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  1. Membrane protein megahertz crystallography at the European XFEL

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    04 Nov 2019 | BioXFEL Publications | Contributor(s): Chris Gisriel, Jesse David Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha Stander, Stella Lisova, Valerio Mariani, Manuela Kuhn, Steve Aplin, Thomas D. Grant, Katerina Dörner, Tokushi Sato, Austin Echelmeier, Jorvani Cruz Villarreal, Mark S. Hunter, Max Oliver Wiedorn, Juraj Knoska, Victoria Mazalova, Shatabdi Roy-Chowdhury, Jay-How Yang, Alex Jones, Richard Bean, Johan Bielecki, Yoonhee Kim, Grant Mills, Britta Weinhausen, Jose D. Meza, Nasser Al-Qudami, Saša Bajt, Gerrit Brehm, Sabine Botha, Djelloul Boukhelef, Sandor Brockhauser, Barry D. Bruce, Matthew Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan Kaushylal Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D Zook, John Spence, Henry Chapman, Anton Barty, Richard Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, Nadia Zatsepin

    http://dx.doi.org/10.1038/s41467-019-12955-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Gisriel, C. et al., 2019. Membrane protein megahertz crystallography at the European XFEL. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-12955-3. Chris …

  2. Mentoring Manual

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    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 …

  3. Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination

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    22 Sep 2017 | BioXFEL Publications | Contributor(s): Xuanxuan Li, John Spence, Brenda Hogue, Haiguang Liu

    http://dx.doi.org/10.1107/s2052252517012398 X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the …

  4. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes

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    24 Feb 2020 | BioXFEL Publications | Contributor(s): Tyler D. Huber, Jonathan Clinger, Yang Liu, Weijun Xu, Mitchell Miller, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1021/acschembio.9b00943 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Huber, T.D. et al., 2020. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chemical Biology, 15(3), pp.695–705. Available at: …

  5. Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus

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    27 Oct 2020 | BioXFEL Publications | Contributor(s): Christopher James Gisriel, Petra Fromme, Jose M. Martin-Garcia

    http://dx.doi.org/10.1007/978-1-0716-1012-1_8 book-chapter Gisriel, C., Fromme, P. & Martin-Garcia, J.M., 2020. Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus. Viruses as Therapeutics, pp.125–162. Available at: …

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

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

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

  7. Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

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    24 Apr 2018 | BioXFEL Publications | Contributor(s): Yannig Gicquel, Robin Schubert, Svetlana Kapis, Gleb Bourenkov, Thomas Schneider, Markus Perbandt, Christian Betzel, Henry Chapman, Michael Heymann

    http://dx.doi.org/10.3791/57133 journal-article Gicquel, Y. et al., 2018. Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography. Journal of Visualized Experiments, (134). Available at: http://dx.doi.org/10.3791/57133. Yannig …

  8. Microfluidic Mixing Injector Holder Enables Routine Structural Enzymology Measurements with Mix-and-Inject Serial Crystallography Using X-ray Free Electron Lasers

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    07 May 2019 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Lois Pollack

    http://dx.doi.org/10.1021/acs.analchem.9b00311 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Calvey, G.D., Katz, A.M. & Pollack, L., 2019. Microfluidic Mixing Injector Holder Enables Routine Structural Enzymology Measurements with Mix-and-Inject Serial Crystallography Using X-ray …

  9. Microfluidic Platforms for Bimolecular and Nanocrystal Separation

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

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

  10. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography

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    07 Aug 2020 | BioXFEL Publications | Contributor(s): Mohammad Vakili, Ramakrishna Vasireddi, Paul V. Gwozdz, Diana Monteiro, Michael Heymann, Robert H. Blick, Martin Trebbin

    http://dx.doi.org/10.1063/5.0012806 journal-article Vakili, M. et al., 2020. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. Review of Scientific Instruments, 91(8), p.085108. Available at: http://dx.doi.org/10.1063/5.0012806. Mohammad Vakili and Ramakrishna …

  11. Microfluidic sample delivery for serial crystallography using XFELs

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    27 Jun 2019 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Mukul Sonker, Alexandra Ros

    http://dx.doi.org/10.1007/s00216-019-01977-x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Echelmeier, A., Sonker, M. & Ros, A., 2019. Microfluidic sample delivery for serial crystallography using XFELs. Analytical and Bioanalytical Chemistry, 411(25), pp.6535–6547. Available …

  12. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight

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    08 Apr 2021 | BioXFEL Publications | Contributor(s): E. H. Snell, J. R. Helliwell

    http://dx.doi.org/10.1080/0889311x.2021.1900833 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Snell, E.H. & Helliwell, J.R., 2021. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight. …

  13. Mighty small: Observing and modeling individual microbes becomes big science

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    05 Nov 2013 | BioXFEL Publications | Contributor(s): J.-U. Kreft, C. M. Plugge, V. Grimm, C. Prats, J. H. J. Leveau, T. Banitz, S. Baines, J. Clark, A. Ros, I. Klapper, C. J. Topping, A. J. Field, A. Schuler, E. Litchman, F. L. Hellweger

    journal-article http://dx.doi.org/10.1073/pnas.1317472110 Kreft, J.-U. et al., 2013. Mighty small: Observing and modeling individual microbes becomes big science. Proceedings of the National Academy of Sciences, 110(45), pp.18027–18028. Available at: http://dx.doi.org/10.1073/pnas.1317472110. …

  14. MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles

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    06 Apr 2022 | BioXFEL Publications | Contributor(s): Jorvani Cruz Villarreal, Rory Kruithoff, Ana Egatz-Gomez, Paul D. Coleman, Robert Ros, Todd R. Sandrin, Alexandra Ros

    http://dx.doi.org/10.1007/s00216-022-04038-y journal-article Cruz Villarreal, J., Kruithoff, R., Egatz-Gomez, A., Coleman, P. D., Ros, R., Sandrin, T. R., & Ros, A. (2022). MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. …

  15. Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

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    12 May 2013 | BioXFEL Publications | Contributor(s): Marius Schmidt

    Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive …

  16. Mix-and-diffuse serial synchrotron crystallography

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    09 Oct 2017 | BioXFEL Publications | Contributor(s): Kenneth R. Beyerlein, Dennis Dierksmeyer, Valerio Mariani, Manuela Kuhn, Iosifina Sarrou, Angelica Ottaviano, Salah Awel, Juraj Knoska, Silje Fuglerud, Olof Jönsson, Stephan Stern, Max Oliver Wiedorn, Oleksandr Yefanov, Luigi Adriano, Richard Bean, Anja Burkhardt, Pontus Fischer, Michael Heymann, Daniel A. Horke, Katharina E. J. Jungnickel, Elena Kovaleva, Olga Lorbeer, Markus Metz, Jan Meyer, Andrew Morgan, Kanupriya Pande, Saravanan Panneerselvam, Carolin Seuring, Aleksandra Tolstikova, Julia Lieske, Steve Aplin, Manfred Roessle, Thomas A. White, Henry Chapman, Alke Meents, Dominik Oberthuer

    http://dx.doi.org/10.1107/s2052252517013124 Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers …

  17. Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers

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    29 Aug 2016 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Chris B. Schaffer, Lois Pollack

    http://dx.doi.org/10.1063/1.4961971 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Calvey, G.D. et al., 2016. Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers. Structural Dynamics, 3(5), p.054301. Available at: …

  18. Model Comparison to Identify Structural Heterogeneity in Protein X-Ray Crystallography

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    04 Feb 2017 | BioXFEL Publications | Contributor(s): Nathan S. Babcock, David A. Sivak, Daniel Keedy, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2016.11.2628 journal-article Babcock, N.S. et al., 2017. Model Comparison to Identify Structural Heterogeneity in Protein X-Ray Crystallography. Biophysical Journal, 112(3), p.486a. Available at: http://dx.doi.org/10.1016/j.bpj.2016.11.2628. Nathan S. Babcock and …

  19. Molecular architecture of the yeast Mediator complex

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    24 Sep 2015 | BioXFEL Publications | Contributor(s): Philip J Robinson, Michael J Trnka, Riccardo Pellarin, Charles H Greenberg, David Bushnell, Ralph Davis, Alma L Burlingame, Andrej Sali, Roger Kornberg

    http://dx.doi.org/10.7554/elife.08719 Philip J Robinson and Michael J Trnka and Riccardo Pellarin and Charles H Greenberg and David A Bushnell and Ralph Davis and Alma L Burlingame and Andrej Sali and Roger D Kornberg Robinson, P.J. et al., 2015. Molecular architecture of the yeast Mediator …

  20. Molecular biophysical characterization of the third FF domain of Homo sapiens Prp40 homolog A

    0.0 out of 5 stars 

    19 Apr 2018 | BioXFEL Publications | Contributor(s): Adalberto Díaz Casas, Gabriela Casanova Sepúlveda, Odalys Sánchez Negrón, Andrea P. Caro Muñiz, Stewart R. Malavé Ramos, Ana R. Cebollero López, Belinda Pastrana-Ríos

    http://dx.doi.org/10.1016/j.molstruc.2018.04.059 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Díaz Casas, A. et al., 2018. Molecular biophysical characterization of the third FF domain of Homo sapiens Prp40 homolog A. Journal of Molecular Structure, 1167, pp.174–179. …

  21. Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV ‐2 spike protein receptor‐binding domain

    0.0 out of 5 stars 

    10 Aug 2021 | BioXFEL Publications | Contributor(s): Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, David Case, Jean Baum

    http://dx.doi.org/10.1002/prot.26208 journal-article Williams, J.K. et al., 2021. Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV ‐2 spike protein receptor‐binding domain. Proteins: Structure, Function, …

  22. Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain

    0.0 out of 5 stars 

    14 Jan 2021 | BioXFEL Publications | Contributor(s): Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, David Case, Jean Baum

    http://dx.doi.org/10.1101/2021.01.08.425965 AbstractSince the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human …

  23. 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 …

  24. Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases

    0.0 out of 5 stars 

    12 Feb 2021 | BioXFEL Publications | Contributor(s): Premila P. Samuel, David Case

    http://dx.doi.org/10.1016/j.bpj.2020.11.1905 journal-article Samuel, P.P. & Case, D.A., 2021. Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases. Biophysical Journal, 120(3), p.298a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1905. Premila P. Samuel and David …

  25. 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.

  26. Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

    0.0 out of 5 stars 

    26 Oct 2020 | BioXFEL Publications | Contributor(s): Shikai Jin, Mitchell Miller, Mingchen Chen, Nicholas P. Schafer, Xingcheng Lin, Xun Chen, George Phillips, Peter G. Wolynes

    http://dx.doi.org/10.1107/s2052252520013494 The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections …

  27. Monochromatic and polychromatic serial crystallography at the Advanced Photon Source

    0.0 out of 5 stars 

    19 Dec 2017 | BioXFEL Publications | Contributor(s): R. F. Fischetti, J. Martin-Garcia, N. Zatsepin, N. Stander, L. Zhu, G. Subramanian, G. Nelson, J. Coe, N. Nagaratnam, S. Roy-Chowdury, D. Kissick, A. Ishchenko, C. Conrad, G. Ketawala, D. James, J. Zook, C. Ogata, N. Venugopalan, S. Xu, A. Meents, V. Srajer, R. Henning, H. Chapman, J. Spence, U. Weierstall, V. Cherezov, P. Fromme, W. Liu

    http://dx.doi.org/10.1107/s0108767317096404 journal-article Fischetti, R.F. et al., 2017. Monochromatic and polychromatic serial crystallography at the Advanced Photon Source. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a368–a369. Available at: …

  28. Morphology of GaAs-quantum-well interfaces grown by liquid-phase epitaxy

    0.0 out of 5 stars 

    26 Jul 2002 | BioXFEL Publications | Contributor(s): U. Morlock, J. Christen, D. Bimberg, E. Bauser, H.-J. Queisser, A. Ourmazd

    http://dx.doi.org/10.1103/physrevb.44.8792 journal-article Morlock, U. et al., 1991. Morphology of GaAs-quantum-well interfaces grown by liquid-phase epitaxy. Physical Review B, 44(16), pp.8792–8797. Available at: http://dx.doi.org/10.1103/physrevb.44.8792. U. Morlock and J. Christen and D. …

  29. Moving in the Right Direction: Protein Vibrational Steering Function

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    14 Mar 2017 | BioXFEL Publications | Contributor(s): Katherine A. Niessen, Mengyang Xu, Alessandro Paciaroni, Andrea Orecchini, Edward Snell, Andrea Markelz

    journal-article http://dx.doi.org/10.1016/j.bpj.2016.12.049 Niessen, K.A. et al., 2017. Moving in the Right Direction: Protein Vibrational Steering Function. Biophysical Journal, 112(5), pp.933–942. Available at: http://dx.doi.org/10.1016/j.bpj.2016.12.049. Katherine A. Niessen and Mengyang Xu …

