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  1. Structure Validation in Phenix

    0.0 out of 5 stars 

    08 Apr 2015 | Teaching Materials

    Paul Adams describes how to use the Phenix crystallographic software package to assess the accuracy of crystallographic models.

  2. Structure Refinement in Phenix

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    08 Apr 2015 | Teaching Materials

    Pavel Afonine describes an introduction to crystallographic structure refinement, structure refinement with Phenix.refine, and real space refinement tools for CryoEM and low resolution X-ray data

  3. Molecular Replacement in Phenix

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    08 Apr 2015 | Teaching Materials

    Paul Adams describes molecular replacement methods to solve the phase problem of crystallography and how to evaluate success in Phenix.  He also describes the latest advances in Phenix molecular replacement methods.

  4. Experimental Phasing

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    08 Apr 2015 | Teaching Materials

    Tom Terwilliger introduces experimental phasing techniques for X-ray crystallography and describes recent developments in SAD phasing using the Phenix software package.

  5. Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies

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    08 Apr 2015 | BioXFEL Publications | Contributor(s): David J. Aceti, Craig A. Bingman, Russell L. Wrobel, Ronnie O. Frederick, Shin-ichi Makino, Karl W. Nichols, Sarata C. Sahu, Lai F. Bergeman, Paul G. Blommel, Claudia C. Cornilescu, Katarzyna A. Gromek, Kory D. Seder, Soyoon Hwang, John G. Primm, Grzegorz Sabat, Frank C. Vojtik, Brian F. Volkman, Zsolt Zolnai, George Phillips, John L. Markley, Brian G. Fox

    http://dx.doi.org/10.1007/s10969-015-9198-1 David J. Aceti and Craig A. Bingman and Russell L. Wrobel and Ronnie O. Frederick and Shin-ichi Makino and Karl W. Nichols and Sarata C. Sahu and Lai F. Bergeman and Paul G. Blommel and Claudia C. Cornilescu and Katarzyna A. Gromek and Kory D. Seder and …

  6. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy

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    08 Apr 2015 | BioXFEL Publications | Contributor(s): Dario Mizrachi, Yujie Chen, Jiayan Liu, Hwei-Ming Peng, Ailong Ke, Lois Pollack, Raymond J. Turner, Richard J. Auchus, Matthew P. DeLisa

    journal-article http://dx.doi.org/10.1038/ncomms7826 Mizrachi, D. et al., 2015. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy. Nature Communications, 6, p.6826. Available at: http://dx.doi.org/10.1038/ncomms7826. Dario Mizrachi and Yujie Chen …

  7. Phase Retrieval with Application to Optical Imaging: A contemporary overview

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    03 Apr 2015 | BioXFEL Publications | Contributor(s): Yoav Shechtman, Yonina C. Eldar, Oren Cohen, Henry Chapman, Jianwei Miao, Mordechai Segev

    http://dx.doi.org/10.1109/msp.2014.2352673 Yoav Shechtman and Yonina C. Eldar and Oren Cohen and Henry Nicholas Chapman and Jianwei Miao and Mordechai Segev Shechtman, Y. et al., 2015. Phase Retrieval with Application to Optical Imaging: A contemporary overview. IEEE Signal Processing Magazine, …

  8. 2015 Phenix Workshop at Rice University

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    03 Apr 2015 | Workshops | Contributor(s): Tom Grant, George Phillips

    The Gulf Coast Consortia, BioXFEL, and Rice University present an instructional workshop on Phenix, the Python-based Hierarchical Environment for Intergrated Xtallography. Topics include experimental phasing, molecular replacement, model refinement and structure validation.

  9. Critical assessment of the emission spectra of various photosystem II core complexes

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    03 Apr 2015 | BioXFEL Publications | Contributor(s): Jinhai Chen, Adam Kell, Khem Acharya, Christopher Kupitz, Petra Fromme, Ryszard Jankowiak

    http://dx.doi.org/10.1007/s11120-015-0128-7 Jinhai Chen and Adam Kell and Khem Acharya and Christopher Kupitz and Petra Fromme and Ryszard Jankowiak Chen, J. et al., 2015. Critical assessment of the emission spectra of various photosystem II core complexes. Photosynthesis Research, 124(3), …

  10. stream2stats

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    01 Apr 2015 | Downloads | Contributor(s): Tom Grant

    'stream2stats' makes quick work of calculating a variety of merging statistics from SFX data and plotting them

