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  1. Introduction to CrystFEL

    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 …

  2. How good are my data?

    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 …

  3. Practical considerations during processing of serial crystallographic XFEL data

    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 …

  4. From cctbx to cctbx.xfel and beyond

    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 …

  5. Handling sample heterogeneity in serial crystallography

    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 …

  6. Winning the Battle of Signal vs. Noise

    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 …

  7. Clustering and main sources of variance of SFX data

    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 …

  8. BioXFEL Expert Panel Discussion

    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

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

    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. …

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

    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: …

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

    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 …

  12. 2014 Data Analysis Workshop

    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 …

  13. Crystallographic Methods - Introduction and Overview

    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

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

    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 …

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

    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: …

  16. Electron microscopy of gold nanoparticles at atomic resolution

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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: …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

  30. 2nd International BioXFEL Conference Logo

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

    Transparent background logo for 2nd BioXFEL Conference

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

    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 …

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

    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 …

  33. Revealing transient structures of nucleosomes as DNA unwinds

    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 …

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

    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: …

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

    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 …

  36. Genomic basis for the convergent evolution of electric organs

    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 …

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

    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. …

  38. First Annual NSF Site Visit Photo

    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.

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

    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. …

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

    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 …

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

    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), …

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

    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 …

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

    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: …

  44. Diffraction before destruction

    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: …

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

    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), …

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

    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 …

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

    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. …

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

    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: …

  49. Phasing coherently illuminated nanocrystals bounded by partial unit cells

    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 …

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

    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. …

  51. Liquid sample delivery techniques for serial femtosecond crystallography

    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: …

  52. 7 A resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

    09 Jun 2014 | BioXFEL Publications | Contributor(s): B. Pedrini, C.-J. Tsai, G. Capitani, C. Padeste, M. S. Hunter, N. A. Zatsepin, A. Barty, W. H. Benner, S. Boutet, G. K. Feld, S. P. Hau-Riege, R. A. Kirian, C. Kupitz, M. Messerschmitt, J. I. Ogren, T. Pardini, B. Segelke, G. J. Williams, J. C. H. Spence, R. Abela, M. Coleman, J. E. Evans, G. F. X. Schertler, M. Frank, X.-D. Li

    http://dx.doi.org/10.1098/rstb.2013.0500 B. Pedrini and C.-J. Tsai and G. Capitani and C. Padeste and M. S. Hunter and N. A. Zatsepin and A. Barty and W. H. Benner and S. Boutet and G. K. Feld and S. P. Hau-Riege and R. A. Kirian and C. Kupitz and M. Messerschmitt and J. I. Ogren and T. Pardini and …

  53. Conformations of macromolecules and their complexes from heterogeneous datasets

    09 Jun 2014 | BioXFEL Publications | Contributor(s): P. Schwander, R. Fung, A. Ourmazd

    http://dx.doi.org/10.1098/rstb.2013.0567 P. Schwander and R. Fung and A. Ourmazd Schwander, P., Fung, R. & Ourmazd, A., 2014. Conformations of macromolecules and their complexes from heterogeneous datasets. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), …

  54. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment

    09 Jun 2014 | BioXFEL Publications | Contributor(s): K. Pande, P. Schwander, M. Schmidt, D. K. Saldin

    http://dx.doi.org/10.1098/rstb.2013.0332 K. Pande and P. Schwander and M. Schmidt and D. K. Saldin Pande, K. et al., 2014. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Philosophical Transactions of the Royal Society B: …

  55. 'Hit and run' serial femtosecond crystallography of a membrane kinase in the lipid cubic phase

    09 Jun 2014 | BioXFEL Publications | Contributor(s): M. Caffrey, D. Li, N. Howe, S. T. A. Shah

    journal-article http://dx.doi.org/10.1098/rstb.2013.0621 NSF-STC Biology with X-ray Lasers (NSF-1231306) Caffrey, M. et al., 2014. “Hit and run” serial femtosecond crystallography of a membrane kinase in the lipid cubic phase. Philosophical Transactions of the Royal Society B: Biological …