  30. Multi-shell model of ion-induced nucleic acid condensation

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    21 Apr 2016 | BioXFEL Publications | Contributor(s): Igor S. Tolokh, Aleksander V. Drozdetski, Lois Pollack, Nathan A. Baker, Alexey V. Onufriev

    http://dx.doi.org/10.1063/1.4945382 journal-article Tolokh, I.S. et al., 2016. Multi-shell model of ion-induced nucleic acid condensation. The Journal of Chemical Physics, 144(15), p.155101. Available at: http://dx.doi.org/10.1063/1.4945382. Igor S. Tolokh and Aleksander V. Drozdetski and Lois …

  31. Multitemperature data and diffuse scattering in X-ray crystallography

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    07 Dec 2015 | Teaching Materials | Contributor(s): James Fraser

    Dr. James Fraser will discuss recent advances in mapping the structural basis of protein conformational dynamics using multitemperature data and diffuse scattering from both conventional synchrotron sources and XFELs.

  32. 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.

  33. Nanocrystallography measurements of early stage synthetic malaria pigment

    0.0 out of 5 stars 

    28 Sep 2017 | BioXFEL Publications | Contributor(s): Ruben A. Dilanian, Victor Streltsov, Hannah D. Coughlan, Harry M. Quiney, Andrew V. Martin, Nectarios Klonis, Con Dogovski, Sébastien Boutet, Marc Messerschmidt, Garth J. Williams, Sophie Williams, Nicholas W. Phillips, Keith A. Nugent, Leann Tilley, Brian Abbey

    http://dx.doi.org/10.1107/s1600576717012663 The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic …

  34. Native phasing of x-ray free-electron laser data for a G protein-coupled receptor

    0.0 out of 5 stars 

    23 Sep 2016 | BioXFEL Publications | Contributor(s): Alexander Batyuk, Lorenzo Galli, Andrii Ishchenko, Gye Won Han, Cornelius Gati, Petr A. Popov, Ming-Yue Lee, Benjamin Stauch, Thomas A. White, Anton Barty, Andrew Aquila, Mark S. Hunter, Mengning Liang, Sébastien Boutet, Mengchen Pu, Zhi-jie Liu, Garrett Charles Nelson, Daniel James, Chufeng Li, Yun Zhao, John Spence, Wei Liu, Petra Fromme, Vsevolod Katritch, Uwe Weierstall, Raymond C. Stevens, Vadim Cherezov

    http://dx.doi.org/10.1126/sciadv.1600292 Alexander Batyuk and Lorenzo Galli and Andrii Ishchenko and Gye Won Han and Cornelius Gati and Petr A. Popov and Ming-Yue Lee and Benjamin Stauch and Thomas A. White and Anton Barty and Andrew Aquila and Mark S. Hunter and Mengning Liang and Sébastien …

  35. Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser

    0.0 out of 5 stars 

    30 Nov 2012 | BioXFEL Publications | Contributor(s): L. Redecke, K. Nass, D. P. DePonte, T. A. White, D. Rehders, A. Barty, F. Stellato, M. Liang, T. R. M. Barends, S. Boutet, G. J. Williams, M. Messerschmidt, M. M. Seibert, A. Aquila, D. Arnlund, S. Bajt, T. Barth, M. J. Bogan, C. Caleman, T.-C. Chao, R. B. Doak, H. Fleckenstein, M. Frank, R. Fromme, L. Galli, I. Grotjohann, M. S. Hunter, L. C. Johansson, S. Kassemeyer, G. Katona, R. A. Kirian, R. Koopmann, C. Kupitz, L. Lomb, A. V. Martin, S. Mogk, R. Neutze, R. L. Shoeman, J. Steinbrener, N. Timneanu, D. Wang, U. Weierstall, N. A. Zatsepin, J. C. H. Spence, P. Fromme, I. Schlichting, M. Duszenko, C. Betzel, H. N. Chapman

    http://dx.doi.org/10.1126/science.1229663 journal-article Redecke, L. et al., 2013. Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser. Science, 339(6116), pp.227–230. Available at: http://dx.doi.org/10.1126/science.1229663. L. Redecke and K. Nass …

  36. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

    0.0 out of 5 stars 

    16 Aug 2021 | BioXFEL Publications | Contributor(s): Serdar Durdagi, Çağdaş Dağ, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Fatma Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan Kaushylal Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan Demirci

    http://dx.doi.org/10.1016/j.str.2021.07.007 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Durdagi, S. et al., 2021. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing. Structure. …

  37. Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

    0.0 out of 5 stars 

    10 Sep 2020 | BioXFEL Publications | Contributor(s): Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan Kaushylal Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan Demirci

    http://dx.doi.org/10.1101/2020.09.09.287987 AbstractThe COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) …

  38. Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales

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    18 Aug 2020 | BioXFEL Publications | Contributor(s): David P. Klebl, Molly S.C. Gravett, Dimitrios Kontziampasis, David J. Wright, Robin S. Bon, Diana Monteiro, Martin Trebbin, Frank Sobott, Howard D. White, Michele C. Darrow, Rebecca F. Thompson, Stephen P. Muench

    http://dx.doi.org/10.1016/j.str.2020.07.018 journal-article Klebl, D.P. et al., 2020. Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales. Structure, 28(11), pp.1238–1248.e4. Available at: http://dx.doi.org/10.1016/j.str.2020.07.018. David P. Klebl …

  39. Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme's Conformational Freedom and Disorder

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    22 May 2015 | BioXFEL Publications | Contributor(s): Eynat Dellus-Gur, Mikael Elias, Emilia Caselli, Fabio Prati, Merijn L.M. Salverda, J. Arjan G.M. De Visser, James Fraser, Dan S. Tawfik

    journal-article http://dx.doi.org/10.1016/j.jmb.2015.05.011 Dellus-Gur, E. et al., 2015. Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme’s Conformational Freedom and Disorder. Journal of Molecular Biology, 427(14), pp.2396–2409. Available at: …

  40. New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering

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    14 Nov 2017 | BioXFEL Publications | Contributor(s): Daniel A Keedy, Zachary B Hill, Justin T Biel, Emily Kang, T. Justin Rettenmaier, Jose Brandao-Neto, Nicholas M Pearce, Frank Von Delft, James A. Wells, James Fraser

    http://dx.doi.org/10.1101/218966 Allostery is an inherent feature of proteins and provides alternative routes to regulating function. Small-molecule allosteric inhibitors are often desirable; however, it remains challenging to identify surface sites in proteins which can bind small molecules and …

