesco Stellato, Uwe Weierstall, Garth J. Williams, Chunhong Yoon, Dingjie Wang, Nadia Zatsepin, Brenda Hogue, Nobuyuki Matoba, Petra Fromme, Tsafrir S. Mor

    CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein ofHuman immunodeficiency virus 1(HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral …

  67. Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam

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    19 Aug 2014 | BioXFEL Publications | Contributor(s): M. R. Sawaya, D. Cascio, M. Gingery, J. Rodriguez, L. Goldschmidt, J.-P. Colletier, M. M. Messerschmidt, S. Boutet, J. E. Koglin, G. J. Williams, A. S. Brewster, K. Nass, J. Hattne, S. Botha, R. B. Doak, R. L. Shoeman, D. P. DePonte, H.-W. Park, B. A. Federici, N. K. Sauter, I. Schlichting, D. S. Eisenberg

    http://dx.doi.org/10.1073/pnas.1413456111 journal-article Sawaya, M.R. et al., 2014. Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proceedings of the National Academy of Sciences, 111(35), pp.12769–12774. Available …

  68. Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers

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    15 Aug 2014 | BioXFEL Publications | Contributor(s): S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, A. Barty, C. Bostedt, J. Bozek, R. Coffee, S. Epp, B. Erk, L. Foucar, R. Hartmann, N. Kimmel, K-U. Kühnel, J. Maurer, M. Messerschmidt, B. Rudek, D. Starodub, J. Thøgersen, G. Weidenspointner, T. A. White, H. Stapelfeldt, D. Rolles, H. N. Chapman, J. Küpper

    http://dx.doi.org/10.1039/c4fd00028e S. Stern and L. Holmegaard and F. Filsinger and A. Rouzée and A. Rudenko and P. Johnsson and A. V. Martin and A. Barty and C. Bostedt and J. Bozek and R. Coffee and S. Epp and B. Erk and L. Foucar and R. Hartmann and N. Kimmel and K-U. Kühnel and J. Maurer and …

  69. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography

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    14 Aug 2014 | BioXFEL Publications | Contributor(s): Wei Liu, Andrii Ishchenko, Vadim Cherezov

    http://dx.doi.org/10.1038/nprot.2014.141 journal-article Liu, W., Ishchenko, A. & Cherezov, V., 2014. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nature Protocols, 9(9), pp.2123–2134. Available at: http://dx.doi.org/10.1038/nprot.2014.141. Wei …

  70. Fixed-target protein serial microcrystallography with an x-ray free electron laser

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    12 Aug 2014 | BioXFEL Publications | Contributor(s): Mark S. Hunter, Brent W. Segelke, Marc Messerschmidt, Garth J. Williams, Nadia Zatsepin, Anton Barty, W. Henry Benner, David B. Carlson, Matthew Coleman, Alexander Graf, Stefan Hau-Riege, Tommaso Pardini, M. Marvin Seibert, James Evans, Sébastien Boutet, Matthias Frank

    http://dx.doi.org/10.1038/srep06026 Mark S. Hunter and Brent Segelke and Marc Messerschmidt and Garth J. Williams and Nadia A. Zatsepin and Anton Barty and W. Henry Benner and David B. Carlson and Matthew Coleman and Alexander Graf and Stefan P. Hau-Riege and Tommaso Pardini and M. Marvin Seibert …

  71. E pluribus unum, no more: from one crystal, many conformations

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    09 Aug 2014 | BioXFEL Publications | Contributor(s): Rahel Woldeyes, David A Sivak, James Fraser

    http://dx.doi.org/10.1016/j.sbi.2014.07.005 Rahel A Woldeyes and David A Sivak and James S Fraser Woldeyes, R.A., Sivak, D.A. & Fraser, J.S., 2014. E pluribus unum, no more: from one crystal, many conformations. Current Opinion in Structural Biology, 28, pp.56–62. Available at: …

  72. Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases

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    06 Aug 2014 | BioXFEL Publications | Contributor(s): Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George Phillips, Brian G Fox

    http://dx.doi.org/10.1186/1754-6834-7-109 journal-article Book, A.J. et al., 2014. Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases. Biotechnology for Biofuels, 7(1), p.109. Available at: http://dx.doi.org/10.1186/1754-6834-7-109. Adam J Book and …