  11. Hit Rate Calculator

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    01 Apr 2015 | Downloads | Contributor(s): Tom Grant

    Data Analysis Scripts 'hits' is a python script that can be used to quickly calculate hits and hit rates from a series of different experimental runs from an SFX experiment when using Cheetah for hit finding. It uses Cheetah's frames.txt file to calculate hits.  By default it will use your own …

  12. peakogram

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    01 Apr 2015 | Downloads | Contributor(s): Tom Grant

    'peakogram' is a script to plot a 2D histogram of peak intensities from SFX data.  Using the Cheetah peaks.txt file from hit finding results, it will plot peak intensity as a function of resolution in pixels, binned by the number of peaks. This plot can be useful for estimating resolution, …

  13. Integrative, dynamic structural biology at atomic resolution—it's about time

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    31 Mar 2015 | BioXFEL Publications | Contributor(s): Henry Van Den Bedem, James Fraser

    http://dx.doi.org/10.1038/nmeth.3324 Henry van den Bedem and James S Fraser Van den Bedem, H. & Fraser, J.S., 2015. Integrative, dynamic structural biology at atomic resolution—it’s about time. Nat Meth, 12(4), pp.307–318. Available at: http://dx.doi.org/10.1038/nmeth.3324. NSF-STC Biology …

  14. Two disparate ligand-binding sites in the human P2Y1 receptor

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    30 Mar 2015 | BioXFEL Publications | Contributor(s): Dandan Zhang, Zhan-Guo Gao, Kaihua Zhang, Evgeny Kiselev, Steven Crane, Jiang Wang, Silvia Paoletta, Cuiying Yi, Limin Ma, Wenru Zhang, Gye Won Han, Hong Liu, Vadim Cherezov, Vsevolod Katritch, Hualiang Jiang, Raymond C. Stevens, Kenneth A. Jacobson, Qiang Zhao, Beili Wu

    http://dx.doi.org/10.1038/nature14287 Dandan Zhang and Zhan-Guo Gao and Kaihua Zhang and Evgeny Kiselev and Steven Crane and Jiang Wang and Silvia Paoletta and Cuiying Yi and Limin Ma and Wenru Zhang and Gye Won Han and Hong Liu and Vadim Cherezov and Vsevolod Katritch and Hualiang Jiang and …

  15. Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus)

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    25 Mar 2015 | BioXFEL Publications | Contributor(s): Lindsay L Traeger, Jeremy D Volkening, Howell Moffett, Jason R Gallant, Po-Hao Chen, Carl D Novina, George Phillips, Rene Anand, Gregg B Wells, Matthew Pinch, Robert Güth, Graciela A Unguez, James S Albert, Harold Zakon, Michael R Sussman, Manoj P Samanta

    http://dx.doi.org/10.1186/s12864-015-1288-8 Lindsay L Traeger and Jeremy D Volkening and Howell Moffett and Jason R Gallant and Po-Hao Chen and Carl D Novina and George N Phillips and Rene Anand and Gregg B Wells and Matthew Pinch and Robert Güth and Graciela A Unguez and James S Albert and Harold …

  16. Fluorescence Recovery After Photobleaching in Lipidic Cubic Phase (LCP-FRAP)

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    22 Mar 2015 | BioXFEL Publications | Contributor(s): Gustavo Fenalti, Enrique E. Abola, Chong Wang, Beili Wu, Vadim Cherezov

    http://dx.doi.org/10.1016/bs.mie.2014.12.008 Gustavo Fenalti and Enrique E. Abola and Chong Wang and Beili Wu and Vadim Cherezov Fenalti, G. et al., 2015. Fluorescence Recovery After Photobleaching in Lipidic Cubic Phase (LCP-FRAP). Membrane Proteins—Engineering, Purification and Crystallization, …

  17. High Throughput Protein Nanocrystal Fractionation in a Microfluidic Sorter

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    20 Mar 2015 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Shatabdi Roy-Chowdhury, Jesse David Coe, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.5b00589 Bahige G. Abdallah and Shatabdi Roy-Chowdhury and Jesse Coe and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2015. High Throughput Protein Nanocrystal Fractionation in a Microfluidic Sorter. Anal. Chem., 87(8), pp.4159–4167. Available at: …