  41. NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins

    0.0 out of 5 stars 

    21 May 2015 | BioXFEL Publications | Contributor(s): James D Zook, Gina Mo, Nicholas J. Sisco, Felicia M. Craciunescu, Debra T. Hansen, Bobby Baravati, Brian R. Cherry, Kathryn Sykes, Rebekka Wachter, Wade D. Van Horn, Petra Fromme

    http://dx.doi.org/10.1016/j.str.2015.03.025 James Zook and Gina Mo and Nicholas J. Sisco and Felicia M. Craciunescu and Debra T. Hansen and Bobby Baravati and Brian R. Cherry and Kathryn Sykes and Rebekka Wachter and Wade D. Van Horn and Petra Fromme Zook, J. et al., 2015. NMR Structure of …

  42. Non-thermal damage to lead tungstate induced by intense short-wavelength laser radiation (Conference Presentation)

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    21 Jun 2017 | BioXFEL Publications | Contributor(s): Vojtech Vozda, Pavel Boháček, Tomáš Burian, Jaromir Chalupský, Vera Hájková, Libor Juha, Ludek Vyšín, Jérôme Gaudin, Philip A. Heimann, Stefan Hau-Riege, Marek Jurek, Dorota Klinger, Jacek Krzywinski, Marc Messerschmidt, Stefan P. Moeller, Robert Nagler, Jerzy B. Pelka, Michael Rowen, William F. Schlotter, Michele L. Swiggers, Harald Sinn, Ryszard Sobierajski, Kai Tiedtke, Sven Toleikis, Thomas Tschentscher, Joshua J. Turner, Hubertus Wabnitz, Art J. Nelson, Maria V. Kozlova, Sam M. Vinko, Thomas Whitcher, Thomas Dzelzainis, Oldrich Renner, Karel Saksl, Roland R. Fäustlin, Ali R. Khorsand, Marta Fajardo, Bianca S. Iwan, Jakob Andreasson, Janos Hajdu, Nicusor Timneanu, Justin S. Wark, David Riley, Richard W. Lee, Mitsuru Nagasono, Makina Yabashi

    http://dx.doi.org/10.1117/12.2270944 proceedings-article Vozda, V. et al., 2017. Non-thermal damage to lead tungstate induced by intense short-wavelength laser radiation (Conference Presentation) L. Juha, S. Bajt, & R. Soufli, eds. Damage to VUV, EUV, and X-ray Optics VI. Available at: …

  43. Nonlinear Optical Imaging of Integral Membrane Protein Crystals in Lipidic Mesophases

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    21 Dec 2009 | BioXFEL Publications | Contributor(s): David J. Kissick, Ellen J. Gualtieri, Garth J. Simpson, Vadim Cherezov

    http://dx.doi.org/10.1021/ac902139w journal-article Kissick, D.J. et al., 2010. Nonlinear Optical Imaging of Integral Membrane Protein Crystals in Lipidic Mesophases. Analytical Chemistry, 82(2), pp.491–497. Available at: http://dx.doi.org/10.1021/ac902139w. David J. Kissick and Ellen J. …

  44. Nonlinear X-ray Compton Scattering

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

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

  45. Nucleation and Growth of Membrane Protein CrystalsIn Meso—A Fluorescence Microscopy Study

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    02 Nov 2015 | BioXFEL Publications | Contributor(s): Andrey Bogorodskiy, Fedor Frolov, Alexey Mishin, Ekaterina Round, Vitaly Polovinkin, Vadim Cherezov, Valentin Gordeliy, Georg Büldt, Thomas Gensch, Valentin Borshchevskiy

    journal-article http://dx.doi.org/10.1021/acs.cgd.5b01061 Bogorodskiy, A. et al., 2015. Nucleation and Growth of Membrane Protein CrystalsIn Meso—A Fluorescence Microscopy Study. Crystal Growth & Design, 15(12), pp.5656–5660. Available at: http://dx.doi.org/10.1021/acs.cgd.5b01061. Andrey …

  46. Numerical modeling reveals improved organelle separation for dielectrophoretic ratchet migration

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    25 Aug 2023 | BioXFEL Publications | Contributor(s): Domin Koh, Mukul Sonker, Edgar A. Arriaga, Alexandra Ros

    http://dx.doi.org/10.1002/elps.202300091 AbstractOrganelle size varies with normal and abnormal cell function. Thus, size‐based particle separation techniques are key to assessing the properties of organelle subpopulations differing in size. Recently, insulator‐based dielectrophoresis (iDEP) …

  47. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

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    08 Sep 2021 | BioXFEL Publications | Contributor(s): Suraj Pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara Zielinski, Sasa Bajt, Salah Awel, Katarina Doerner, Matthias Frank, Luca Gelisio, Rebecca Jeanne Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell Miller, Grant Mills, Garrett Charles Nelson, Jose L. Olmos, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John Spence, Peter Schwander, Anton Barty, Henry Chapman, Petra Fromme, Adrian P. Mancuso, George Phillips, Richard Bean, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1107/s2052252521008125 Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source …

  48. Observations of phase changes in monoolein during high viscous injection

    0.0 out of 5 stars 

    21 Mar 2022 | BioXFEL Publications | Contributor(s): Daniel J. Wells, Peter Berntsen, Eugeniu Balaur, Cameron M. Kewish, Patrick Adams, Andrew Aquila, Jack Binns, Sébastien Boutet, Hayden Broomhall, Carl Caleman, Andrew Christofferson, Charlotte E. Conn, Caroline Dahlqvist, Leonie Flueckiger, Francisco Gian Roque, Tamar L. Greaves, Majid Hejazian, Mark S. Hunter, Marjan Hadian Jazi, H. Olof Jönsson, Sachini Kadaoluwa Pathirannahalage, Richard Kirian, Alex Kozlov, Ruslan P. Kurta, Hugh Marman, Derek Mendez, Andrew Morgan, Keith Nugent, Dominik Oberthuer, Harry Quiney, Juliane Reinhardt, Saumitra Saha, Jonas A. Sellberg, Raymond Sierra, Max Oliver Wiedorn, Brian Abbey, Andrew V. Martin, Connie Darmanin

    http://dx.doi.org/10.1107/s1600577522001862 Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and …

