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When Your Crystals Bite

14 Oct 2015 | Teaching Materials | Contributor(s): George Phillips

Dr. George Phillips describes properties of crystals such as twinning and other defects and how they can adversely affect crystallographic analysis.

Where and how to house big data on small fragments

05 May 2025 | BioXFEL Publications | Contributor(s): Daniel A. Erlanson, Stephen K. Burley, Daren Fearon, James Fraser, Dale Kreitler, Maria Cristina Nonato, Naoki Sakai, Jan Wollenhaupt, Manfred S. Weiss

https://doi.org/10.1038/s41467-025-59233-z journal-article Erlanson, D. A., Burley, S. K., Fearon, D., Fraser, J. S., Kreitler, D., Nonato, M. C., Sakai, N., Wollenhaupt, J., & Weiss, M. S. (2025). Where and how to house big data on small fragments. Nature Communications, 16(1). …

Winning the Battle of Signal vs. Noise

29 Aug 2014 | Teaching Materials

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

WNT5A Inhibits Hepatocyte Proliferation and Concludes β-Catenin Signaling in Liver Regeneration

19 Jun 2015 | BioXFEL Publications | Contributor(s): Jing Yang, Antonella Cusimano, Jappmann K. Monga, Morgan E. Preziosi, Filippo Pullara, Guillermo Calero, Richard Lang, Terry P. Yamaguchi, Kari N. Nejak-Bowen, Satdarshan P. Monga

journal-article http://dx.doi.org/10.1016/j.ajpath.2015.04.021 Yang, J. et al., 2015. WNT5A Inhibits Hepatocyte Proliferation and Concludes β-Catenin Signaling in Liver Regeneration. The American Journal of Pathology, 185(8), pp.2194–2205. Available at: …

workspace

17 Oct 2013 | Tools

workspace

X-ray and UV radiation-damage-induced phasing using synchrotron serial crystallography

06 Apr 2018 | BioXFEL Publications | Contributor(s): Nicolas Foos, Carolin Seuring, Robin Schubert, Anja Burkhardt, Olof Svensson, Alke Meents, Henry Chapman, Max H. Nanao

http://dx.doi.org/10.1107/s2059798318001535 Specific radiation damage can be used to determine phases de novo from macromolecular crystals. This method is known as radiation-damage-induced phasing (RIP). One limitation of the method is that the dose of individual data sets must be minimized, which …

X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7

12 Jun 2012 | BioXFEL Publications | Contributor(s): J.W. Fairman, N. Dautin, D. Wojtowicz, L. Wei, N. Noinaj, T.J. Barnard, E. Udho, A. Finkelstein, T.M. Przytycka, V. Cherezov, S.K. Buchanan

http://dx.doi.org/10.2210/pdb4e1s/pdb component Fairman, J.W. et al., 2012. X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7. Available at: http://dx.doi.org/10.2210/pdb4e1s/pdb. J.W. Fairman and N. Dautin and D. Wojtowicz and L. Wei and N. Noinaj …

X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis

12 Jun 2012 | BioXFEL Publications | Contributor(s): J.W. Fairman, N. Dautin, D. Wojtowicz, L. Wei, N. Noinaj, T.J. Barnard, E. Udho, A. Finkelstein, T.M. Przytycka, V. Cherezov, S.K. Buchanan

http://dx.doi.org/10.2210/pdb4e1t/pdb component Fairman, J.W. et al., 2012. X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis. Available at: http://dx.doi.org/10.2210/pdb4e1t/pdb. J.W. Fairman and N. Dautin and D. Wojtowicz and L. Wei and N. …

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

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

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

X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis

19 Dec 2018 | BioXFEL Publications | Contributor(s): Scott C. Jensen, Brendan Sullivan, Daniel A. Hartzler, Jose Meza Aguilar, Salah Awel, Saša Bajt, Shibom Basu, Richard Bean, Henry Chapman, Chelsie E Conrad, Matthias Frank, Raimund Fromme, Jose M. Martin-Garcia, Thomas D. Grant, Michael Heymann, Mark S. Hunter, Gihan Kaushylal Ketawala, Richard Kirian, Juraj Knoska, Christopher Kupitz, Xuanxuan Li, Mengning Liang, Stella Lisova, Valerio Mariani, Victoria Mazalova, Marc Messerschmidt, Michael Moran, Garrett Charles Nelson, Dominik Oberthür, Alex Schaffer, Raymond G. Sierra, Natalie Vaughn, Uwe Weierstall, Max Oliver Wiedorn, P. Lourdu Xavier, Jay-How Yang, Oleksandr Yefanov, Nadia Zatsepin, Andrew Aquila, Petra Fromme, Sébastien Boutet, Gerald T. Seidler, Yulia Pushkar

http://dx.doi.org/10.1021/acs.jpclett.8b03595 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Jensen, S.C. et al., 2019. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. The …