  18. Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography

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    20 Mar 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, Lillian R Kenner, Matthew Warkentin, Rahel Woldeyes, Michael Thompson, Aaron S Brewster, Andrew H Van Benschoten, Elizabeth L Baxter, Jesse B Hopkins, Monarin Uervirojnangkoorn, Scott E McPhillps, Jinhu Song, Roberto Alonso-Mori, James Holton, William I Weis, Axel T Brunger, S. Michael Soltis, Henrik Lemke, Ana Gonzalez, Nicholas K Sauter, Aina E Cohen, Henry Van Den Bedem, Robert E Thorne, James Fraser

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function. Here we compare the …

  19. Solution to the phase problem for surface X-ray diffraction

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    14 Mar 2015 | BioXFEL Publications | Contributor(s): P.F. Lyman, V.L. Shneerson, R. Fung, R.J. Harder, S.S. Parihar, H.T. Johnson-Steigelman, D.K. Saldin

    http://dx.doi.org/10.1107/s0108767308096505 journal-article Lyman, P.F. et al., 2008. Solution to the phase problem for surface X-ray diffraction. Acta Crystallographica Section A Foundations of Crystallography, 64(a1), pp.C109–C109. Available at: http://dx.doi.org/10.1107/s0108767308096505. …

  20. GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1–2 September 2014

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    13 Mar 2015 | BioXFEL Publications | Contributor(s): Alexander Heifetz, Gebhard F.X. Schertler, Roland Seifert, Christopher G. Tate, Patrick M. Sexton, Vsevolod V. Gurevich, Daniel Fourmy, Vadim Cherezov, Fiona H. Marshall, R. Ian Storer, Isabel Moraes, Irina G. Tikhonova, Christofer S. Tautermann, Peter Hunt, Tom Ceska, Simon Hodgson, Mike J. Bodkin, Shweta Singh, Richard J. Law, Philip C. Biggin

    http://dx.doi.org/10.1007/s00210-015-1111-8 Alexander Heifetz and Gebhard F. X. Schertler and Roland Seifert and Christopher G. Tate and Patrick M. Sexton and Vsevolod V. Gurevich and Daniel Fourmy and Vadim Cherezov and Fiona H. Marshall and R. Ian Storer and Isabel Moraes and Irina G. Tikhonova …

  21. Fabrication of wedged multilayer Laue lenses

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    12 Mar 2015 | BioXFEL Publications | Contributor(s): M. Prasciolu, A. F. G. Leontowich, J. Krzywinski, A. Andrejczuk, H. N. Chapman, S. Bajt

    http://dx.doi.org/10.1364/ome.5.000748 M. Prasciolu and A. F. G. Leontowich and J. Krzywinski and A. Andrejczuk and H. N. Chapman and S. Bajt Prasciolu, M. et al., 2015. Fabrication of wedged multilayer Laue lenses. Opt. Mater. Express, 5(4), p.748. Available at: …

  22. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage

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    11 Mar 2015 | BioXFEL Publications | Contributor(s): Justin D Flory, Trey Johnson, Chad R Simmons, Su Lin, Giovanna Ghirlanda, Petra Fromme

    http://dx.doi.org/10.4161/1949095x.2014.992181 journal-article Flory, J.D. et al., 2014. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage. Artificial DNA: PNA & XNA, 5(3), p.e992181. Available at: http://dx.doi.org/10.4161/1949095x.2014.992181. Justin D Flory …

  23. Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

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    09 Mar 2015 | BioXFEL Publications | Contributor(s): Helen M. Ginn, Marc Messerschmidt, Xiaoyun Ji, Hanwen Zhang, Danny Axford, Richard J. Gildea, Graeme Winter, Aaron S. Brewster, Johan Hattne, Armin Wagner, Jonathan M. Grimes, Gwyndaf Evans, Nicholas K. Sauter, Geoff Sutton, David I. Stuart

    http://dx.doi.org/10.1038/ncomms7435 Helen M. Ginn and Marc Messerschmidt and Xiaoyun Ji and Hanwen Zhang and Danny Axford and Richard J. Gildea and Graeme Winter and Aaron S. Brewster and Johan Hattne and Armin Wagner and Jonathan M. Grimes and Gwyndaf Evans and Nicholas K. Sauter and Geoff Sutton …

  24. Biostructural Science Inspired by Next-Generation X-Ray Sources

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    06 Mar 2015 | BioXFEL Publications | Contributor(s): Sol M. Gruner, Eaton E Lattman

    http://dx.doi.org/10.1146/annurev-biophys-060414-033813 Sol M. Gruner and Eaton E. Lattman Gruner, S.M. & Lattman, E.E., 2015. Biostructural Science Inspired by Next-Generation X-Ray Sources. Annual Review of Biophysics, 44(1), pp.33–51. Available at: …