  49. OleD Loki as a Catalyst for Tertiary Amine and Hydroxamate Glycosylation

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    09 Jan 2017 | BioXFEL Publications | Contributor(s): Ryan R. Hughes, Khaled A. Shaaban, Jianjun Zhang, Hongnan Cao, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1002/cbic.201600676 journal-article Hughes, R.R. et al., 2017. OleD Loki as a Catalyst for Tertiary Amine and Hydroxamate Glycosylation. ChemBioChem, 18(4), pp.363–367. Available at: http://dx.doi.org/10.1002/cbic.201600676. Ryan R. Hughes and Khaled A. Shaaban and Jianjun …

  50. OnDA: online data analysis and feedback for serial X-ray imaging

    0.0 out of 5 stars 

    24 May 2016 | BioXFEL Publications | Contributor(s): Valerio Mariani, Andrew Morgan, Chun Hong Yoon, Thomas J. Lane, Thomas A. White, Christopher O'Grady, Manuela Kuhn, Steve Aplin, Jason Koglin, Anton Barty, Henry Chapman

    This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments:OnDA(online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These …

  51. Ondrej Krivanek's early scientific research

    0.0 out of 5 stars 

    01 Mar 2017 | BioXFEL Publications | Contributor(s): John Spence

    http://dx.doi.org/10.1016/j.ultramic.2016.12.006 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Spence, J.C.H., 2017. Ondrej Krivanek’s early scientific research. Ultramicroscopy, 180, pp.8–13. Available at: http://dx.doi.org/10.1016/j.ultramic.2016.12.006. John C.H. Spence

  52. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites

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    28 May 2015 | BioXFEL Publications | Contributor(s): Marcus Fischer, Brian K. Shoichet, James Fraser

    http://dx.doi.org/10.1002/cbic.201500196 Marcus Fischer and Brian K. Shoichet and James S. Fraser Fischer, M., Shoichet, B.K. & Fraser, J.S., 2015. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. ChemBioChem, 16(11), pp.1560–1564. Available …

  53. One dimensional focusing with high numerical aperture multilayer Laue lens

    0.0 out of 5 stars 

    28 Jan 2016 | BioXFEL Publications | Contributor(s): Saša Bajt, Mauro Prasciolu, Andrew J. Morgan, Henry Chapman, Jacek Krzywinski, Andrzej Andrejczuk

    http://dx.doi.org/10.1063/1.4937543 Saša Bajt and Mauro Prasciolu and Andrew J. Morgan and Henry N. Chapman and Jacek Krzywinski and Andrzej Andrejczuk Bajt, S. et al., 2016. One dimensional focusing with high numerical aperture multilayer Laue lens. Available at: …

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

    0.0 out of 5 stars 

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

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

  55. Open data set of live cyanobacterial cells imaged using an X-ray laser

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    29 Jul 2016 | BioXFEL Publications | Contributor(s): Gijs Van Der Schot, Martin Svenda, Filipe R.N.C. Maia, Max F. Hantke, Daniel P. DePonte, M. Marvin Seibert, Andrew Aquila, Joachim Schulz, Richard Kirian, Mengning Liang, Francesco Stellato, Sadia Bari, Bianca Iwan, Jakob Andreasson, Nicusor Timneanu, Johan Bielecki, Daniel Westphal, Francisca Nunes De Almeida, Duško Odić, Dirk Hasse, Gunilla H. Carlsson, Daniel S.D. Larsson, Anton Barty, Andrew V. Martin, Sebastian Schorb, Christoph Bostedt, John D. Bozek, Sebastian Carron, Ken Ferguson, Daniel Rolles, Artem Rudenko, Sascha W. Epp, Lutz Foucar, Benedikt Rudek, Benjamin Erk, Robert Hartmann, Nils Kimmel, Peter Holl, Lars Englert, N. Duane Loh, Henry Chapman, Inger Andersson, Janos Hajdu, Tomas Ekeberg

    http://dx.doi.org/10.1038/sdata.2016.58 Gijs van der Schot and Martin Svenda and Filipe R.N.C. Maia and Max F. Hantke and Daniel P. DePonte and M. Marvin Seibert and Andrew Aquila and Joachim Schulz and Richard A. Kirian and Mengning Liang and Francesco Stellato and Sadia Bari and Bianca Iwan and …

  56. Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

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    06 Jul 2016 | BioXFEL Publications | Contributor(s): Aleksander V. Drozdetski, Igor S. Tolokh, Lois Pollack, Nathan Baker, Alexey V. Onufriev

    http://dx.doi.org/10.1103/physrevlett.117.028101 journal-article Drozdetski, A.V. et al., 2016. Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA. Physical Review Letters, 117(2). Available at: http://dx.doi.org/10.1103/physrevlett.117.028101. Aleksander V. Drozdetski and …

  57. Optical Cryoimaging Reveals a Heterogeneous Distribution of Mitochondrial Redox State in ex vivo Guinea Pig Hearts and its Alteration during Ischemia and Reperfusion

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    15 Jun 2016 | BioXFEL Publications | Contributor(s): Mahsa Ranji, Mohammad M. Motlagh, Fahimeh Salehpor, Reyhaneh Sepehr, James S. Heisner, Ranjan K. Dash, Amadou K. S. Camara

    journal-article http://dx.doi.org/10.1109/jtehm.2016.2570219 Ranji, M. et al., 2016. Optical Cryoimaging Reveals a Heterogeneous Distribution of Mitochondrial Redox State in ex vivo Guinea Pig Hearts and its Alteration during Ischemia and Reperfusion. IEEE Journal of Translational Engineering in …

  58. Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging

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    22 Apr 2022 | BioXFEL Publications | Contributor(s): Salah Awel, Sebastian Lavin-Varela, Nils Roth, Daniel A. Horke, Andrei V. Rode, Richard Kirian, Jochen Küpper, Henry Chapman

    http://dx.doi.org/10.1103/physrevapplied.17.044044 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Awel, S., Lavin-Varela, S., Roth, N., Horke, D. A., Rode, A. V., Kirian, R. A., Küpper, J., & Chapman, H. N. (2022). Optical Funnel to Guide and Focus Virus Particles for X-Ray …

  59. Optical measurements of long-range protein vibrations

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

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

  60. Optically Induced Forces Imposed in an Optical Funnel on a Stream of Particles in Air or Vacuum

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    11 Dec 2015 | BioXFEL Publications | Contributor(s): Niko Eckerskorn, Richard Bowman, Richard Kirian, Salah Awel, Max Oliver Wiedorn, Jochen Küpper, Miles J. Padgett, Henry Chapman, Andrei V. Rode

    http://dx.doi.org/10.1103/physrevapplied.4.064001 Niko Eckerskorn and Richard Bowman and Richard A. Kirian and Salah Awel and Max Wiedorn and Jochen Küpper and Miles J. Padgett and Henry N. Chapman and Andrei V. Rode Eckerskorn, N. et al., 2015. Optically Induced Forces Imposed in an Optical …