  73. Structure and Substrate Specificity of a Eukaryotic Fucosidase fromFusarium graminearum

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    02 Aug 2014 | BioXFEL Publications | Contributor(s): Hongnan Cao, Jonathan D. Walton, Phil Brumm, George Phillips

    http://dx.doi.org/10.1074/jbc.m114.583286 journal-article Cao, H. et al., 2014. Structure and Substrate Specificity of a Eukaryotic Fucosidase fromFusarium graminearum. Journal of Biological Chemistry, 289(37), pp.25624–25638. Available at: http://dx.doi.org/10.1074/jbc.m114.583286. Hongnan …

  74. Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19

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    31 Jul 2014 | BioXFEL Publications | Contributor(s): Sherif I. Elshahawi, Theresa A. Ramelot, Jayaraman Seetharaman, Jing Chen, Shanteri Singh, Yunhuang Yang, Kari Pederson, Madan K. Kharel, Rong Xiao, Scott Lew, Ragothaman M. Yennamalli, Mitchell Miller, Fengbin Wang, Liang Tong, Gaetano T. Montelione, Michael A. Kennedy, Craig A. Bingman, Haining Zhu, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1021/cb500327m Sherif I. Elshahawi and Theresa A. Ramelot and Jayaraman Seetharaman and Jing Chen and Shanteri Singh and Yunhuang Yang and Kari Pederson and Madan K. Kharel and Rong Xiao and Scott Lew and Ragothaman M. Yennamalli and Mitchell D. Miller and Fengbin Wang and …

  75. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules

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    31 Jul 2014 | BioXFEL Publications | Contributor(s): Rebecca Boll, Arnaud Rouzée, Marcus Adolph, Denis Anielski, Andrew Aquila, Sadia Bari, Cédric Bomme, Christoph Bostedt, John D. Bozek, Henry Chapman, Lauge Christensen, Ryan Coffee, Niccola Coppola, Sankar De, Piero Decleva, Sascha W. Epp, Benjamin Erk, Frank Filsinger, Lutz Foucar, Tais Gorkhover, Lars Gumprecht, André Hömke, Lotte Holmegaard, Per Johnsson, Jens S. Kienitz, Thomas Kierspel, Faton Krasniqi, Kai-Uwe Kühnel, Jochen Maurer, Marc Messerschmidt, Robert Moshammer, Nele L. M. Müller, Benedikt Rudek, Evgeny Savelyev, Ilme Schlichting, Carlo Schmidt, Frank Scholz, Sebastian Schorb, Joachim Schulz, Jörn Seltmann, Mauro Stener, Stephan Stern, Simone Techert, Jan Thøgersen, Sebastian Trippel, Jens Viefhaus, Marc Vrakking, Henrik Stapelfeldt, Jochen Küpper, Joachim Ullrich, Artem Rudenko, Daniel Rolles

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump–probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular …

  76. Endosomal GPCR signaling turned off by negative feedback actions of PKA and v-ATPase

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    27 Jul 2014 | BioXFEL Publications | Contributor(s): Alexandre Gidon, Mohammad M Al-Bataineh, Frederic G Jean-Alphonse, Hilary P Stevenson, Tomoyuki Watanabe, Claire Louet, Ashok Khatri, Guillermo Calero, Núria M Pastor-Soler, Thomas J Gardella, Jean-Pierre Vilardaga

    http://dx.doi.org/10.1038/nchembio.1589 journal-article Gidon, A. et al., 2014. Endosomal GPCR signaling turned off by negative feedback actions of PKA and v-ATPase. Nature Chemical Biology, 10(9), pp.707–709. Available at: http://dx.doi.org/10.1038/nchembio.1589. Alexandre Gidon and Mohammad …

  77. Identifying, studying and making good use of macromolecular crystals

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    25 Jul 2014 | BioXFEL Publications | Contributor(s): Guillermo Calero, Aina E. Cohen, Joseph Luft, Janet Newman, Edward Snell

    Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name …

  78. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye–Semiconductor Interface

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    25 Jul 2014 | BioXFEL Publications | Contributor(s): Katrin R. Siefermann, Chaitanya D. Pemmaraju, Stefan Neppl, Andrey Shavorskiy, Amy A. Cordones, Josh Vura-Weis, Daniel S. Slaughter, Felix P. Sturm, Fabian Weise, Hendrik Bluhm, Matthew L. Strader, Hana Cho, Ming-Fu Lin, Camila Bacellar, Champak Khurmi, Jinghua Guo, Giacomo Coslovich, Joseph S. Robinson, Robert A. Kaindl, Robert W Schoenlein, Ali Belkacem, Daniel M. Neumark, Stephen R. Leone, Dennis Nordlund, Hirohito Ogasawara, Oleg Krupin, Joshua J. Turner, William F. Schlotter, Michael R. Holmes, Marc Messerschmidt, Michael P. Minitti, Sheraz Gul, Jin Z. Zhang, Nils Huse, David Prendergast, Oliver Gessner

    http://dx.doi.org/10.1021/jz501264x journal-article Siefermann, K.R. et al., 2014. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye–Semiconductor Interface. The Journal of Physical Chemistry Letters, 5(15), pp.2753–2759. Available at: http://dx.doi.org/10.1021/jz501264x. Katrin …

