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Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

27 Dec 2016 | BioXFEL Publications | Contributor(s): Yujie Chen, Joshua M. Tokuda, Traci Topping, Steve P. Meisburger, Suzette A. Pabit, Lisa M. Gloss, Lois Pollack

http://dx.doi.org/10.1073/pnas.1611118114 journal-article Chen, Y. et al., 2016. Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. …

https://www.bioxfel.org/resources/1376

Carbamate Insecticides Target Human Melatonin Receptors

27 Dec 2016 | BioXFEL Publications | Contributor(s): Marina Popovska-Gorevski, Margarita L. Dubocovich, Rajendram V. Rajnarayanan

http://dx.doi.org/10.1021/acs.chemrestox.6b00301 journal-article Popovska-Gorevski, M., Dubocovich, M.L. & Rajnarayanan, R.V., 2017. Carbamate Insecticides Target Human Melatonin Receptors. …

https://www.bioxfel.org/resources/1668

Conformational variation of proteins at room temperature is not dominated by radiation damage

21 Dec 2016 | BioXFEL Publications | Contributor(s): Silvia Russi, Ana González, Lillian R. Kenner, Daniel A. Keedy, James Fraser, Henry Van Den Bedem

Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the …

https://www.bioxfel.org/resources/1199

LCLS Beam-time Schedules

20 Dec 2016 | Downloads

All Schedules on LCLS Website LCLS Run 15 Schedule (June 2017 - Nov 2017)LCLS Run 14 Schedule (Aug 2016 - Dec 2016)LCLS Run 13 Schedule (Mar 2016 - Aug 2016)LCLS Run 12 Schedule (Oct 2015 - Mar …

https://www.bioxfel.org/resources/1191

Structural enzymology using X-ray free electron lasers

15 Dec 2016 | BioXFEL Publications | Contributor(s): Christopher Kupitz, Jose L. Olmos, Mark Holl, Lee Tremblay, Kanupriya Pande, Suraj Pandey, Dominik Oberthür, Mark S. Hunter, Mengning Liang, Andrew Aquila, Jason Tenboer, George Douglas Calvey, Andrea Katz, Yujie Chen, Max Oliver Wiedorn, Juraj Knoska, Alke Meents, Valerio Majriani, Tyler Norwood, Ishwor Poudyal, Thomas Grant, Mitchell Miller, Weijun Xu, Aleksandra Tolstikova, Andrew Morgan, Markus Metz, Jose M. Martin-Garcia, James D Zook, Shatabdi Roy-Chowdhury, Jesse David Coe, Nirupa Nagaratnam, Domingo Meza, Raimund Fromme, Shibom Basu, Matthias Frank, Thomas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry Chapman, Nadia Zatsepin, Garrett Charles Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George Phillips, Marius Schmidt

http://dx.doi.org/10.1063/1.4972069 Christopher Kupitz and Jose L. Olmos and Mark Holl and Lee Tremblay and Kanupriya Pande and Suraj Pandey and Dominik Oberthür and Mark Hunter and Mengning Liang …

https://www.bioxfel.org/resources/1210

Visualizing single-stranded nucleic acids in solution

13 Dec 2016 | BioXFEL Publications | Contributor(s): Alex Plumridge, Steve P. Meisburger, Lois Pollack

http://dx.doi.org/10.1093/nar/gkw1297 journal-article Plumridge, A., Meisburger, S.P. & Pollack, L., 2016. Visualizing single-stranded nucleic acids in solution. Nucleic Acids Research, p.gkw1297. …

https://www.bioxfel.org/resources/1369

Continuous Separation of DNA Molecules by Size Using Insulator-Based Dielectrophoresis