  56. Performance of a beam-multiplexing diamond crystal monochromator at the Linac Coherent Light Source

    06 Jun 2014 | BioXFEL Publications | Contributor(s): Diling Zhu, Yiping Feng, Stanislav Stoupin, Sergey A. Terentyev, Henrik T. Lemke, David M. Fritz, Matthieu Chollet, J. M. Glownia, Roberto Alonso-Mori, Marcin Sikorski, Sanghoon Song, Tim B. Van Driel, Garth J. Williams, Marc Messerschmidt, Sébastien Boutet, Vladimir D. Blank, Yuri V. Shvyd'ko, Aymeric Robert

    http://dx.doi.org/10.1063/1.4880724 journal-article Zhu, D. et al., 2014. Performance of a beam-multiplexing diamond crystal monochromator at the Linac Coherent Light Source. Review of Scientific Instruments, 85(6), p.063106. Available at: http://dx.doi.org/10.1063/1.4880724. Diling Zhu and …

  57. BioXFEL Annual Report 2014

    04 Jun 2014 | Downloads | Contributor(s): Jill Szczesek

    BioXFEL will create a diverse and inclusive community of scholars who will transform our ability to visualize the building blocks of life at a molecular scale, advancing from today's static pictures to recording detailed motions. These "movies" will lead to deeper understanding and to the …

  58. Temporal and Spatial Temperature Measurement in Insulator-Based Dielectrophoretic Devices

    03 Jun 2014 | BioXFEL Publications | Contributor(s): Asuka Nakano, Jinghui Luo, Alexandra Ros

    http://dx.doi.org/10.1021/ac501083h journal-article Nakano, A., Luo, J. & Ros, A., 2014. Temporal and Spatial Temperature Measurement in Insulator-Based Dielectrophoretic Devices. Analytical Chemistry, 86(13), pp.6516–6524. Available at: http://dx.doi.org/10.1021/ac501083h. Asuka Nakano and …

  59. Introduction to XFELs in Structural Biology

    03 Jun 2014 | Seminars | Contributor(s): Edward Snell

    Dr. Edward Snell gives a brief overview of how X-ray free electron lasers work and how they can be used to investigate structural aspects of biological systems never before accessible to experiment.

  60. Intro to Structural Biology

    02 Jun 2014 | Seminars | Contributor(s): Dan Gewirth

    Dr. Dan Gewirth of the Hauptman-Woodward Medical Research Institute gives a brief overview of structural biology and its importance as a tool to understanding biological processes. Be sure to grab the MP3 audio file to follow along with the PowerPoint slides.

  61. Time-Resolved Spectra from Millivolt EELS Data

    30 May 2014 | BioXFEL Publications | Contributor(s): Chufeng Li, GANESH SUBRAMANIAN, John Spence

    http://dx.doi.org/10.1017/s1431927614000890 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Li, C., Subramanian, G. & Spence, J.C.H., 2014. Time-Resolved Spectra from Millivolt EELS Data. Microscopy and Microanalysis, 20(03), pp.837–846. Available at: …

  62. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

    29 May 2014 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, Henry Van den Bedem, David A. Sivak, Gregory A. Petsko, Dagmar Ringe, Mark A. Wilson, James S. Fraser

    http://dx.doi.org/10.1016/j.str.2014.04.016 Daniel A. Keedy and Henry van den Bedem and David A. Sivak and Gregory A. Petsko and Dagmar Ringe and Mark A. Wilson and James S. Fraser Keedy, D.A. et al., 2014. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis …

  63. Use of transmission electron microscopy to identify nanocrystals of challenging protein targets

    28 May 2014 | BioXFEL Publications | Contributor(s): H. P. Stevenson, A. M. Makhov, M. Calero, A. L. Edwards, O. B. Zeldin, I. I. Mathews, G. Lin, C. O. Barnes, H. Santamaria, T. M. Ross, S. M. Soltis, C. Khosla, V. Nagarajan, J. F. Conway, A. E. Cohen, G. Calero

    http://dx.doi.org/10.1073/pnas.1400240111 journal-article Stevenson, H.P. et al., 2014. Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proceedings of the National Academy of Sciences, 111(23), pp.8470–8475. Available at: …

  64. Silicon Mirrors for High-Intensity X-Ray Pump and Probe Experiments

    28 May 2014 | BioXFEL Publications | Contributor(s): Tom Pardini, Sébastien Boutet, Joseph Bradley, Tilo Döppner, 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

    journal-article http://dx.doi.org/10.1103/physrevapplied.1.044007 Pardini, T. et al., 2014. Silicon Mirrors for High-Intensity X-Ray Pump and Probe Experiments. Physical Review Applied, 1(4). Available at: http://dx.doi.org/10.1103/physrevapplied.1.044007. Tom Pardini and Sébastien Boutet and …