  25. Investigation of femtosecond collisional ionization rates in a solid-density aluminium plasma

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    03 Mar 2015 | BioXFEL Publications | Contributor(s): S. M. Vinko, O. Ciricosta, T. R. Preston, D. S. Rackstraw, C.R.D. Brown, T. Burian, J. Chalupský, B. I. Cho, H.-K. Chung, K. Engelhorn, R. W. Falcone, R. Fiokovinini, V. Hájková, P. A. Heimann, L. Juha, H. J. Lee, R. W. Lee, M. Messerschmidt, B. Nagler, W. Schlotter, J. J. Turner, L. Vysin, U. Zastrau, J. S. Wark

    http://dx.doi.org/10.1038/ncomms7397 S. M. Vinko and O. Ciricosta and T. R. Preston and D. S. Rackstraw and C.R.D. Brown and T. Burian and J. Chalupský and B. I. Cho and H.-K. Chung and K. Engelhorn and R. W. Falcone and R. Fiokovinini and V. Hájková and P. A. Heimann and L. Juha and H. J. Lee …

  26. Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser

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    02 Mar 2015 | BioXFEL Publications | Contributor(s): Tomas Ekeberg, Martin Svenda, Chantal Abergel, Filipe R. N. C. Maia, Virginie Seltzer, Jean-Michel Claverie, Max Hantke, Olof Jönsson, Carl Nettelblad, Gijs Van Der Schot, Mengning Liang, Daniel P. DePonte, Anton Barty, M. Marvin Seibert, Bianca Iwan, Inger Andersson, N. Duane Loh, Andrew V. Martin, Henry Chapman, Christoph Bostedt, John D. Bozek, Ken R. Ferguson, Jacek Krzywinski, Sascha W. Epp, Daniel Rolles, Artem Rudenko, Robert Hartmann, Nils Kimmel, Janos Hajdu

    http://dx.doi.org/10.1103/physrevlett.114.098102 Tomas Ekeberg and Martin Svenda and Chantal Abergel and Filipe R. N. C. Maia and Virginie Seltzer and Jean-Michel Claverie and Max Hantke and Olof Jönsson and Carl Nettelblad and Gijs van der Schot and Mengning Liang and Daniel P. DePonte and …

  27. Coronavirus envelope (E) protein remains at the site of assembly

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    26 Feb 2015 | BioXFEL Publications | Contributor(s): Pavithra Venkatagopalan, Sasha M. Daskalova, Lisa A. Lopez, Kelly A. Dolezal, Brenda Hogue

    journal-article http://dx.doi.org/10.1016/j.virol.2015.02.005 Venkatagopalan, P. et al., 2015. Coronavirus envelope (E) protein remains at the site of assembly. Virology, 478, pp.75–85. Available at: http://dx.doi.org/10.1016/j.virol.2015.02.005. Pavithra Venkatagopalan and Sasha M. Daskalova …

  28. Toxicity of Eosinophil MBP Is Repressed by Intracellular Crystallization and Promoted by Extracellular Aggregation

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    26 Feb 2015 | BioXFEL Publications | Contributor(s): Alice Soragni, Shida Yousefi, Christina Stoeckle, Angela B. Soriaga, Michael R. Sawaya, Evelyne Kozlowski, Inès Schmid, Susanne Radonjic-Hoesli, Sebastien Boutet, Garth J. Williams, Marc Messerschmidt, M. Marvin Seibert, Duilio Cascio, Nadia A. Zatsepin, Manfred Burghammer, Christian Riekel, Jacques-Philippe Colletier, Roland Riek, David S. Eisenberg, Hans-Uwe Simon

    http://dx.doi.org/10.1016/j.molcel.2015.01.026 Alice Soragni and Shida Yousefi and Christina Stoeckle and Angela B. Soriaga and Michael R. Sawaya and Evelyne Kozlowski and Inès Schmid and Susanne Radonjic-Hoesli and Sebastien Boutet and Garth J. Williams and Marc Messerschmidt and M. Marvin …