X-ray focusing with efficient high-NA multilayer Laue lenses

23 Mar 2018 | BioXFEL Publications | Contributor(s): Saša Bajt, Mauro Prasciolu, Holger Fleckenstein, Martin Domaracký, Henry Chapman, Andrew J Morgan, Oleksandr Yefanov, Marc Messerschmidt, Yang Du, Kevin T Murray, Valerio Mariani, Manuela Kuhn, Steven Aplin, Kanupriya Pande, Pablo Villanueva-Perez, Karolina Stachnik, Joe Chen, Andrzej Andrejczuk, Alke Meents, Anja Burkhardt, David Pennicard, Xiaojing Huang, Hanfei Yan, Evgeny Nazaretski, Yong S Chu, Christian E Hamm

http://dx.doi.org/10.1038/lsa.2017.162 journal-article Bajt, S. et al., 2017. X-ray focusing with efficient high-NA multilayer Laue lenses. Light: Science & Applications, 7(3), p.17162. Available at: http://dx.doi.org/10.1038/lsa.2017.162. Saša Bajt and Mauro Prasciolu and Holger Fleckenstein …

X-ray Free Electron Lasers

27 Dec 2018 | BioXFEL Publications

http://dx.doi.org/10.1007/978-3-030-00551-1 book Boutet, S., Fromme, P. & Hunter, M.S. eds., 2018. X-ray Free Electron Lasers. Available at: http://dx.doi.org/10.1007/978-3-030-00551-1.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

11 Apr 2016 | BioXFEL Publications | Contributor(s): X. Edward Zhou, Xiang Gao, Anton Barty, Yanyong Kang, Yuanzheng He, Wei Liu, Andrii Ishchenko, Thomas A. White, Oleksandr Yefanov, Gye Won Han, Qingping Xu, Parker W. De Waal, Kelly M. Suino-Powell, Sébastien Boutet, Garth J. Williams, Meitian Wang, Dianfan Li, Martin Caffrey, Henry Chapman, John Spence, Petra Fromme, Uwe Weierstall, Raymond C. Stevens, Vadim Cherezov, Karsten Melcher, H. Eric Xu

http://dx.doi.org/10.1038/sdata.2016.21 X. Edward Zhou and Xiang Gao and Anton Barty and Yanyong Kang and Yuanzheng He and Wei Liu and Andrii Ishchenko and Thomas A. White and Oleksandr Yefanov and Gye Won Han and Qingping Xu and Parker W. de Waal and Kelly M. Suino-Powell and Sébastien Boutet and …

X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene

09 Sep 2016 | BioXFEL Publications | Contributor(s): Brian Abbey, Ruben A. Dilanian, Connie Darmanin, Rebecca A. Ryan, Corey T. Putkunz, Andrew V. Martin, David Wood, Victor Streltsov, Michael W. M. Jones, Naylyn Gaffney, Felix Hofmann, Garth J. Williams, Sébastien Boutet, Marc Messerschmidt, M. Marvin Seibert, Sophie Williams, Evan Curwood, Eugeniu Balaur, Andrew G. Peele, Keith A. Nugent, Harry M. Quiney

http://dx.doi.org/10.1126/sciadv.1601186 Brian Abbey and Ruben A. Dilanian and Connie Darmanin and Rebecca A. Ryan and Corey T. Putkunz and Andrew V. Martin and David Wood and Victor Streltsov and Michael W. M. Jones and Naylyn Gaffney and Felix Hofmann and Garth J. Williams and Sébastien Boutet …

X-ray lasers and crystallography

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

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

X-Ray Lasers in Biology

24 Apr 2017 | BioXFEL Publications | Contributor(s): John Spence

http://dx.doi.org/10.1016/bs.aiep.2017.01.008 book-chapter NSF-STC Biology with X-ray Lasers (NSF-1231306) Spence, J.C.H., 2017. X-Ray Lasers in Biology. Advances in Imaging and Electron Physics, pp.103–152. Available at: http://dx.doi.org/10.1016/bs.aiep.2017.01.008. John C.H. Spence