12 Dec 2016 | BioXFEL Publications | Contributor(s): Paul V. Jones, Gabriel L. Salmon, Alexandra Ros

journal-article http://dx.doi.org/10.1021/acs.analchem.6b03369 Jones, P.V., Salmon, G.L. & Ros, A., 2017. Continuous Separation of DNA Molecules by Size Using Insulator-Based Dielectrophoresis. …

https://www.bioxfel.org/resources/1263

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

06 Dec 2016 | BioXFEL Publications | Contributor(s): Yi Zheng, Ling Qin, Natalia V. Ortiz Zacarías, Henk De Vries, Gye Won Han, Martin Gustavsson, Marta Dabros, Chunxia Zhao, Robert J. Cherney, Percy Carter, Dean Stamos, Ruben Abagyan, Vadim Cherezov, Raymond C. Stevens, Adriaan P. IJzerman, Laura H. Heitman, Andrew Tebben, Irina Kufareva, Tracy M. Handel

http://dx.doi.org/10.1038/nature20605 journal-article Zheng, Y. et al., 2016. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature, 540(7633), pp.458–461. …

https://www.bioxfel.org/resources/1451

Lecture Series

01 Dec 2016 | Teaching Materials

BioXFEL Lecture Series videos are kept here.

https://www.bioxfel.org/resources/1189

Journal Club Seminars

01 Dec 2016 | Teaching Materials

Videos of all past Journal Clubs 

https://www.bioxfel.org/resources/1188

Editorial overview: Biophysical and molecular biological methods

28 Nov 2016 | BioXFEL Publications | Contributor(s): Petra Fromme, Andrej Sali

http://dx.doi.org/10.1016/j.sbi.2016.11.015 journal-article Fromme, P. & Sali, A., 2016. Editorial overview: Biophysical and molecular biological methods. Current Opinion in Structural Biology, 40, …

https://www.bioxfel.org/resources/1413

Structure of photosystem II and substrate binding at room temperature

18 Nov 2016 | BioXFEL Publications | Contributor(s): Iris Diane Young, Mohamed Ibrahim, Ruchira Chatterjee, Sheraz Gul, Franklin D. Fuller, Sergey Koroidov, Aaron S. Brewster, Rosalie Tran, Roberto Alonso-Mori, Thomas Kroll, Tara Michels-Clark, Hartawan Laksmono, Raymond G. Sierra, Claudiu A. Stan, Rana Hussein, Miao Zhang, Lacey Douthit, Markus Kubin, Casper De Lichtenberg, Long Vo Pham, Håkan Nilsson, Mun Hon Cheah, Dmitriy Shevela, Claudio Saracini, Mackenzie A. Bean, Ina Seuffert, Dimosthenis Sokaras, Tsu-Chien Weng, Ernest Pastor, Clemens Weninger, Thomas Fransson, Louise Lassalle, Philipp Bräuer, Pierre Aller, Peter T. Docker, Babak Andi, Allen M. Orville, James M. Glownia, Silke Nelson, Marcin Sikorski, Diling Zhu, Mark S. Hunter, Thomas J. Lane, Andy Aquila, Jason E. Koglin, Joseph Robinson, Mengning Liang, Sébastien Boutet, Artem Y. Lyubimov, Monarin Uervirojnangkoorn, Nigel W. Moriarty, Dorothee Liebschner, Pavel V. Afonine, David G. Waterman, Gwyndaf Evans, Philippe Wernet, Holger Dobbek, William I. Weis, Axel T. Brunger, Petrus H. Zwart, Paul D. Adams, Athina Zouni, Johannes Messinger, Uwe Bergmann, Nicholas K. Sauter, Jan Kern, Vittal K. Yachandra, Junko Yano

http://dx.doi.org/10.1038/nature20161 Iris D. Young and Mohamed Ibrahim and Ruchira Chatterjee and Sheraz Gul and Franklin D. Fuller and Sergey Koroidov and Aaron S. Brewster and Rosalie Tran and …

https://www.bioxfel.org/resources/1214

Simulations of single-pulse Laue diffraction from proteins with radiation from synchrotron and XFEL sources