  79. 2nd International BioXFEL Conference Logo

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    11 Jul 2014 | Downloads | Contributor(s): Tom Grant

    Transparent background logo for 2nd BioXFEL Conference

  80. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy

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    09 Jul 2014 | BioXFEL Publications | Contributor(s): Jan Kern, Rosalie Tran, Roberto Alonso-Mori, Sergey Koroidov, Nathaniel Echols, Johan Hattne, Mohamed Ibrahim, Sheraz Gul, Hartawan Laksmono, Raymond G. Sierra, Richard J. Gildea, Guangye Han, Julia Hellmich, Benedikt Lassalle-Kaiser, Ruchira Chatterjee, Aaron S. Brewster, Claudiu A. Stan, Carina Glöckner, Alyssa Lampe, Dörte DiFiore, Despina Milathianaki, Alan R. Fry, M. Marvin Seibert, Jason E. Koglin, Erik Gallo, Jens Uhlig, Dimosthenis Sokaras, Tsu-Chien Weng, Petrus H. Zwart, David Skinner, Michael J. Bogan, Marc Messerschmidt, Pieter Glatzel, Garth J. Williams, Sébastien Boutet, Paul D. Adams, Athina Zouni, Johannes Messinger, Nicholas K. Sauter, Uwe Bergmann, Junko Yano, Vittal K. Yachandra

    journal-article http://dx.doi.org/10.1038/ncomms5371 Kern, J. et al., 2014. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications, 5. Available at: http://dx.doi.org/10.1038/ncomms5371. Jan Kern and Rosalie Tran and Roberto …

  81. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser

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    08 Jul 2014 | BioXFEL Publications | Contributor(s): Christopher Kupitz, Shibom Basu, Ingo Grotjohann, Raimund Fromme, Nadia Zatsepin, Kimberly N. Rendek, Mark S. Hunter, Robert L. Shoeman, Thomas A. White, Dingjie Wang, Daniel James, Jay-How Yang, Danielle E. Cobb, Brenda Reeder, Raymond G. Sierra, Haiguang Liu, Anton Barty, Andrew L. Aquila, Daniel Deponte, Richard Kirian, Sadia Bari, Jesse J. Bergkamp, Kenneth R. Beyerlein, Michael J. Bogan, Carl Caleman, Tzu-Chiao Chao, Chelsie E Conrad, Katherine M. Davis, Holger Fleckenstein, Lorenzo Galli, Stefan Hau-Riege, Stephan Kassemeyer, Hartawan Laksmono, Mengning Liang, Lukas Lomb, Stefano Marchesini, Andrew V. Martin, Marc Messerschmidt, Despina Milathianaki, Karol Nass, Alexandra Ros, Shatabdi Roy-Chowdhury, Kevin Schmidt, Marvin Seibert, Jan Steinbrener, Francesco Stellato, Lifen Yan, Chunhong Yoon, Thomas A. Moore, Ana L. Moore, Yulia Pushkar, Garth J. Williams, Sébastien Boutet, R. Bruce Doak, Uwe Weierstall, Matthias Frank, Henry Chapman, John Spence, Petra Fromme

    http://dx.doi.org/10.1038/nature13453 Christopher Kupitz and Shibom Basu and Ingo Grotjohann and Raimund Fromme and Nadia A. Zatsepin and Kimberly N. Rendek and Mark S. Hunter and Robert L. Shoeman and Thomas A. White and Dingjie Wang and Daniel James and Jay-How Yang and Danielle E. Cobb and …

  82. Revealing transient structures of nucleosomes as DNA unwinds

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    03 Jul 2014 | BioXFEL Publications | Contributor(s): Yujie Chen, Joshua M. Tokuda, Traci Topping, Julie L. Sutton, Steve P. Meisburger, Suzette A. Pabit, Lisa M. Gloss, Lois Pollack

    http://dx.doi.org/10.1093/nar/gku562 journal-article Chen, Y. et al., 2014. Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Research, 42(13), pp.8767–8776. Available at: http://dx.doi.org/10.1093/nar/gku562. Yujie Chen and Joshua M. Tokuda and Traci Topping and …