X-ray scattering exhibits time-resolved view of rhodopsin activation

10 Feb 2023 | BioXFEL Publications | Contributor(s): C. Swathi K. Menon, Konstantinos Karpos, Thomas D. Grant, Andrey V. Struts, Steven D.E. Fried, Suchithranga M.D.C. Perera, Irina V. Kosheleva, Leslie Salas-Estrada, Alan Grossfield, Petra Fromme, Richard Kirian, Michael F. Brown

http://dx.doi.org/10.1016/j.bpj.2022.11.1170 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Perera, S. M. D. C., Kosheleva, I. V., Salas-Estrada, L., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2023). X-ray scattering exhibits …

X-ray two-photon absorption with high fluence XFEL pulses

07 Sep 2015 | BioXFEL Publications | Contributor(s): J Hoszowska, J Szlachetko, J-Cl Dousse, W Błachucki, Y Kayser, Ch Milne, M Pajek, S Boutet, M Messerschmidt, G Williams, C T Chantler

http://dx.doi.org/10.1088/1742-6596/635/10/102009 J Hoszowska and J Szlachetko and J-Cl Dousse and W Błachucki and Y Kayser and Ch Milne and M Pajek and S Boutet and M Messerschmidt and G Williams and C T Chantler Hoszowska, J. et al., 2015. X-ray two-photon absorption with high fluence XFEL …

X-ray-Based Techniques to Study the Nano–Bio Interface

02 Mar 2021 | BioXFEL Publications | Contributor(s): Carlos Sanchez-Cano, Ramon A. Alvarez-Puebla, John M. Abendroth, Tobias Beck, Robert Blick, Yuan Cao, Frank Caruso, Indranath Chakraborty, Henry Chapman, Chunying Chen, Bruce E. Cohen, Andre L. C. Conceição, David P. Cormode, Daxiang Cui, Kenneth A. Dawson, Gerald Falkenberg, Chunhai Fan, Neus Feliu, Mingyuan Gao, Elisabetta Gargioni, Claus-C. Glüer, Florian Grüner, Moustapha Hassan, Yong Hu, Yalan Huang, Samuel Huber, Nils Huse, Yanan Kang, Ali Khademhosseini, Thomas F. Keller, Christian Körnig, Nicholas A. Kotov, Dorota Koziej, Xing-Jie Liang, Beibei Liu, Sijin Liu, Yang Liu, Ziyao Liu, Luis M. Liz-Marzán, Xiaowei Ma, Andres Machicote, Wolfgang Maison, Adrian P. Mancuso, Saad Megahed, Bert Nickel, Ferdinand Otto, Cristina Palencia, Sakura Pascarelli, Arwen Pearson, Oula Peñate-Medina, Bing Qi, Joachim Rädler, Joseph J. Richardson, Axel Rosenhahn, Kai Rothkamm, Michael Rübhausen, Milan K. Sanyal, Raymond E. Schaak, Heinz-Peter Schlemmer, Marius Schmidt, Oliver Schmutzler, Theo Schotten, Florian Schulz, A. K. Sood, Kathryn M. Spiers, Theresa Staufer, Dominik M. Stemer, Andreas Stierle, Xing Sun, Gohar Tsakanova, Paul S. Weiss, Horst Weller, Fabian Westermeier, Ming Xu, Huijie Yan, Yuan Zeng, Ying Zhao, Yuliang Zhao, Dingcheng Zhu, Ying Zhu, Wolfgang J. Parak

http://dx.doi.org/10.1021/acsnano.0c09563 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sanchez-Cano, C. et al., 2021. X-ray-Based Techniques to Study the Nano–Bio Interface. ACS Nano, 15(3), pp.3754–3807. Available at: http://dx.doi.org/10.1021/acsnano.0c09563. Carlos …

XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia

09 Mar 2020 | BioXFEL Publications | Contributor(s): James D Zook, Mrinal Shekhar, Debra Hansen, Chelsie E Conrad, Thomas Grant, Chitrak Gupta, Thomas White, Anton Barty, Shibom Basu, Yun Zhao, Nadia Zatsepin, Andrii Ishchenko, Alex Batyuk, Cornelius Gati, Chufeng Li, Lorenzo Galli, Jesse David Coe, Mark S. Hunter, Meng Liang, Uwe Weierstall, Garret Nelson, Daniel James, Benjamin Stauch, Felicia Craciunescu, Darren Gary Thifault, Wei Liu, Vadim Cherezov, Abhishek Singharoy, Petra Fromme

http://dx.doi.org/10.1016/j.str.2020.02.005 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zook, J. et al., 2020. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure. Available at: …

XFEL data analysis for structural biology

21 Jul 2016 | BioXFEL Publications | Contributor(s): Haiguang Liu, John Spence

http://dx.doi.org/10.1007/s40484-016-0076-z Haiguang Liu and John C. H. Spence Liu, H. & Spence, J.C.H., 2016. XFEL data analysis for structural biology. Quantitative Biology, 4(3), pp.159–176. Available at: http://dx.doi.org/10.1007/s40484-016-0076-z. NSF-STC Biology with X-ray Lasers …

XFEL Game - Windows Download

25 Oct 2016 | Downloads | Contributor(s): fiacre

Windows Version

XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity

24 Apr 2019 | BioXFEL Publications | Contributor(s): Linda C. Johansson, Benjamin Stauch, John D. McCorvy, Gye Won Han, Nilkanth N Patel, Xi-Ping Huang, Alexander Batyuk, Cornelius Gati, Samuel T. Slocum, Chufeng Li, Jessica M. Grandner, Shuming Hao, Reid H. J. Olsen, Alexandra R. Tribo, Sahba Zaare, Lan Zhu, Nadia Zatsepin, Uwe Weierstall, Saïd Yous, Raymond C. Stevens, Wei Liu, Bryan L. Roth, Vsevolod Katritch, Vadim Cherezov

http://dx.doi.org/10.1038/s41586-019-1144-0 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Johansson, L.C. et al., 2019. XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. Nature. Available at: http://dx.doi.org/10.1038/s41586-019-1144-0. …

XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction

19 Dec 2017 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Rahel Woldeyes, Takanori Nakane, Kotaro Koiwai, Ayumi Yamashita, Tomoyuki Tanaka, Toshi Arima, Jun Kobayashi, Tetsuya Masuda, Mamoru Suzuki, Michihiro Sugahara, Rie Tanaka, Eriko Nango, So Iwata, Fumiaki Yumoto, James Fraser, William F. DeGrado

http://dx.doi.org/10.1107/s0108767317099603 journal-article Thomaston, J.L. et al., 2017. XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction. Acta Crystallographica Section A Foundations and Advances, 73(a1), …

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

23 Aug 2017 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Rahel Woldeyes, Takanori Nakane, Ayumi Yamashita, Tomoyuki Tanaka, Kotaro Koiwai, Aaron S. Brewster, Benjamin A. Barad, Yujie Chen, Thomas Lemmin, Monarin Uervirojnangkoorn, Toshi Arima, Jun Kobayashi, Tetsuya Masuda, Mamoru Suzuki, Michihiro Sugahara, Nicholas K. Sauter, Rie Tanaka, Osamu Nureki, Kensuke Tono, Yasumasa Joti, Eriko Nango, So Iwata, Fumiaki Yumoto, James Fraser, William F. DeGrado

http://dx.doi.org/10.1073/pnas.1705624114 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Thomaston, J.L. et al., 2017. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proceedings of the National Academy of …

XFELs for structure and dynamics in biology

10 May 2017 | BioXFEL Publications | Contributor(s): J. C. H. Spence

http://dx.doi.org/10.1107/s2052252517005760 The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are …

XFELs open a new era in structural chemical biology

17 Nov 2015 | BioXFEL Publications | Contributor(s): Petra Fromme

http://dx.doi.org/10.1038/nchembio.1968 Petra Fromme Fromme, P., 2015. XFELs open a new era in structural chemical biology. Nat Chem Biol, 11(12), pp.895–899. Available at: http://dx.doi.org/10.1038/nchembio.1968. NSF-STC Biology with X-ray Lasers (NSF-1231306) journal-article

XRayView

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, …

Zatsepin_IUCr2015_SFX_software.pdf

21 Jul 2015 | PDF

Zatsepin_IUCr2015_SFX_software.pdf