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  1. Sub-Femtosecond Free-Electron Laser Pulses

    0.0 out of 5 stars 

    07 May 2015 | 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/10.1364/cleo_si.2015.stu2n.7 W. Helml and A. R. Maier and W. Schweinberger and I. Grguraš and P. Radcliffe and G. Doumy and C. Roedig and J. Gagnon and M. Messerschmidt and S. Schorb and C. Bostedt and F. Grüner and L. F. DiMauro and D. Cubaynes and J. D. Bozek and Th. …

  2. 2D Crystallography

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    06 May 2015 | Teaching Materials

    Dr. Mattias Frank discusses new possibilities in the field of 2D crystallography made possible by XFEL sources.

  3. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

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    05 May 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, James Fraser, Henry Van Den Bedem

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated …

  4. Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges

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    30 Apr 2015 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, A. Dashti, P. Schwander, R. Fung, A. Ourmazd

    http://dx.doi.org/10.1063/1.4919740 A. Hosseinizadeh and A. Dashti and P. Schwander and R. Fung and A. Ourmazd Hosseinizadeh, A. et al., 2015. Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges. Structural Dynamics, 2(4), p.041601. Available at: …

  5. Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

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    29 Apr 2015 | BioXFEL Publications | Contributor(s): L. Galli, S.-K. Son, M. Klinge, S. Bajt, A. Barty, R. Bean, C. Betzel, K. R. Beyerlein, C. Caleman, R. B. Doak, M. Duszenko, H. Fleckenstein, C. Gati, B. Hunt, R. A. Kirian, M. Liang, M. H. Nanao, K. Nass, D. Oberthür, L. Redecke, R. Shoeman, F. Stellato, C. H. Yoon, T. A. White, O. Yefanov, J. Spence, H. N. Chapman

    http://dx.doi.org/10.1063/1.4919398 L. Galli and S.-K. Son and M. Klinge and S. Bajt and A. Barty and R. Bean and C. Betzel and K. R. Beyerlein and C. Caleman and R. B. Doak and M. Duszenko and H. Fleckenstein and C. Gati and B. Hunt and R. A. Kirian and M. Liang and M. H. Nanao and K. Nass and D. …

  6. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with AMP

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    28 Apr 2015 | BioXFEL Publications | Contributor(s): Do Jin Kim, Eduard Bitto, Craig A. Bingman, Hyun-Jung Kim, Byung Woo Han, George Phillips

    http://dx.doi.org/10.1002/prot.24821 Do Jin Kim and Eduard Bitto and Craig A. Bingman and Hyun-Jung Kim and Byung Woo Han and George N. Phillips Kim, D.J. et al., 2015. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in …

  7. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

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    25 Apr 2015 | BioXFEL Publications | Contributor(s): Haitao Zhang, Hamiyet Unal, Cornelius Gati, Gye Won Han, Wei Liu, Nadia A. Zatsepin, Daniel James, Dingjie Wang, Garrett Charles Nelson, Uwe Weierstall, Michael R. Sawaya, Qingping Xu, Marc Messerschmidt, Garth J. Williams, Sébastien Boutet, Oleksandr M. Yefanov, Thomas A. White, Chong Wang, Andrii Ishchenko, Kalyan C. Tirupula, Russell Desnoyer, Jesse David Coe, Chelsie E. Conrad, Petra Fromme, Raymond C. Stevens, Vsevolod Katritch, Sadashiva S. Karnik, Vadim Cherezov

    http://dx.doi.org/10.1016/j.cell.2015.04.011 Haitao Zhang and Hamiyet Unal and Cornelius Gati and Gye Won Han and Wei Liu and Nadia A. Zatsepin and Daniel James and Dingjie Wang and Garrett Nelson and Uwe Weierstall and Michael R. Sawaya and Qingping Xu and Marc Messerschmidt and Garth J. …

  8. Structure determination with weak anomalous signal

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    24 Apr 2015 | BioXFEL Publications | Contributor(s): Thomas Charles Terwilliger, Li-Wei Hung, Paul D. Adams, Nathanial D Echols, Ralf Grosse-Kunstleve, James Holton, Gabor Bunkoczi, Randy J. Read, David Akey, Janet Smith

    http://dx.doi.org/10.2172/1178320 Thomas Charles Terwilliger and Li-Wei Hung and Paul D. Adams and Nathanial D Echols and Ralf Grosse-Kunstleve and James Holton and Gabor Bunkoczi and Randy J. Read and David Akey and Janet Smith Terwilliger, T.C. et al., 2015. Structure determination with weak …