  65. A new view on crystal harvesting

    28 May 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Thomas D. Grant, Jennifer R. Wolfley, Edward Snell

    X-ray crystallography typically requires the mounting of crystals, which can make the sample difficult to manipulate when it is small and the microscope objective is close to the crystallization plate. By simply moving the objective to the bottom of a clear crystallization plate (inverting the …

  66. Using a commodity high-definition television for collaborative structural biology

    28 May 2014 | BioXFEL Publications | Contributor(s): Ragothaman Yennamalli, Raj Arangarasan, Aaron Bryden, Michael Gleicher, George Phillips

    Visualization of protein structures using stereoscopic systems is frequently needed by structural biologists working to understand a protein's structure–function relationships. Often several scientists are working as a team and need simultaneous interaction with each other and the graphics …

  67. BioXFEL Strategic Plan 2013-2018

    28 May 2014 | Downloads | Contributor(s): Jill Szczesek

    We present a strategic plan for the operation of BioXFEL, a National Science Foundation Science and Technology Center, Biology with X-ray Lasers. The plan is the organic product of a meeting facilitated by Giant Leap at Arizona State University in February 2014, and covers the period 2013 – 2018.

  68. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    25 May 2014 | BioXFEL Publications | Contributor(s): Marcus Fischer, Ryan G. Coleman, James Fraser, Brian K. Shoichet

    http://dx.doi.org/10.1038/nchem.1954 journal-article Fischer, M. et al., 2014. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry, 6(7), pp.575–583. Available at: http://dx.doi.org/10.1038/nchem.1954. Marcus …

  69. Small Angle X-Ray Scattering as a Complementary Tool for High-Throughput Structural Studies

    21 May 2014 | Publications | Contributor(s): Tom Grant, Edward Snell

    Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. …

  70. Low Temperature Assembly of Functional 3D DNA-PNA-Protein Complexes

    14 May 2014 | BioXFEL Publications | Contributor(s): Justin D. Flory, Chad R. Simmons, Su Lin, Trey Johnson, Alessio Andreoni, James D Zook, Giovanna Ghirlanda, Yan Liu, Hao Yan, Petra Fromme

    http://dx.doi.org/10.1021/ja501228c journal-article Flory, J.D. et al., 2014. Low Temperature Assembly of Functional 3D DNA-PNA-Protein Complexes. Journal of the American Chemical Society, 136(23), pp.8283–8295. Available at: http://dx.doi.org/10.1021/ja501228c. Justin D. Flory and Chad R. …

  71. Fast k-NNG Construction with GPU-Based Quick Multi-Select

    08 May 2014 | BioXFEL Publications | Contributor(s): Ivan Komarov, Ali Dashti, Roshan M. D'Souza

    http://dx.doi.org/10.1371/journal.pone.0092409 journal-article Komarov, I., Dashti, A. & D’Souza, R.M., 2014. Fast k-NNG Construction with GPU-Based Quick Multi-Select M. Gomez-Gesteira, ed. PLoS ONE, 9(5), p.e92409. Available at: http://dx.doi.org/10.1371/journal.pone.0092409. Ivan Komarov …

  72. Introduction to Biological Small Angle Scattering

    08 May 2014 | Seminars | Contributor(s): Tom Grant

    (YouTube Video Below) An introductory course to small angle X-ray scattering intended for beginners in the field and those interesting in learning more about solution-based scattering. Topics covered include: - What is small angle scattering? - Reciprocal space to real space - Electron density and …

  73. X-ray lasers and crystallography

    29 Apr 2014 | BioXFEL Publications | Contributor(s): John Spence

    journal-article http://dx.doi.org/10.1107/s2052252514009567 Spence, J.C.H., 2014. X-ray lasers and crystallography. IUCrJ, 1(3), pp.151–152. Available at: http://dx.doi.org/10.1107/s2052252514009567. John C.H. Spence

  74. BioXFEL Science Graphic

    25 Apr 2014 | Downloads | Contributor(s): Edward J Sobczak

  75. Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms

    14 Apr 2014 | BioXFEL Publications | Contributor(s): V. Schweikhard, C. Meng, K. Murakami, C. D. Kaplan, R. D. Kornberg, S. M. Block

    journal-article http://dx.doi.org/10.1073/pnas.1405181111 Schweikhard, V. et al., 2014. Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proceedings of the National Academy of Sciences, 111(18), pp.6642–6647. …