  61. Optimal Pulse Processing, Pile-Up Decomposition, and Applications of Silicon Drift Detectors at LCLS

    0.0 out of 5 stars 

    11 Oct 2017 | BioXFEL Publications | Contributor(s): G. Blaj, C. J. Kenney, A. Dragone, G. Carini, S. Herrmann, P. Hart, A. Tomada, J. Koglin, G. Haller, S. Boutet, M. Messerschmidt, G. Williams, M. Chollet, G. Dakovski, S. Nelson, J. Pines, S. Song, J. Thayer

    http://dx.doi.org/10.1109/tns.2017.2762281 journal-article Blaj, G. et al., 2017. Optimal Pulse Processing, Pile-Up Decomposition, and Applications of Silicon Drift Detectors at LCLS. IEEE Transactions on Nuclear Science, 64(11), pp.2854–2868. Available at: …

  62. Optimizing crystallization hits - small to large and large to small

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    14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft

    Joe Luft describes methods for optimizing initial results from crystallization screening trials for both macro and nanocrystals.

  63. ORACLE reveals a bright future to fight bacteria

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    15 Apr 2021 | BioXFEL Publications | Contributor(s): Willow Coyote-Maestas, James Fraser

    http://dx.doi.org/10.7554/elife.68277 A new way to alter the genome of bacteriophages helps produce large libraries of variants, allowing these bacteria-killing viruses to be designed to target species harmful to human health. journal-article Coyote-Maestas, W., & Fraser, J. S. (2021). ORACLE …

  64. Orientation and analysis of XFEL serial diffraction patterns from fibrous molecular assemblies

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    05 Jul 2018 | BioXFEL Publications | Contributor(s): David H. Wojtas, Kartik Ayyer, Mengning Liang, Estelle Mossou, Carolin Seuring, V. Trevor Forsyth, Henry Chapman, Rick P. Millane

    http://dx.doi.org/10.1109/ivcnz.2017.8402508 proceedings-article Wojtas, D.H. et al., 2017. Orientation and analysis of XFEL serial diffraction patterns from fibrous molecular assemblies. 2017 International Conference on Image and Vision Computing New Zealand (IVCNZ). Available at: …

  65. Outrunning damage: Electrons vs X-rays—timescales and mechanisms

    0.0 out of 5 stars 

    01 Jun 2017 | BioXFEL Publications | Contributor(s): John Spence

    http://dx.doi.org/10.1063/1.4984606 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Spence, J.C.H., 2017. Outrunning damage: Electrons vs X-rays—timescales and mechanisms. Structural Dynamics, 4(4), p.044027. Available at: http://dx.doi.org/10.1063/1.4984606. John C. …

  66. Overview of Serial Femtosecond Crystallography

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    14 Oct 2015 | Teaching Materials | Contributor(s): Petra Fromme

    Dr. Petra Fromme discusses an introductory overview to the field of serial crystallography and recent results showing the potential power of the technique.

  67. 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, …

  68. PEGylated Serp-1 Markedly Reduces Pristane-Induced Experimental Diffuse Alveolar Hemorrhage, Altering uPAR Distribution, and Macrophage Invasion

    0.0 out of 5 stars 

    18 Feb 2021 | BioXFEL Publications | Contributor(s): Qiuyun Guo, Jordan R. Yaron, John W. Wallen, Kyle F. Browder, Ryan Boyd, Tien L. Olson, Michelle Burgin, Peaches Ulrich, Emily Aliskevich, Lauren N. Schutz, Petra Fromme, Liqiang Zhang, Alexandra R. Lucas

    http://dx.doi.org/10.3389/fcvm.2021.633212 Diffuse alveolar hemorrhage (DAH) is one of the most serious clinical complications of systemic lupus erythematosus (SLE). The prevalence of DAH is reported to range from 1 to 5%, but while DAH is considered a rare complication there is a reported 50–80% …

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

    0.0 out of 5 stars 

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

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

  70. Performance of silicon drift detectors at LCLS

    0.0 out of 5 stars 

    25 Oct 2017 | BioXFEL Publications | Contributor(s): G. Blaj, C. J. Kenney, S. Boutet, G. Carini, M. Chollet, G. Dakovski, G. Haller, P. Hart, S. Herrmann, J. Koglin, M. Messerschmidt, S. Nelson, J. Pines, S. Song, J. Thayer, A. Tomada, G. Williams

    http://dx.doi.org/10.1109/nssmic.2016.8069827 proceedings-article Blaj, G. et al., 2016. Performance of silicon drift detectors at LCLS. 2016 IEEE Nuclear Science Symposium, Medical Imaging Conference and Room-Temperature Semiconductor Detector Workshop (NSS/MIC/RTSD). Available at: …

  71. Peripheral Blood Biomarkers Associated With Toxicity and Treatment Characteristics After 131 I- Metaiodobenzylguanidine Therapy in Patients With Neuroblastoma

    0.0 out of 5 stars 

    15 May 2017 | BioXFEL Publications | Contributor(s): Kevin Campbell, Erin E. Karski, Aleksandra Olow, David A. Edmondson, Ayano C. Kohlgruber, Matthew Coleman, Daphne A. Haas-Kogan, Katherine K. Matthay, Steven G. DuBois

    http://dx.doi.org/10.1016/j.ijrobp.2017.05.008 journal-article Campbell, K. et al., 2017. Peripheral Blood Biomarkers Associated With Toxicity and Treatment Characteristics After 131 I- Metaiodobenzylguanidine Therapy in Patients With Neuroblastoma. International Journal of Radiation …

  72. Phase retrieval for randomly terminated finite crystals

    0.0 out of 5 stars 

    05 Jan 2016 | BioXFEL Publications | Contributor(s): Joe Chen, Rick A. Kirian, Richard J. Bean, Kenneth R. Beyerlein, Miriam Barthelmess, Chun Hong Yoon, Fenglin Wang, Flavio Capotondi, Emanuele Pedersoli, Anton Barty, Henry Chapman, Philip J. Bones, Romain D. Arnal, Rick P. Millane, John Spence

    http://dx.doi.org/10.1107/s2053273315099714 Joe P. J. Chen and Rick 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 and Philip J. Bones and Romain D. …