  29. Protein dielectrophoresis and the link to dielectric properties

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    20 Feb 2015 | BioXFEL Publications | Contributor(s): Fernanda Camacho-Alanis, Alexandra Ros

    http://dx.doi.org/10.4155/bio.14.306 Fernanda Camacho-Alanis and Alexandra Ros Camacho-Alanis, F. & Ros, A., 2015. Protein dielectrophoresis and the link to dielectric properties. Bioanalysis, 7(3), pp.353–371. Available at: http://dx.doi.org/10.4155/bio.14.306. journal-article

  30. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams

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    16 Feb 2015 | BioXFEL Publications | Contributor(s): Karol Nass, Lutz Foucar, Thomas R. M. Barends, Elisabeth Hartmann, Sabine Botha, Robert L. Shoeman, R. Bruce Doak, Roberto Alonso-Mori, Andrew Aquila, Saša Bajt, Anton Barty, Richard Bean, Kenneth R. Beyerlein, Maike Bublitz, Nikolaj Drachmann, Jonas Gregersen, H. Olof Jönsson, Wolfgang Kabsch, Stephan Kassemeyer, Jason E. Koglin, Michael Krumrey, Daniel Mattle, Marc Messerschmidt, Poul Nissen, Linda Reinhard, Oleg Sitsel, Dimosthenis Sokaras, Garth J. Williams, Stefan Hau-Riege, Nicusor Timneanu, Carl Caleman, Henry Chapman, Sébastien Boutet, Ilme Schlichting

    Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX),Clostridium …

  31. Structural basis for bifunctional peptide recognition at human δ-opioid receptor

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    16 Feb 2015 | BioXFEL Publications | Contributor(s): Gustavo Fenalti, Nadia Zatsepin, Cecilia Betti, Patrick Giguere, Gye Won Han, Andrii Ishchenko, Wei Liu, Karel Guillemyn, Haitao Zhang, Daniel James, Dingjie Wang, Uwe Weierstall, John Spence, Sébastien Boutet, Marc Messerschmidt, Garth J Williams, Cornelius Gati, Oleksandr M Yefanov, Thomas A White, Dominik Oberthuer, Markus Metz, Chun Hong Yoon, Anton Barty, Henry Chapman, Shibom Basu, Jesse David Coe, Chelsie E Conrad, Raimund Fromme, Petra Fromme, Dirk Tourwé, Peter W Schiller, Bryan L Roth, Steven Ballet, Vsevolod Katritch, Raymond C Stevens, Vadim Cherezov

    http://dx.doi.org/10.1038/nsmb.2965 Gustavo Fenalti and Nadia A Zatsepin and Cecilia Betti and Patrick Giguere and Gye Won Han and Andrii Ishchenko and Wei Liu and Karel Guillemyn and Haitao Zhang and Daniel James and Dingjie Wang and Uwe Weierstall and John C H Spence and Sébastien Boutet and …

  32. Direct Phasing of Finite Crystals Illuminated with a Free-Electron Laser

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    12 Feb 2015 | BioXFEL Publications | Contributor(s): Richard Kirian, Richard J. Bean, Kenneth R. Beyerlein, Miriam Barthelmess, Chun Hong Yoon, Fenglin Wang, Flavio Capotondi, Emanuele Pedersoli, Anton Barty, Henry Chapman

    http://dx.doi.org/10.1103/physrevx.5.011015 Richard A. Kirian and Richard J. Bean and Kenneth R. Beyerlein and Miriam Barthelmess and Chun Hong Yoon and Fenglin Wang and Flavio Capotondi and Emanuele Pedersoli and Anton Barty and Henry N. Chapman Kirian, R.A. et al., 2015. Direct Phasing of …

  33. Imaging single cells in a beam of live cyanobacteria with an X-ray laser

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    11 Feb 2015 | BioXFEL Publications | Contributor(s): Gijs Van Der Schot, Martin Svenda, Filipe R. N. C. Maia, Max Hantke, Daniel P. DePonte, M. Marvin Seibert, Andrew Aquila, Joachim Schulz, Richard Kirian, Mengning Liang, Francesco Stellato, Bianca Iwan, Jakob Andreasson, Nicusor Timneanu, Daniel Westphal, F. Nunes Almeida, Dusko Odic, Dirk Hasse, Gunilla H. Carlsson, Daniel S. D. Larsson, Anton Barty, Andrew V. Martin, Sebastian Schorb, Christoph Bostedt, John D. Bozek, Daniel Rolles, Artem Rudenko, Sascha Epp, Lutz Foucar, Benedikt Rudek, Robert Hartmann, Nils Kimmel, Peter Holl, Lars Englert, Ne-Te Duane Loh, Henry Chapman, Inger Andersson, Janos Hajdu, Tomas Ekeberg

    http://dx.doi.org/10.1038/ncomms6704 Gijs van der Schot and Martin Svenda and Filipe R. N. C. Maia and Max Hantke and Daniel P. DePonte and M. Marvin Seibert and Andrew Aquila and Joachim Schulz and Richard Kirian and Mengning Liang and Francesco Stellato and Bianca Iwan and Jakob Andreasson and …