  76. Mapping the decay of double core hole states of atoms and molecules

    10 Apr 2014 | BioXFEL Publications | Contributor(s): M Mucke, V Zhaunerchyk, R J Squibb, M Kamińska, J H D Eland, P V D Meulen, P Salén, P Linusson, R D Thomas, M Larsson, L J Frasinski, M Siano, T Osipov, L Fang, B Murphy, N Berrah, L Foucar, J Ullrich, K Motomura, S Mondal, K Ueda, R Richter, K C Prince, M N Piancastelli, M Glownia, J Cryan, R Coffee, C Bostedt, J Bozek, S Schorb, M Messerschmidt, O Takahashi, S Wada, R Feifel

    journal-article http://dx.doi.org/10.1088/1742-6596/488/3/032021 Mucke, M. et al., 2014. Mapping the decay of double core hole states of atoms and molecules. Journal of Physics: Conference Series, 488(3), p.032021. Available at: http://dx.doi.org/10.1088/1742-6596/488/3/032021. M Mucke and V …

  77. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein

    09 Apr 2014 | BioXFEL Publications | Contributor(s): Jasper J. Van Thor, Mark M. Warren, Craig N. Lincoln, Matthieu Chollet, Henrik Till Lemke, David M. Fritz, Marius Schmidt, Jason Tenboer, Zhong Ren, Vukica Srajer, Keith Moffat, Tim Graber

    http://dx.doi.org/10.1039/c4fd00011k Jasper J. van Thor and Mark M. Warren and Craig N. Lincoln and Matthieu Chollet and Henrik Till Lemke and David M. Fritz and Marius Schmidt and Jason Tenboer and Zhong Ren and Vukica Srajer and Keith Moffat and Tim Graber Van Thor, J.J. et al., 2014. Signal to …

  78. Experience with the CSPAD during dedicated detector runs at LCLS

    31 Mar 2014 | BioXFEL Publications | Contributor(s): G A Carini, S Boutet, M Chollet, A Dragone, G Haller, P A Hart, S C Herrmann, C J Kenney, J Koglin, M Messerschmidt, S Nelson, J Pines, A Robert, S Song, J B Thayer, G J Williams, D Zhu

    http://dx.doi.org/10.1088/1742-6596/493/1/012011 journal-article Carini, G.A. et al., 2014. Experience with the CSPAD during dedicated detector runs at LCLS. Journal of Physics: Conference Series, 493, p.012011. Available at: http://dx.doi.org/10.1088/1742-6596/493/1/012011. G A Carini and S …

  79. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer

    27 Mar 2014 | BioXFEL Publications | Contributor(s): Marius Schmidt, Dilano Saldin

    http://dx.doi.org/10.1063/1.4869472 Marius Schmidt and Dilano K. Saldin Schmidt, M. & Saldin, D.K., 2014. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer. Structural Dynamics, 1(2), p.024701. Available at: …

  80. Nonlinear X-ray Compton Scattering

    27 Mar 2014 | BioXFEL Publications | Contributor(s): Matthias Fuchs

    proceedings-article http://dx.doi.org/10.1364/hilas.2014.hth2b.3 Fuchs, M., 2014. Nonlinear X-ray Compton Scattering. Research in Optical Sciences. Available at: http://dx.doi.org/10.1364/hilas.2014.hth2b.3. Matthias Fuchs

  81. Approaches to time-resolved diffraction using an XFEL

    25 Mar 2014 | BioXFEL Publications | Contributor(s): John Spence

    http://dx.doi.org/10.1039/c4fd00025k John C. H. Spence Spence, J.C.H., 2014. Approaches to time-resolved diffraction using an XFEL. Faraday Discuss., 171, pp.429–438. Available at: http://dx.doi.org/10.1039/c4fd00025k. NSF-STC Biology with X-ray Lasers (NSF-1231306) We describe several schemes …

  82. Reply to 'Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein'

    21 Mar 2014 | BioXFEL Publications | Contributor(s): Yang Ouk Jung, Jae Hyuk Lee, Joonghan Kim, Marius Schmidt, Keith Moffat, Vukica Šrajer, Hyotcherl Ihee

    http://dx.doi.org/10.1038/nchem.1897 Yang Ouk Jung and Jae Hyuk Lee and Joonghan Kim and Marius Schmidt and Keith Moffat and Vukica Šrajer and Hyotcherl Ihee Jung, Y.O. et al., 2014. Reply to “Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.” …