  73. Phase retrieval in the presence of multiplicative noise

    0.0 out of 5 stars 

    06 Sep 2017 | BioXFEL Publications | Contributor(s): Joe Chen, Richard Kirian

    http://dx.doi.org/10.1117/12.2275182 proceedings-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chen, J.P.J. & Kirian, R.A., 2017. Phase retrieval in the presence of multiplicative noise J. J. Dolne & R. P. Millane, eds. Unconventional and Indirect Imaging, Image Reconstruction, and …

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

    0.0 out of 5 stars 

    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, …

  75. Phase-retrieval algorithms for direct phasing of coherent nanocrystal diffraction

    0.0 out of 5 stars 

    19 Dec 2017 | BioXFEL Publications | Contributor(s): Joe Chen, Richard Kirian

    http://dx.doi.org/10.1107/s0108767317097653 journal-article Chen, J.P.J. & Kirian, R.A., 2017. Phase-retrieval algorithms for direct phasing of coherent nanocrystal diffraction. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a239–a239. Available at: …

  76. Phasing coherently illuminated nanocrystals bounded by partial unit cells

    5.0 out of 5 stars 

    31 Dec 2012 | Publications | Contributor(s): R. Kirian, R. Bean, K. Beyerlein, O. Yevanof, T. White, A. Barty, Henry Chapman

    With the use of highly coherent femtosecond X-ray pulses from a free-electron laser, it is possible to record protein nanocrystal diffraction patterns with far more information than is present in conventional crystallographic diffraction data. It has been suggested that diffraction phases may be …

  77. Phasing coherently illuminated nanocrystals bounded by partial unit cells

    0.0 out of 5 stars 

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

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

  78. Phasing Serial Crystallography Data

    0.0 out of 5 stars 

    27 Dec 2018 | BioXFEL Publications | Contributor(s): Richard Kirian, Joe Chen, John Spence

    http://dx.doi.org/10.1007/978-3-030-00551-1_8 book-chapter NSF-STC Biology with X-ray Lasers (NSF-1231306) Kirian, R.A., Chen, J.P.J. & Spence, J.C.H., 2018. Phasing Serial Crystallography Data. X-ray Free Electron Lasers, pp.235–252. Available at: http://dx.doi.org/10.1007/978-3-030-00551-1_8. …

  79. Photocycle Populations with Femtosecond Excitation of Crystalline Photoactive Yellow Protein

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    01 May 2016 | BioXFEL Publications | Contributor(s): Christopher D.M. Hutchison, Marius Kaucikas, Jason Tenboer, Christopher Kupitz, Keith Moffat, Marius Schmidt, Jasper J. Van Thor

    http://dx.doi.org/10.1016/j.cplett.2016.04.087 Christopher D.M. Hutchison and Marius Kaucikas and Jason Tenboer and Christopher Kupitz and Keith Moffat and Marius Schmidt and Jasper J. van Thor Hutchison, C.D.M. et al., 2016. Photocycle populations with femtosecond excitation of crystalline …

  80. Photoreversible interconversion of a phytochrome photosensory module in the crystalline state

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    18 Dec 2019 | BioXFEL Publications | Contributor(s): E. Sethe Burgie, Jonathan Clinger, Mitchell Miller, Aaron S. Brewster, Pierre Aller, Agata Butryn, Franklin D. Fuller, Sheraz Gul, Iris Diane Young, Cindy C. Pham, In-Sik Kim, Asmit Bhowmick, Lee J. O’Riordan, Kyle D. Sutherlin, Joshua V. Heinemann, Alexander Batyuk, Roberto Alonso-Mori, Mark S. Hunter, Jason E. Koglin, Junko Yano, Vittal K. Yachandra, Nicholas K. Sauter, Aina E. Cohen, Jan Kern, Allen M. Orville, George Phillips, Richard D. Vierstra

    http://dx.doi.org/10.1073/pnas.1912041116 A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within …

  81. Picosecond to microsecond TR-XAS: intermediates in the photolysis of methylcobalamin

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    19 Dec 2017 | BioXFEL Publications | Contributor(s): GANESH SUBRAMANIAN, Gerdenis Kodis, Andrew Chizmeshya, Qingyu Kong, Xiaoyi Zhang, Uwe Weierstall, John Spence

    http://dx.doi.org/10.1107/s2053273317084455 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Subramanian, G. et al., 2017. Picosecond to microsecond TR-XAS: intermediates in the photolysis of methylcobalamin. Acta Crystallographica Section A Foundations and Advances, 73(a2), …

  82. Pink-beam serial crystallography

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    30 Oct 2017 | BioXFEL Publications | Contributor(s): A. Meents, M. O. Wiedorn, V. Srajer, R. Henning, I. Sarrou, J. Bergtholdt, M. Barthelmess, P. Y. A. Reinke, D. Dierksmeyer, A. Tolstikova, S. Schaible, M. Messerschmidt, C. M. Ogata, D. J. Kissick, M. H. Taft, D. J. Manstein, J. Lieske, D. Oberthuer, R. F. Fischetti, H. N. Chapman

    http://dx.doi.org/10.1038/s41467-017-01417-3 journal-article Meents, A. et al., 2017. Pink-beam serial crystallography. Nature Communications, 8(1). Available at: http://dx.doi.org/10.1038/s41467-017-01417-3. A. Meents and M. O. Wiedorn and V. Srajer and R. Henning and I. Sarrou and J. …

  83. PNA-Peptide Assembly in a 3D DNA Nanocage at Room Temperature

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    25 Mar 2013 | BioXFEL Publications | Contributor(s): Justin D. Flory, Sandip Shinde, Su Lin, Yan Liu, Hao Yan, Giovanna Ghirlanda, Petra Fromme

    http://dx.doi.org/10.1021/ja400762c journal-article Flory, J.D. et al., 2013. PNA-Peptide Assembly in a 3D DNA Nanocage at Room Temperature. Journal of the American Chemical Society, 135(18), pp.6985–6993. Available at: http://dx.doi.org/10.1021/ja400762c. Justin D. Flory and Sandip Shinde and …

  84. Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap

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    16 Nov 2015 | BioXFEL Publications | Contributor(s): Lin Gan, Fernanda Camacho-Alanis, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.5b02524 Lin Gan and Fernanda Camacho-Alanis and Alexandra Ros Gan, L., Camacho-Alanis, F. & Ros, A., 2015. Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap. Anal. Chem., 87(24), …