  9. LucY: A Versatile New Fluorescent Reporter Protein

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    23 Apr 2015 | BioXFEL Publications | Contributor(s): Michele E. Auldridge, Hongnan Cao, Saurabh Sen, Laura P. Franz, Craig A. Bingman, Ragothaman M. Yennamalli, George Phillips, David Mead, Eric J. Steinmetz

    http://dx.doi.org/10.1371/journal.pone.0124272 Michele E. Auldridge and Hongnan Cao and Saurabh Sen and Laura P. Franz and Craig A. Bingman and Ragothaman M. Yennamalli and George N. Phillips and David Mead and Eric J. Steinmetz Auldridge, M.E. et al., 2015. LucY: A Versatile New Fluorescent …

  10. The Structure of the PanD/PanZ Protein Complex Reveals Negative Feedback Regulation of Pantothenate Biosynthesis by Coenzyme A

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    23 Apr 2015 | BioXFEL Publications | Contributor(s): Diana C.F. Monteiro, Vijay Patel, Christopher P. Bartlett, Shingo Nozaki, Thomas D. Grant, James A. Gowdy, Gary S. Thompson, Arnout P. Kalverda, Edward H. Snell, Hironori Niki, Arwen R. Pearson, Michael E. Webb

    http://dx.doi.org/10.1016/j.chembiol.2015.03.017 Diana C.F. Monteiro and Vijay Patel and Christopher P. Bartlett and Shingo Nozaki and Thomas D. Grant and James A. Gowdy and Gary S. Thompson and Arnout P. Kalverda and Edward H. Snell and Hironori Niki and Arwen R. Pearson and Michael E. …

  11. 2015 Serial Crystallography Data Analysis Workshop at ACA Annual Meeting.

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    23 Apr 2015 | Workshops | Contributor(s): Nadia Zatsepin, Tom Grant

    We are running a serial femtosecond crystallography data analysis workshop at ACA 2015 in Philadelphia, PA, focused on "Serial Crystallography Data Analysis with Cheetah and CrystFEL: Concepts and Tutorials".  www.amercrystalassn.org/2015-wk.02   Workshop format: The workshop will start with an …

  12. The linac coherent light source single particle imaging road map

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    21 Apr 2015 | BioXFEL Publications | Contributor(s): A. Aquila, A. Barty, C. Bostedt, S. Boutet, G. Carini, D. DePonte, P. Drell, S. Doniach, K. H. Downing, T. Earnest, H. Elmlund, V. Elser, M. Gühr, J. Hajdu, J. Hastings, S. P. Hau-Riege, Z. Huang, E. E. Lattman, F. R. N. C. Maia, S. Marchesini, A. Ourmazd, C. Pellegrini, R. Santra, I. Schlichting, C. Schroer, J. C. H. Spence, I. A. Vartanyants, S. Wakatsuki, W. I. Weis, G. J. Williams

    http://dx.doi.org/10.1063/1.4918726 A. Aquila and A. Barty and C. Bostedt and S. Boutet and G. Carini and D. dePonte and P. Drell and S. Doniach and K. H. Downing and T. Earnest and H. Elmlund and V. Elser and M. Gühr and J. Hajdu and J. Hastings and S. P. Hau-Riege and Z. Huang and E. E. Lattman …

  13. Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data

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    21 Apr 2015 | BioXFEL Publications | Contributor(s): Thomas Barends, Thomas A. White, Anton Barty, Lutz Foucar, Marc Messerschmidt, Roberto Alonso-Mori, Sabine Botha, Henry Chapman, R. Bruce Doak, Lorenzo Galli, Cornelius Gati, Matthias Gutmann, Jason Koglin, Anders Markvardsen, Karol Nass, Dominik Oberthur, Robert L. Shoeman, Ilme Schlichting, Sébastien Boutet

    Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo …

  14. framesorter

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    20 Apr 2015 | Downloads

    Framesorter is a script for parsing the output from Cheetah  

  15. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Jesse David Coe, Christopher Kupitz, Shibom Basu, Chelsie E Conrad, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme

    http://dx.doi.org/10.1016/bs.mie.2015.01.011 Jesse Coe and Christopher Kupitz and Shibom Basu and Chelsie E. Conrad and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme Coe, J. et al., 2015. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free …