  83. Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT fromSulfolobus solfataricus

    20 Mar 2014 | BioXFEL Publications | Contributor(s): Fengbin Wang, Shanteri Singh, Jianjun Zhang, Tyler D. Huber, Kate E. Helmich, Manjula Sunkara, Katherine A. Hurley, Randal D. Goff, Craig A. Bingman, Andrew J. Morris, Jon S. Thorson, George Phillips

    http://dx.doi.org/10.1111/febs.12784 journal-article Wang, F. et al., 2014. Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT fromSulfolobus solfataricus. FEBS Journal, 281(18), pp.4224–4239. Available at: …

  84. Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse

    17 Mar 2014 | BioXFEL Publications | Contributor(s): J. Szlachetko, C. J. Milne, J. Hoszowska, J.-Cl. Dousse, W. Błachucki, J. Sà, Y. Kayser, M. Messerschmidt, R. Abela, S. Boutet, C. David, G. Williams, M. Pajek, B. D. Patterson, G. Smolentsev, J. A. Van Bokhoven, M. Nachtegaal

    http://dx.doi.org/10.1063/1.4868260 journal-article Szlachetko, J. et al., 2014. Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse. Structural Dynamics, 1(2), p.021101. Available at: http://dx.doi.org/10.1063/1.4868260. J. Szlachetko …

  85. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    16 Mar 2014 | BioXFEL Publications | Contributor(s): Johan Hattne, Nathaniel Echols, Rosalie Tran, Jan Kern, Richard J Gildea, Aaron S Brewster, Roberto Alonso-Mori, Carina Glöckner, Julia Hellmich, Hartawan Laksmono, Raymond G Sierra, Benedikt Lassalle-Kaiser, Alyssa Lampe, Guangye Han, Sheraz Gul, Dörte DiFiore, Despina Milathianaki, Alan R Fry, Alan Miahnahri, William E White, Donald W Schafer, M Marvin Seibert, Jason E Koglin, Dimosthenis Sokaras, Tsu-Chien Weng, Jonas Sellberg, Matthew J Latimer, Pieter Glatzel, Petrus H Zwart, Ralf W Grosse-Kunstleve, Michael J Bogan, Marc Messerschmidt, Garth J Williams, Sébastien Boutet, Johannes Messinger, Athina Zouni, Junko Yano, Uwe Bergmann, Vittal K Yachandra, Paul D Adams, Nicholas K Sauter

    journal-article http://dx.doi.org/10.1038/nmeth.2887 Hattne, J. et al., 2014. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods, 11(5), pp.545–548. Available at: http://dx.doi.org/10.1038/nmeth.2887. Johan Hattne and Nathaniel Echols …

  86. Opacity effects in a solid-density aluminium plasma created by photo-excitation with an X-ray laser

    14 Mar 2014 | BioXFEL Publications | Contributor(s): D.S. Rackstraw, S.M. Vinko, O. Ciricosta, B.I. Cho, K. Engelhorn, H.-K. Chung, C.R.D. Brown, T. Burian, J. Chalupský, R.W. Falcone, C. Graves, V. Hájková, A. Higginbotham, L. Juha, J. Krzywinski, H.J. Lee, M. Messerschmidt, C. Murphy, Y. Ping, A. Scherz, W. Schlotter, S. Toleikis, J.J. Turner, L. Vysin, T. Wang, B. Wu, U. Zastrau, D. Zhu, B. Nagler, R.W. Lee, P.A. Heimann, J.S. Wark

    http://dx.doi.org/10.1016/j.hedp.2014.02.003 journal-article Rackstraw, D.S. et al., 2014. Opacity effects in a solid-density aluminium plasma created by photo-excitation with an X-ray laser. High Energy Density Physics, 11, pp.59–69. Available at: http://dx.doi.org/10.1016/j.hedp.2014.02.003. …

  87. An integrated approach for thermal stabilization of a mesophilic adenylate kinase

    11 Mar 2014 | BioXFEL Publications | Contributor(s): Sojin Moon, Du-kyo Jung, George Phillips, Euiyoung Bae

    http://dx.doi.org/10.1002/prot.24549 journal-article Moon, S. et al., 2014. An integrated approach for thermal stabilization of a mesophilic adenylate kinase. Proteins: Structure, Function, and Bioinformatics, 82(9), pp.1947–1959. Available at: http://dx.doi.org/10.1002/prot.24549. Sojin Moon …