  85. Polo: an open-source graphical user interface for crystallization screening

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    19 Feb 2021 | BioXFEL Publications | Contributor(s): Ethan T Holleman, Erica Duguid, Lisa J. Keefe, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s1600576721000108 Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at …

  86. Polyclonal Antibody Production for Membrane Proteins via Genetic Immunization

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    24 Feb 2016 | BioXFEL Publications | Contributor(s): Debra T. Hansen, Mark D. Robida, Felicia M. Craciunescu, Andrey V. Loskutov, Katerina Dörner, John-Charles Rodenberry, Xiao Wang, Tien L. Olson, Hetal Patel, Petra Fromme, Kathryn F. Sykes

    http://dx.doi.org/10.1038/srep21925 Debra T. Hansen and Mark D. Robida and Felicia M. Craciunescu and Andrey V. Loskutov and Katerina Dörner and John-Charles Rodenberry and Xiao Wang and Tien L. Olson and Hetal Patel and Petra Fromme and Kathryn F. Sykes Hansen, D.T. et al., 2016. Polyclonal …

  87. Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: Beyond the wormlike chain model

    0.0 out of 5 stars 

    20 Apr 2013 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, Julie L. Sutton, Huimin Chen, Suzette A. Pabit, Serdal Kirmizialtin, Ron Elber, Lois Pollack

    http://dx.doi.org/10.1002/bip.22265 journal-article Meisburger, S.P. et al., 2013. Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: Beyond the wormlike chain model. Biopolymers, p.n/a–n/a. Available at: http://dx.doi.org/10.1002/bip.22265. Steve …

  88. Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature

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    13 Mar 2023 | BioXFEL Publications | Contributor(s): Sarthak Saha, Can Özden, Alfred Samkutty, Silvia Russi, Aina Cohen, Margaret M. Stratton, Sarah Perry

    http://dx.doi.org/10.1039/d2lc01194h Here we have reported novel polymeric devices to control fluid flow using surface forces and capillary action to facilitate counter-diffusive, on-chip protein crystallization. journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Saha, S., Özden, C., …

  89. Possibilities for serial femtosecond crystallography sample delivery at future light sourcesa)

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    14 May 2015 | BioXFEL Publications | Contributor(s): L. M. G. Chavas, L. Gumprecht, H. N. Chapman

    http://dx.doi.org/10.1063/1.4921220 L. M. G. Chavas and L. Gumprecht and H. N. Chapman Chavas, L.M.G., Gumprecht, L. & Chapman, H.N., 2015. Possibilities for serial femtosecond crystallography sample delivery at future light sourcesa). Structural Dynamics, 2(4), p.041709. Available at: …

  90. Post-refinement method for snapshot serial crystallography

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    13 Oct 2015 | Teaching Materials

    A post-refinement procedure has been devised for ‘snapshot’ diffraction data consisting entirely of partially recorded reflections, each diffraction pattern from a crystal in an orientation unrelated to the others. Initial estimates of the diffraction geometry are used to calculate initial …

  91. Post-sample aperture for low background diffraction experiments at X-ray free-electron lasers

    0.0 out of 5 stars 

    16 Oct 2017 | BioXFEL Publications | Contributor(s): Max Oliver Wiedorn, Salah Awel, Andrew J. Morgan, Miriam Barthelmess, Richard Bean, Kenneth R. Beyerlein, Leonard M. G. Chavas, Niko Eckerskorn, Holger Fleckenstein, Michael Heymann, Daniel A. Horke, Juraj Knoška, Valerio Mariani, Dominik Oberthür, Nils Roth, Oleksandr Yefanov, Anton Barty, Saša Bajt, Jochen Küpper, Andrei V. Rode, Richard Kirian, Henry Chapman

    http://dx.doi.org/10.1107/s1600577517011961 The success of diffraction experiments from weakly scattering samples strongly depends on achieving an optimal signal-to-noise ratio. This is particularly important in single-particle imaging experiments where diffraction signals are typically very weak …

  92. Poster Template PPT

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    19 Jan 2023 | Downloads | Contributor(s): Nicole Terranova

    …

  93. Practical considerations during processing of serial crystallographic XFEL data

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    29 Aug 2014 | Teaching Materials

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

  94. Practical Considerations for Crystallographic Data Analysis

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    14 Oct 2015 | Teaching Materials | Contributor(s): Tom Grant

    Dr. Thomas Grant explains how crystal quality affects diffraction data and how you can detect and ameliorate problems in crystallographic data.

  95. Practical considerations for the analysis of time-resolved x-ray data

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    16 Aug 2023 | BioXFEL Publications | Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1063/4.0000196 The field of time-resolved macromolecular crystallography has been expanding rapidly after free electron lasers for hard x rays (XFELs) became available. Techniques to collect and process data from XFELs spread to synchrotron light sources. Although time-scales …

  96. 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 …

  97. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    0.0 out of 5 stars 

    27 Jul 2015 | BioXFEL Publications | Contributor(s): Andrew H. Van Benschoten, Pavel V. Afonine, Thomas C. Terwilliger, Michael E. Wall, Colin J. Jackson, Nicholas K. Sauter, Paul D. Adams, Alexandre Urzhumtsev, James Fraser

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible …

  98. Preface for Special Issue on Biology with X-ray Lasers 2

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    17 Aug 2015 | BioXFEL Publications | Contributor(s): Abbas Ourmazd

    journal-article http://dx.doi.org/10.1063/1.4928768 Ourmazd, A., 2015. Preface for Special Issue on Biology with X-ray Lasers 2. Structural Dynamics, 2(4), p.041501. Available at: http://dx.doi.org/10.1063/1.4928768. Abbas Ourmazd

  99. Preparation and Delivery of Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography

    0.0 out of 5 stars 

    16 Feb 2016 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Vadim Cherezov, Wei Liu

    http://dx.doi.org/10.1016/j.bpj.2015.11.383 Andrii Ishchenko and Vadim Cherezov and Wei Liu Ishchenko, A., Cherezov, V. & Liu, W., 2016. Preparation and Delivery of Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography. Biophysical Journal, 110(3), p.59a. Available at: …

  100. Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography

    0.0 out of 5 stars 

    20 Sep 2016 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Vadim Cherezov, Wei Liu

    http://dx.doi.org/10.3791/54463 Andrii Ishchenko and Vadim Cherezov and Wei Liu Ishchenko, A., Cherezov, V. & Liu, W., 2016. Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography. Journal of Visualized Experiments, (115). Available at: …