  16. TFIIF and TFIIS Enhance the Mechanical Persistence of Transcript Elongation by RNA Polymerase II

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Volker Schweikhard, Cong A. Meng, Kenji Murakami, Craig D. Kaplan, Roger Kornberg, Steven M. Block

    journal-article http://dx.doi.org/10.1016/j.bpj.2013.11.4469 Schweikhard, V. et al., 2014. TFIIF and TFIIS Enhance the Mechanical Persistence of Transcript Elongation by RNA Polymerase II. Biophysical Journal, 106(2), p.486a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.4469. Volker …

  17. High-Resolution NMR Spectroscopy Reveals Structure of Lipoprotein flpp3

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): James D Zook, Nicholas Sisco, Gina Mo, Debra Hansen, Felicia Craciunescu, Brian Cherry, Kathryn Sykes, Wade Van Horn, Petra Fromme

    http://dx.doi.org/10.1016/j.bpj.2013.11.1142 journal-article Zook, J.D. et al., 2014. High-Resolution NMR Spectroscopy Reveals Structure of Lipoprotein flpp3. Biophysical Journal, 106(2), p.193a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.1142. James D. Zook and Nicholas Sisco and …

  18. Fast Binding Kinetics of RNA Aptamers Measured using a Novel Microfluidic Mixer

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Alexander L. Van Slyke, Juan Wang, Avtar Singh, Lois Pollack, Warren R. Zipfel

    http://dx.doi.org/10.1016/j.bpj.2013.11.4364 journal-article Van Slyke, A.L. et al., 2014. Fast Binding Kinetics of RNA Aptamers Measured using a Novel Microfluidic Mixer. Biophysical Journal, 106(2), p.796a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.4364. Alexander L. Van Slyke and …

  19. Detection of Protein Nanocrystals Based on the Reversibility of Crystallization

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Katerina Dörner, Jose Martin Garcia, Christopher Kupitz, Rebekka M. Wachter, Petra Fromme

    http://dx.doi.org/10.1016/j.bpj.2013.11.2597 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Dörner, K. et al., 2014. Detection of Protein Nanocrystals Based on the Reversibility of Crystallization. Biophysical Journal, 106(2), p.458a. Available at: …

  20. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Michael E. Wall, Thomas C. Terwilliger, James Fraser, Paul D. Adams, Nicholas K. Sauter, Andrew VanBenschoten

    http://dx.doi.org/10.1016/j.bpj.2013.11.2171 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins. Biophysical Journal, 106(2), p.384a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.2171. Michael E. Wall and Thomas C. Terwilliger …

  21. Sequence Analysis and Biophysical Characterization Reveals the Presence of a Long Disordered Region in the CapA Membrane Protein from F. Tularensis

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Jose M. Martin, Debra T. Hansen, Andrrey Loskutov, Mark D. Robida, Felicia M. Craciunescu, Kathryn Sykes, Rebekka M. Wachter, Petra Fromme, James P. Allen

    http://dx.doi.org/10.1016/j.bpj.2013.11.3806 journal-article Martin, J.M. et al., 2014. Sequence Analysis and Biophysical Characterization Reveals the Presence of a Long Disordered Region in the CapA Membrane Protein from F. Tularensis. Biophysical Journal, 106(2), p.688a. Available at: …

  22. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source

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    16 Apr 2015 | BioXFEL Publications | Contributor(s): Ken R. Ferguson, Maximilian Bucher, John D. Bozek, Sebastian Carron, Jean-Charles Castagna, Ryan Coffee, G. Ivan Curiel, Michael Holmes, Jacek Krzywinski, Marc Messerschmidt, Michael Minitti, Ankush Mitra, Stefan Moeller, Peter Noonan, Timur Osipov, Sebastian Schorb, Michele Swiggers, Alexander Wallace, Jing Yin, Christoph Bostedt

    The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is …

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

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    15 Apr 2015 | Publications

    Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for …

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

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    14 Apr 2015 | 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.24798 R. Sophia Weerth and Karolina Michalska and Craig A. Bingman and Ragothaman M. Yennamalli and Hui Li and Robert Jedrzejczak and Fengbin Wang and Gyorgy Babnigg and Andrzej Joachimiak and Michael G. Thomas and George N. Phillips Sophia Weerth, R. et al., 2015. …

  25. The Coherent X-ray Imaging instrument at the Linac Coherent Light Source

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    14 Apr 2015 | BioXFEL Publications | Contributor(s): Mengning Liang, Garth J. Williams, Marc Messerschmidt, M. Marvin Seibert, Paul A. Montanez, Matt Hayes, Despina Milathianaki, Andrew Aquila, Mark S. Hunter, Jason E. Koglin, Donald W. Schafer, Serge Guillet, Armin Busse, Robert Bergan, William Olson, Kay Fox, Nathaniel Stewart, Robin Curtis, Alireza Alan Miahnahri, Sébastien Boutet