  88. X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

    05 Mar 2014 | BioXFEL Publications | Contributor(s): Jochen Küpper, Stephan Stern, Lotte Holmegaard, Frank Filsinger, Arnaud Rouzée, Artem Rudenko, Per Johnsson, Andrew V. Martin, Marcus Adolph, Andrew Aquila, Saša Bajt, Anton Barty, Christoph Bostedt, John Bozek, Carl Caleman, Ryan Coffee, Nicola Coppola, Tjark Delmas, Sascha Epp, Benjamin Erk, Lutz Foucar, Tais Gorkhover, Lars Gumprecht, Andreas Hartmann, Robert Hartmann, Günter Hauser, Peter Holl, Andre Hömke, Nils Kimmel, Faton Krasniqi, Kai-Uwe Kühnel, Jochen Maurer, Marc Messerschmidt, Robert Moshammer, Christian Reich, Benedikt Rudek, Robin Santra, Ilme Schlichting, Carlo Schmidt, Sebastian Schorb, Joachim Schulz, Heike Soltau, John Spence, Dmitri Starodub, Lothar Strüder, Jan Thøgersen, Marc J. J. Vrakking, Georg Weidenspointner, Thomas A. White, Cornelia Wunderer, Gerard Meijer, Joachim Ullrich, Henrik Stapelfeldt, Daniel Rolles, Henry Chapman

    http://dx.doi.org/10.1103/physrevlett.112.083002 Jochen Küpper and Stephan Stern and Lotte Holmegaard and Frank Filsinger and Arnaud Rouzée and Artem Rudenko and Per Johnsson and Andrew V. Martin and Marcus Adolph and Andrew Aquila and Saša Bajt and Anton Barty and Christoph Bostedt and John …

  89. Purification and Biophysical Characterization of the CapA Membrane Protein FTT0807 fromFrancisella tularensis

    04 Mar 2014 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Debra T. Hansen, James D Zook, Andrey V. Loskutov, Mark D. Robida, Felicia M. Craciunescu, Kathryn F. Sykes, Rebekka M. Wachter, Petra Fromme, James P. Allen

    http://dx.doi.org/10.1021/bi401644s journal-article Martin-Garcia, J.M. et al., 2014. Purification and Biophysical Characterization of the CapA Membrane Protein FTT0807 fromFrancisella tularensis. Biochemistry, 53(12), pp.1958–1970. Available at: http://dx.doi.org/10.1021/bi401644s. Jose M. …

  90. Insulator-based dielectrophoresis of mitochondria

    04 Mar 2014 | BioXFEL Publications | Contributor(s): Jinghui Luo, Bahige G. Abdallah, Gregory G. Wolken, Edgar A. Arriaga, Alexandra Ros

    journal-article http://dx.doi.org/10.1063/1.4866852 Luo, J. et al., 2014. Insulator-based dielectrophoresis of mitochondria. Biomicrofluidics, 8(2), p.021801. Available at: http://dx.doi.org/10.1063/1.4866852. Jinghui Luo and Bahige G. Abdallah and Gregory G. Wolken and Edgar A. Arriaga and …

  91. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography

    14 Feb 2014 | BioXFEL Publications | Contributor(s): Uwe Weierstall, Daniel James, Chong Wang, Thomas A. White, Dingjie Wang, Wei Liu, John Spence, R. Bruce Doak, Garrett Charles Nelson, Petra Fromme, Raimund Fromme, Ingo Grotjohann, Christopher Kupitz, Nadia Zatsepin, Haiguang Liu, Shibom Basu, Daniel Wacker, Gye Won Han, Vsevolod Katritch, Sébastien Boutet, Marc Messerschmidt, Garth J. Williams, Jason E. Koglin, M. Marvin Seibert, Markus Klinker, Cornelius Gati, Robert L. Shoeman, Anton Barty, Henry Chapman, Richard Kirian, Kenneth R. Beyerlein, Raymond C. Stevens, Dianfan Li, Syed T. A. Shah, Nicole Howe, Martin Caffrey, Vadim Cherezov

    journal-article Uwe Weierstall and Daniel James and Chong Wang and Thomas A. White and Dingjie Wang and Wei Liu and John C. H. Spence and R. Bruce Doak and Garrett Nelson and Petra Fromme and Raimund Fromme and Ingo Grotjohann and Christopher Kupitz and Nadia A. Zatsepin and Haiguang Liu and …