  34. Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

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    09 Feb 2015 | BioXFEL Publications | Contributor(s): Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James Fraser

    Advances in electron cryomicroscopy allow for the building of de novo atomic models into high resolution Coulomb potential maps. While established validation metrics independently assess map quality and model geometry, methods to assess the precise fitting of an atomic model into the map and to …

  35. Nanocrystallography

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    04 Feb 2015 | Teaching Materials

    Joe Luft describes the theory and practice behind crystallography and nanocrystallography and discuss recent advances in the production, characterization, and optimization of nanocrystals.

  36. Towards RIP using free-electron laser SFX data

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    04 Feb 2015 | BioXFEL Publications | Contributor(s): Lorenzo Galli, Sang-Kil Son, Thomas A. White, Robin Santra, Henry Chapman, Max H. Nanao

    Here, it is shown that simulated native serial femtosecond crystallography (SFX) cathepsin B data can be phased by rapid ionization of sulfur atoms. Utilizing standard software adopted for radiation-damage-induced phasing (RIP), the effects on both substructure determination and phasing of the …

  37. A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS

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    29 Jan 2015 | BioXFEL Publications | Contributor(s): Jesse B. Hopkins, Andrea Katz, Steve P. Meisburger, Matthew A. Warkentin, Robert E. Thorne, Lois Pollack

    http://dx.doi.org/10.1107/s1600576714027782 The application of small-angle X-ray scattering (SAXS) for high-throughput characterization of biological macromolecules in solution is limited by radiation damage. By cryocooling samples, radiation damage and required sample volumes can be reduced by …

  38. Molecular dynamics simulation of a psychrophilic adenylate kinase

    0.0 out of 5 stars 

    29 Jan 2015 | BioXFEL Publications | Contributor(s): Euiyoung Bae, Sojin Moon, George Phillips

    http://dx.doi.org/10.1007/s13765-015-0033-y Euiyoung Bae and Sojin Moon and George N. Phillips Bae, E., Moon, S. & Phillips, G.N., 2015. Molecular dynamics simulation of a psychrophilic adenylate kinase. Journal of the Korean Society for Applied Biological Chemistry, 58(2), pp.209–212. Available …

  39. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine

    0.0 out of 5 stars 

    23 Jan 2015 | BioXFEL Publications | Contributor(s): L. Qin, I. Kufareva, L. G. Holden, C. Wang, Y. Zheng, C. Zhao, G. Fenalti, H. Wu, G. W. Han, V. Cherezov, R. Abagyan, R. C. Stevens, T. M. Handel

    http://dx.doi.org/10.1126/science.1261064 L. Qin and I. Kufareva and L. G. Holden and C. Wang and Y. Zheng and C. Zhao and G. Fenalti and H. Wu and G. W. Han and V. Cherezov and R. Abagyan and R. C. Stevens and T. M. Handel Qin, L. et al., 2015. Crystal structure of the chemokine receptor CXCR4 in …

  40. Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser

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    20 Jan 2015 | BioXFEL Publications | Contributor(s): Carl Caleman, Nicuşor Tîmneanu, Andrew V. Martin, H. Olof Jönsson, Andrew Aquila, Anton Barty, Howard A. Scott, Thomas A. White, Henry Chapman

    http://dx.doi.org/10.1364/oe.23.001213 Carl Caleman and Nicuşor Tîmneanu and Andrew V. Martin and H. Olof Jönsson and Andrew Aquila and Anton Barty and Howard A. Scott and Thomas A. White and Henry N. Chapman Caleman, C. et al., 2015. Ultrafast self-gating Bragg diffraction of exploding …

  41. Career Trends: Exploring Careers Beyond the Bench

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    20 Jan 2015 | Publications