    The Coherent X-ray Imaging (CXI) instrument specializes in hard X-ray, in-vacuum, high power density experiments in all areas of science. Two main sample chambers, one containing a 100 nm focus and one a 1 µm focus, are available, each with multiple diagnostics, sample injection, pump–probe …

  26. Mentoring Manual

    0.0 out of 5 stars 

    14 Apr 2015 | Teaching Materials

    This manual was written by the members of the Institute for Broadening Participation and their affiliates. "Each section of this manual is devoted to the perspective and experience of each of the distinct roles in program-based mentoring environments, and organized according to the major …

  27. Simulations on time-resolved structure determination of uncrystallized biomolecules in the presence of shot noise

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    10 Apr 2015 | BioXFEL Publications | Contributor(s): K. Pande, M. Schmidt, P. Schwander, D. K. Saldin

    http://dx.doi.org/10.1063/1.4916980 K. Pande and M. Schmidt and P. Schwander and D. K. Saldin Pande, K. et al., 2015. Simulations on time-resolved structure determination of uncrystallized biomolecules in the presence of shot noise. Structural Dynamics, 2(2), p.024103. Available at: …

  28. Characterization and use of the spent beam for serial operation of LCLS

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    10 Apr 2015 | BioXFEL Publications | Contributor(s): Sébastien Boutet, Lutz Foucar, Thomas R. M. Barends, Sabine Botha, R. Bruce Doak, Jason E. Koglin, Marc Messerschmidt, Karol Nass, Ilme Schlichting, M. Marvin Seibert, Robert L. Shoeman, Garth J. Williams

    X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort …

  29. Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source

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    09 Apr 2015 | BioXFEL Publications | Contributor(s): Y. Feng, R. Alonso-Mori, T. R. M. Barends, V. D. Blank, S. Botha, M. Chollet, D. S. Damiani, R. B. Doak, J. M. Glownia, J. M. Koglin, H. T. Lemke, M. Messerschmidt, K. Nass, S. Nelson, I. Schlichting, R. L. Shoeman, Yu. V. Shvyd'ko, M. Sikorski, S. Song, S. Stoupin, S. Terentyev, G. J. Williams, D. Zhu, A. Robert, S. Boutet

    Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, …

  30. Structure Validation in Phenix

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    08 Apr 2015 | Teaching Materials

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

  31. 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

  32. Molecular Replacement in Phenix

    0.0 out of 5 stars 

    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.

  33. 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.

  34. 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 …

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

    0.0 out of 5 stars 

    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 …

  36. 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, …

  37. 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.

  38. 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), …

  39. 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

  40. Hit Rate Calculator

    0.0 out of 5 stars 

    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 …

  41. peakogram

    0.0 out of 5 stars 

    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, …

  42. 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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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, …

  46. 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: …

  47. 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 …

  48. 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. …

  49. 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 …

  50. 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: …

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

    0.0 out of 5 stars 

    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 …

  52. 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 …

  53. 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: …

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

    0.0 out of 5 stars 

    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 …

  55. 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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

  58. Protein dielectrophoresis and the link to dielectric properties

    0.0 out of 5 stars 

    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

  59. 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 …

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

    0.0 out of 5 stars 

    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 …

  61. 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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

  64. 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.

  65. 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 …

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

    0.0 out of 5 stars 

    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 …

  67. 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 …

  68. 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 …

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

    0.0 out of 5 stars 

    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 …

  70. Career Trends: Exploring Careers Beyond the Bench

    0.0 out of 5 stars 

    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 …

  71. 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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

  75. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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: …

  77. 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 …

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

    0.0 out of 5 stars 

    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 …

  79. 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  

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

    0.0 out of 5 stars 

    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., …

  81. 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

  82. 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 …

  83. Trajectories of the ribosome as a Brownian nanomachine

    0.0 out of 5 stars 

    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 …

  84. 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. …

  85. 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: …

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

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

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

  87. 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.

  88. 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 …

  89. 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: …

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

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

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

  91. 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. …

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

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

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

  93. 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: …

  94. 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 …

  95. European XFEL Users Meeting

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    28 Oct 2014 | Downloads

  96. Crystallographic Methods - Crystallographic Symmetry - Part III

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

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

  97. 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)

  98. 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)

  99. 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, …

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

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

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