  92. Femtosecond X-ray diffraction from two-dimensional protein crystals

    10 Feb 2014 | BioXFEL Publications | Contributor(s): Matthias Frank, David B. Carlson, Mark S. Hunter, Garth J. Williams, Marc Messerschmidt, Nadia Zatsepin, Anton Barty, W. Henry Benner, Kaiqin Chu, Alexander T. Graf, Stefan Hau-Riege, Richard Kirian, Celestino Padeste, Tommaso Pardini, Bill Pedrini, Brent W. Segelke, M. Marvin Seibert, John Spence, Ching-Ju Tsai, Stephen M. Lane, Xiao-Dan Li, Gebhard F.X. Schertler, Sebastien Boutet, Matthew Coleman, James E. Evans

    X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to …

  93. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation

    07 Feb 2014 | BioXFEL Publications | Contributor(s): R. Paul, R. E. Jinkerson, K. Buss, J. Steel, R. Mohr, W. R. Hess, M. Chen, P. Fromme

    journal-article http://dx.doi.org/10.1128/genomea.01166-13 Paul, R. et al., 2014. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation. Genome Announcements, 2(1), pp.e01166–13–e01166–13. Available at: …

  94. Diffuse X-Ray Scattering to Model Protein Motions

    04 Feb 2014 | BioXFEL Publications | Contributor(s): Michael E. Wall, Paul D. Adams, James S. Fraser, Nicholas K. Sauter

    http://dx.doi.org/10.1016/j.str.2014.01.002 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering to Model Protein Motions. Structure, 22(2), pp.182–184. Available at: http://dx.doi.org/10.1016/j.str.2014.01.002. Michael E. Wall and Paul D. Adams and James S. Fraser and …

  95. Crystallography: Sources of inspiration

    28 Jan 2014 | BioXFEL Publications | Contributor(s): Sean McSweeney, Petra Fromme

    http://dx.doi.org/10.1038/505620a Sean McSweeney and Petra Fromme McSweeney, S. & Fromme, P., 2014. Crystallography: Sources of inspiration. Nature, 505(7485), pp.620–621. Available at: http://dx.doi.org/10.1038/505620a. journal-article

  96. A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation

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

    http://dx.doi.org/10.1093/nar/gkt1375 journal-article Desai, K.K. et al., 2014. A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation. Nucleic Acids Research, 42(6), pp.3931–3942. Available at: http://dx.doi.org/10.1093/nar/gkt1375. …

  97. Optical measurements of long-range protein vibrations

    16 Jan 2014 | BioXFEL Publications | Contributor(s): Gheorghe Acbas, Katherine A. Niessen, Edward Snell, A.G. Markelz

    journal-article http://dx.doi.org/10.1038/ncomms4076 Acbas, G. et al., 2014. Optical measurements of long-range protein vibrations. Nature Communications, 5. Available at: http://dx.doi.org/10.1038/ncomms4076. Gheorghe Acbas and Katherine A. Niessen and Edward H. Snell and A.G. Markelz

  98. Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics

    15 Jan 2014 | BioXFEL Publications | Contributor(s): Joe Chen, John Spence, Rick P. Millane

    X-ray free-electron lasers solve a number of difficulties in protein crystallography by providing intense but ultra-short pulses of X-rays, allowing collection of useful diffraction data from nanocrystals. Whereas the diffraction from large crystals corresponds only to samples of the Fourier …

  99. Direct phasing in femtosecond nanocrystallography. II. Phase retrieval

    15 Jan 2014 | BioXFEL Publications | Contributor(s): Joe Chen, John Spence, Rick P. Millane

    X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental diffraction data [Spenceet al.(2011).Opt. Express,19, …

  100. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

    13 Jan 2014 | BioXFEL Publications | Contributor(s): R. B. Fenwick, H. Van Den Bedem, J. S. Fraser, P. E. Wright

    http://dx.doi.org/10.1073/pnas.1323440111 journal-article Fenwick, R.B. et al., 2014. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proceedings of the National Academy of Sciences, 111(4), pp.E445–E454. Available at: …