  83. Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

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    02 Jul 2014 | BioXFEL Publications | Contributor(s): Diana Fusco, Timothy J. Barnum, Andrew E. Bruno, Joseph Luft, Edward Snell, Sayan Mukherjee, Patrick Charbonneau

    http://dx.doi.org/10.1371/journal.pone.0101123 journal-article Fusco, D. et al., 2014. Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms B. Kobe, ed. PLoS ONE, 9(7), p.e101123. Available at: …

  84. Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography

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    27 Jun 2014 | BioXFEL Publications | Contributor(s): Andrew E. Bruno, Amanda M. Ruby, Joseph Luft, Thomas D. Grant, Jayaraman Seetharaman, Gaetano T. Montelione, John F. Hunt, Edward Snell

    journal-article http://dx.doi.org/10.1371/journal.pone.0100782 NSF-STC Biology with X-ray Lasers (NSF-1231306) Bruno, A.E. et al., 2014. Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular …

  85. Genomic basis for the convergent evolution of electric organs

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    26 Jun 2014 | BioXFEL Publications | Contributor(s): J. R. Gallant, L. L. Traeger, J. D. Volkening, H. Moffett, P.-H. Chen, C. D. Novina, G. N. Phillips, R. Anand, G. B. Wells, M. Pinch, R. Guth, G. A. Unguez, J. S. Albert, H. H. Zakon, M. P. Samanta, M. R. Sussman

    http://dx.doi.org/10.1126/science.1254432 journal-article Gallant, J.R. et al., 2014. Genomic basis for the convergent evolution of electric organs. Science, 344(6191), pp.1522–1525. Available at: http://dx.doi.org/10.1126/science.1254432. J. R. Gallant and L. L. Traeger and J. D. Volkening …

  86. Crystallization screening: the influence of history on current practice

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    26 Jun 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Janet Newman, Edward Snell

    While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. …

  87. First Annual NSF Site Visit Photo

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    23 Jun 2014 | Downloads | Contributor(s): Edward J Sobczak

    The BioXFEL Center meets at Hauptman-Woodward in Buffalo for its first annual NSF site visit.

  88. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature

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    17 Jun 2014 | BioXFEL Publications | Contributor(s): J. A. Sellberg, C. Huang, T. A. McQueen, N. D. Loh, H. Laksmono, D. Schlesinger, R. G. Sierra, D. Nordlund, C. Y. Hampton, D. Starodub, D. P. DePonte, M. Beye, C. Chen, A. V. Martin, A. Barty, K. T. Wikfeldt, T. M. Weiss, C. Caronna, J. Feldkamp, L. B. Skinner, M. M. Seibert, M. Messerschmidt, G. J. Williams, S. Boutet, L. G. M. Pettersson, M. J. Bogan, A. Nilsson

    journal-article http://dx.doi.org/10.1038/nature13266 Sellberg, J.A. et al., 2014. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature. Nature, 510(7505), pp.381–384. Available at: http://dx.doi.org/10.1038/nature13266. J. A. Sellberg and C. Huang and T. …

  89. Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles

    0.0 out of 5 stars 

    16 Jun 2014 | BioXFEL Publications | Contributor(s): Jo E. Lomax, Christopher M. Bianchetti, Aram Chang, George Phillips, Brian G. Fox, Ronald T. Raines

    http://dx.doi.org/10.1016/j.jmb.2014.06.007 journal-article Lomax, J.E. et al., 2014. Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles. Journal of Molecular Biology, 426(17), pp.3041–3056. Available at: http://dx.doi.org/10.1016/j.jmb.2014.06.007. Jo E. Lomax …

  90. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases

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    13 Jun 2014 | BioXFEL Publications | Contributor(s): Sojin Moon, Ryan M. Bannen, Thomas J. Rutkoski, George Phillips, Euiyoung Bae

    http://dx.doi.org/10.1002/prot.24627 journal-article Moon, S. et al., 2014. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins: Structure, Function, and Bioinformatics, 82(10), …

  91. Enabling membrane protein structure and dynamics with X-ray free electron lasers

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    11 Jun 2014 | BioXFEL Publications | Contributor(s): Geoffrey K Feld, Matthias Frank

    http://dx.doi.org/10.1016/j.sbi.2014.05.002 journal-article Feld, G.K. & Frank, M., 2014. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Current Opinion in Structural Biology, 27, pp.69–78. Available at: http://dx.doi.org/10.1016/j.sbi.2014.05.002. Geoffrey K …