15 Nov 2016 | BioXFEL Publications | Contributor(s): Victoria Kabanova, Marius Schmidt, Friedrich Schotte, Marco Cammarata, Michael Wulff

http://dx.doi.org/10.1107/s2053273316097898 journal-article Kabanova, V. et al., 2016. Simulations of single-pulse Laue diffraction from proteins with radiation from synchrotron and XFEL sources. …

https://www.bioxfel.org/resources/1358

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

15 Nov 2016 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Valerie Panneels, Garrett Charles Nelson, Cornelius Gati, Tetsunari Kimura, Christopher Milne, Despina Milathianaki, Minoru Kubo, Wenting Wu, Chelsie E Conrad, Jesse David Coe, Richard Bean, Yun Zhao, Petra Bath, Robert Dods, Rajiv Harimoorthy, Kenneth Beyerlein, Jan Rheinberger, Daniel James, Daniel DePonte, Chufeng Li, Leonardo Sala, Garth Williams, Mark S. Hunter, Jason E. Koglin, Peter Berntsen, Eriko Nango, So Iwata, Henry Chapman, Petra Fromme, Matthias Frank, Rafael Abela, Sébastien Boutet, Anton Barty, Thomas A. White, Uwe Weierstall, John Spence, Richard Neutze, Gebhard F.X. Schertler, Jörg Standfuss

http://dx.doi.org/10.1107/s2053273316099368 Przemyslaw Nogly and Valerie Panneels and Garrett Nelson and Cornelius Gati and Tetsunari Kimura and Christopher Milne and Despina Milathianaki and Minoru …

https://www.bioxfel.org/resources/1205

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

11 Nov 2016 | BioXFEL Publications | Contributor(s): Andrew E. Bruno, Alexei S. Soares, Robin L. Owen, Edward Snell

http://dx.doi.org/10.1107/s160057671601431x Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. …

https://www.bioxfel.org/resources/1359

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

11 Nov 2016 | BioXFEL Publications | Contributor(s): J. R. Stagno, Y. Liu, Y. R. Bhandari, C. E. Conrad, S. Panja, M. Swain, L. Fan, G. Nelson, C. Li, D. R. Wendel, T. A. White, J. D. Coe, M. O. Wiedorn, J. Knoska, D. Oberthuer, R. A. Tuckey, P. Yu, M. Dyba, S. G. Tarasov, U. Weierstall, T. D. Grant, C. D. Schwieters, J. Zhang, A. R. Ferré-D’Amaré, P. Fromme, D. E. Draper, M. Liang, M. S. Hunter, S. Boutet, K. Tan, X. Zuo, X. Ji, A. Barty, N. A. Zatsepin, H. N. Chapman, J. C. H. Spence, S. A. Woodson, Y.-X. Wang

http://dx.doi.org/10.1038/nature20599 J. R. Stagno and Y. Liu and Y. R. Bhandari and C. E. Conrad and S. Panja and M. Swain and L. Fan and G. Nelson and C. Li and D. R. Wendel and T. A. White and J. …

https://www.bioxfel.org/resources/1213

Development of a photophoretic optical guide for femtosecond x-ray diffractive imaging of aerosolized nanoparticles (Conference Presentation)

10 Nov 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Salah Awel, Max Oliver Wiedorn, Daniel Horke, Nils Roth, Niko O. Eckerskorn, Jochen Küpper, Henry Chapman, Andrei V. Rode

http://dx.doi.org/10.1117/12.2239171 Richard A. Kirian and Salah Awel and Max Wiedorn and Daniel Horke and Nils Roth and Niko O. Eckerskorn and Jochen Küpper and Henry N. Chapman and Andrei V. Rode …

https://www.bioxfel.org/resources/1203

4th BioXFEL Conference

04 Nov 2016 | Downloads

…

https://www.bioxfel.org/resources/1186

Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

04 Nov 2016 | BioXFEL Publications | Contributor(s): Mark S. Hunter, Chun Hong Yoon, Hasan Demirci, Raymond G. Sierra, E. Han Dao, Radman Ahmadi, Fulya Aksit, Andrew L. Aquila, Halilibrahim Ciftci, Serge Guillet, Matt J. Hayes, Thomas J. Lane, Meng Liang, Ulf Lundström, Jason E. Koglin, Paul Mgbam, Yashas Rao, Lindsey Zhang, Soichi Wakatsuki, James Holton, Sébastien Boutet