    Last month, the U.S. National Science Foundation (NSF) released a report* with some grim news that confirmed what is painfully obvious to recent Ph.D. graduates in science, technology, engineering, and mathematics (STEM) fields: Unemployment for this cohort is on the rise (at 2.4% in 2010, up …

  42. Investigation of NO2 adsorption on reduced graphene oxide

    0.0 out of 5 stars 

    15 Jan 2015 | BioXFEL Publications | Contributor(s): E.C. Mattson, K. Pande, S. Cui, M. Weinert, J.H. Chen, C.J. Hirschmugl

    journal-article http://dx.doi.org/10.1016/j.cplett.2015.01.018 Mattson, E.C. et al., 2015. Investigation of NO2 adsorption on reduced graphene oxide. Chemical Physics Letters, 622, pp.86–91. Available at: http://dx.doi.org/10.1016/j.cplett.2015.01.018. E.C. Mattson and K. Pande and S. Cui and …

  43. Soft x-ray free-electron laser induced damage to inorganic scintillators

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    07 Jan 2015 | BioXFEL Publications | Contributor(s): Tomáš Burian, Věra Hájková, Jaromír Chalupský, Luděk Vyšín, Pavel Boháček, Martin Přeček, Jan Wild, Cigdem Özkan, Nicola Coppola, Shafagh Dastjani Farahani, Joachim Schulz, Harald Sinn, Thomas Tschentscher, Jérôme Gaudin, Saša Bajt, Kai Tiedtke, Sven Toleikis, Henry Chapman, Rolf A. Loch, Marek Jurek, Ryszard Sobierajski, Jacek Krzywinski, Stefan Moeller, Marion Harmand, Germano Galasso, Mitsuru Nagasono, Karel Saskl, Pavol Sovák, Libor Juha

    http://dx.doi.org/10.1364/ome.5.000254 Tomáš Burian and Věra Hájková and Jaromír Chalupský and Luděk Vyšín and Pavel Boháček and Martin Přeček and Jan Wild and Cigdem Özkan and Nicola Coppola and Shafagh Dastjani Farahani and Joachim Schulz and Harald Sinn and Thomas Tschentscher and …

  44. From deep TLS validation to ensembles of atomic models built from elemental motions

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    02 Jan 2015 | BioXFEL Publications | Contributor(s): Alexandre Urzhumtsev, Pavel Afonine, Andrew H Van Benschoten, James Fraser, Paul D Adams

    The widely used Translation Libration Screw (TLS) approximation describes concerted motions of atomic groups in X-ray refinement. TLS refinement often provides a better interpretation of diffraction data and the resulting rigid body motions may subsequently be assigned biochemical significance. In …

  45. Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

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    02 Jan 2015 | BioXFEL Publications | Contributor(s): Andrew Van Benschoten, Pavel Afonine, Thomas Terwilliger, Michael Wall, Colin Jackson, Nicholas Sauter, Paul Adams, Alexandre Urzhumtsev, James Fraser

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. While Bragg diffraction describes the average positional distribution of crystalline atoms, many different models can fit this distribution equally well. Diffuse X-ray …

  46. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

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    02 Jan 2015 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Daniel James, Dingjie Wang, Thomas A. White, Nadia Zatsepin, Anastasya Shilova, Garrett Charles Nelson, Haiguang Liu, Linda Johansson, Michael Heymann, Kathrin Jaeger, Markus Metz, Cecilia Wickstrand, Wenting Wu, Petra Båth, Peter Berntsen, Dominik Oberthuer, Valerie Panneels, Vadim Cherezov, Henry Chapman, Gebhard F.X. Schertler, Richard Neutze, John Spence, Isabel Moraes, Manfred Burghammer, Joerg Standfuss, Uwe Weierstall

    journal-article Przemyslaw Nogly and Daniel James and Dingjie Wang and Thomas A. White and Nadia Zatsepin and Anastasya Shilova and Garrett Nelson and Haiguang Liu and Linda Johansson and Michael Heymann and Kathrin Jaeger and Markus Metz and Cecilia Wickstrand and Wenting Wu and Petra Båth and …

  47. Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes

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    24 Dec 2014 | BioXFEL Publications | Contributor(s): Gira Bhabha, Justin T. Biel, James Fraser

    http://dx.doi.org/10.1021/ar5003158 Gira Bhabha and Justin T. Biel and James S. Fraser Bhabha, G., Biel, J.T. & Fraser, J.S., 2015. Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes. Acc. Chem. Res., 48(2), pp.423–430. Available at: …