  92. Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules

    0.0 out of 5 stars 

    10 Jun 2014 | BioXFEL Publications | Contributor(s): D Rolles, R Boll, M Adolph, A Aquila, C Bostedt, J D Bozek, H N Chapman, R Coffee, N Coppola, P Decleva, T Delmas, S W Epp, B Erk, F Filsinger, L Foucar, L Gumprecht, A Hömke, T Gorkhover, L Holmegaard, P Johnsson, Ch Kaiser, F Krasniqi, K-U Kühnel, J Maurer, M Messerschmidt, R Moshammer, W Quevedo, I Rajkovic, A Rouzée, B Rudek, I Schlichting, C Schmidt, S Schorb, C D Schröter, J Schulz, H Stapelfeldt, M Stener, S Stern, S Techert, J Thøgersen, M J J Vrakking, A Rudenko, J Küpper, J Ullrich

    http://dx.doi.org/10.1088/0953-4075/47/12/124035 journal-article Rolles, D. et al., 2014. Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules. Journal of Physics B: Atomic, Molecular and Optical Physics, 47(12), p.124035. Available at: …

  93. Diffraction before destruction

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): H. N. Chapman, C. Caleman, N. Timneanu

    http://dx.doi.org/10.1098/rstb.2013.0313 H. N. Chapman and C. Caleman and N. Timneanu Chapman, H.N., Caleman, C. & Timneanu, N., 2014. Diffraction before destruction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130313–20130313. Available at: …

  94. Femtosecond crystallography of membrane proteins in the lipidic cubic phase

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): W. Liu, D. Wacker, C. Wang, E. Abola, V. Cherezov

    http://dx.doi.org/10.1098/rstb.2013.0314 W. Liu and D. Wacker and C. Wang and E. Abola and V. Cherezov Liu, W. et al., 2014. Femtosecond crystallography of membrane proteins in the lipidic cubic phase. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), …

  95. Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): C. Kupitz, I. Grotjohann, C. E. Conrad, S. Roy-Chowdhury, R. Fromme, P. Fromme

    http://dx.doi.org/10.1098/rstb.2013.0316 C. Kupitz and I. Grotjohann and C. E. Conrad and S. Roy-Chowdhury and R. Fromme and P. Fromme Kupitz, C. et al., 2014. Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model …

  96. Coherent convergent-beam time-resolved X-ray diffraction

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): J. C. H. Spence, N. A. Zatsepin, C. Li

    http://dx.doi.org/10.1098/rstb.2013.0325 J. C. H. Spence and N. A. Zatsepin and C. Li Spence, J.C.H., Zatsepin, N.A. & Li, C., 2014. Coherent convergent-beam time-resolved X-ray diffraction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130325–20130325. …

  97. High-resolution structure of viruses from random diffraction snapshots

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, P. Schwander, A. Dashti, R. Fung, R. M. D'Souza, A. Ourmazd

    http://dx.doi.org/10.1098/rstb.2013.0326 A. Hosseinizadeh and P. Schwander and A. Dashti and R. Fung and R. M. D'Souza and A. Ourmazd Hosseinizadeh, A. et al., 2014. High-resolution structure of viruses from random diffraction snapshots. Philosophical Transactions of the Royal Society B: …

  98. Phasing coherently illuminated nanocrystals bounded by partial unit cells

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): R. A. Kirian, R. J. Bean, K. R. Beyerlein, O. M. Yefanov, T. A. White, A. Barty, H. N. Chapman

    http://dx.doi.org/10.1098/rstb.2013.0331 R. A. Kirian and R. J. Bean and K. R. Beyerlein and O. M. Yefanov and T. A. White and A. Barty and H. N. Chapman Kirian, R.A. et al., 2014. Phasing coherently illuminated nanocrystals bounded by partial unit cells. Philosophical Transactions of the Royal …

  99. Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): O. Yefanov, C. Gati, G. Bourenkov, R. A. Kirian, T. A. White, J. C. H. Spence, H. N. Chapman, A. Barty

    http://dx.doi.org/10.1098/rstb.2013.0333 O. Yefanov and C. Gati and G. Bourenkov and R. A. Kirian and T. A. White and J. C. H. Spence and H. N. Chapman and A. Barty Yefanov, O. et al., 2014. Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography. …

  100. Liquid sample delivery techniques for serial femtosecond crystallography

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): U. Weierstall

    http://dx.doi.org/10.1098/rstb.2013.0337 U. Weierstall Weierstall, U., 2014. Liquid sample delivery techniques for serial femtosecond crystallography. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130337–20130337. Available at: …