  48. The accurate assessment of small-angle X-ray scattering data

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    24 Dec 2014 | BioXFEL Publications | Contributor(s): Thomas D. Grant, Joseph Luft, Lester G. Carter, Tsutomu Matsui, Thomas M. Weiss, Anne Martel, Edward Snell

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents …

  49. Generic GPCR residue numbers – aligning topology maps while minding the gaps

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    22 Dec 2014 | BioXFEL Publications | Contributor(s): Vignir Isberg, Chris De Graaf, Andrea Bortolato, Vadim Cherezov, Vsevolod Katritch, Fiona H. Marshall, Stefan Mordalski, Jean-Philippe Pin, Raymond C. Stevens, Gerrit Vriend, David E. Gloriam

    http://dx.doi.org/10.1016/j.tips.2014.11.001 Vignir Isberg and Chris de Graaf and Andrea Bortolato and Vadim Cherezov and Vsevolod Katritch and Fiona H. Marshall and Stefan Mordalski and Jean-Philippe Pin and Raymond C. Stevens and Gerrit Vriend and David E. Gloriam Isberg, V. et al., 2015. Generic …

  50. 2015 BioXFEL International Conference Invited Speakers Abstracts

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    17 Dec 2014 | Downloads

    This is a compilation of the abstracts of the Invited Speakers of the 2015 BioXFEL Conference in Ponce, Puerto Rico.  For more information please visit the event page www.bioxfel.org/events/details/6  

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

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    05 Dec 2014 | Publications

    Authors: Tenboer, J., Basu, S., Zatsepin, N., Pande, K., Milathianaki, D., Frank, M., Hunter, M., Boutet, S., Williams, G. J., Koglin, J. E., Oberthuer, D., Heymann, M., Kupitz, C., Conrad, C., Coe, J., Roy-Chowdhury, S., Weierstall, U., James, D., Wang, D., Grant, T., Barty, A., Yefanov, O., …

  52. 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

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

    0.0 out of 5 stars 

    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 …

  54. 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 …

  55. 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. …

  56. 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: …

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

    0.0 out of 5 stars 

    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 …

  58. 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.

  59. 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 …

  60. 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: …

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

    0.0 out of 5 stars 

    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: …

  62. 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. …

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

    0.0 out of 5 stars 

    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), …

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

    0.0 out of 5 stars 

    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: …

  65. 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 …

  66. European XFEL Users Meeting

    0.0 out of 5 stars 

    28 Oct 2014 | Downloads

  67. Crystallographic Methods - Crystallographic Symmetry - Part III

    0.0 out of 5 stars 

    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)

  68. Crystallographic Methods - Crystallographic Symmetry - Part II

    0.0 out of 5 stars 

    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)

  69. Crystallographic Methods - Crystallographic Symmetry - Part I

    0.0 out of 5 stars 

    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)

  70. 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, …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

  73. 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: …

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

    0.0 out of 5 stars 

    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

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

    0.0 out of 5 stars 

    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

  76. 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. …

  77. 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

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

    0.0 out of 5 stars 

    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

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

    0.0 out of 5 stars 

    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: …

  80. Microfluidic Platforms for Bimolecular and Nanocrystal Separation

    5.0 out of 5 stars 

    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 …

  81. 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 …

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

    0.0 out of 5 stars 

    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

  83. Crystallographic Methods - Geometrical Crystallography - Part I

    0.0 out of 5 stars 

    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

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

    0.0 out of 5 stars 

    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

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

    0.0 out of 5 stars 

    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: …

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

    0.0 out of 5 stars 

    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

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

    0.0 out of 5 stars 

    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

  88. 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., …

  89. 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

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

    0.0 out of 5 stars 

    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 …

  91. Crystallographic Methods - Geometrical Crystallography - Part II

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    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

  92. 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 …

  93. Cheetah Tutorial

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    03 Sep 2014 | Teaching Materials

    Anton Barty (CFEL)

  94. CASS and SFX SAD Tutorial

    0.0 out of 5 stars 

    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.

  95. CrystFEL Tutorial

    0.0 out of 5 stars 

    03 Sep 2014 | Teaching Materials

    Tom White (CFEL)

  96. cctbx.xfel Tutorial

    0.0 out of 5 stars 

    03 Sep 2014 | Teaching Materials

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

  97. 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.

  98. 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

  99. 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.

  100. 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 …