http://dx.doi.org/10.1038/ncomms13388 Mark S. Hunter and Chun Hong Yoon and Hasan DeMirci and Raymond G. Sierra and E. Han Dao and Radman Ahmadi and Fulya Aksit and Andrew L. Aquila and Halilibrahim …

https://www.bioxfel.org/resources/1212

Advanced Transmission Electron Microscopy

25 Oct 2016 | BioXFEL Publications | Contributor(s): Jian Min Zuo, John Spence

http://dx.doi.org/10.1007/978-1-4939-6607-3 book Zuo, J.M. & Spence, J.C.H., 2017. Advanced Transmission Electron Microscopy. Available at: http://dx.doi.org/10.1007/978-1-4939-6607-3. Jian Min …

https://www.bioxfel.org/resources/1458

XFEL Game - Windows Download

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

Windows Version

https://www.bioxfel.org/resources/Game-Windows

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

19 Oct 2016 | BioXFEL Publications | Contributor(s): Petra Edlund, Heikki Takala, Elin Claesson, Léocadie Henry, Robert Dods, Heli Lehtivuori, Matthijs Panman, Kanupriya Pande, Thomas White, Takanori Nakane, Oskar Berntsson, Emil Gustavsson, Petra Båth, Vaibhav Modi, Shatabdi Roy-Chowdhury, James D Zook, Peter Berntsen, Suraj Pandey, Ishwor Poudyal, Jason Tenboer, Christopher Kupitz, Anton Barty, Petra Fromme, Jake D. Koralek, Tomoyuki Tanaka, John Spence, Mengning Liang, Mark S. Hunter, Sebastien Boutet, Eriko Nango, Keith Moffat, Gerrit Groenhof, Janne Ihalainen, Emina A. Stojković, Marius Schmidt, Sebastian Westenhoff

http://dx.doi.org/10.1038/srep35279 Petra Edlund and Heikki Takala and Elin Claesson and Léocadie Henry and Robert Dods and Heli Lehtivuori and Matthijs Panman and Kanupriya Pande and Thomas White …

https://www.bioxfel.org/resources/1244

Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin

19 Oct 2016 | BioXFEL Publications | Contributor(s): Justin T Biel, Michael Thompson, Christian N Cunningham, Jacob E Corn, James Fraser

http://dx.doi.org/10.1101/081646 Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory …

https://www.bioxfel.org/resources/1365

Learned motivation drives circadian physiology in the absence of the master circadian clock

12 Oct 2016 | BioXFEL Publications | Contributor(s): Oliver Rawashdeh, Shannon J. Clough, Randall L. Hudson, Margarita L. Dubocovich

http://dx.doi.org/10.1096/fj.201600926r journal-article Rawashdeh, O. et al., 2017. Learned motivation drives circadian physiology in the absence of the master circadian clock. The FASEB Journal, …

https://www.bioxfel.org/resources/1664

Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex

12 Oct 2016 | BioXFEL Publications | Contributor(s): Artem Y Lyubimov, Monarin Uervirojnangkoorn, Oliver B Zeldin, Qiangjun Zhou, Minglei Zhao, Aaron S Brewster, Tara Michels-Clark, James Holton, Nicholas K Sauter, William I Weis, Axel T Brunger

X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical …

https://www.bioxfel.org/resources/1200

Successful Strategies to Determine High-Resolution Structures of GPCRs

11 Oct 2016 | BioXFEL Publications | Contributor(s): Jin Xiang, Eugene Chun, Chang Liu, Liang Jing, Zina Al-Sahouri, Lan Zhu, Wei Liu

journal-article http://dx.doi.org/10.1016/j.tips.2016.09.009 NSF-STC Biology with X-ray Lasers (NSF-1231306) Xiang, J. et al., 2016. Successful Strategies to Determine High-Resolution Structures of …

https://www.bioxfel.org/resources/1260

Reconstruction of an object from diffraction intensities averaged over multiple object clusters

29 Sep 2016 | BioXFEL Publications | Contributor(s): J P J Chen, R D Arnal, A J Morgan, R J Bean, K R Beyerlein, H N Chapman, P J Bones, R P Millane, R A Kirian

http://dx.doi.org/10.1088/2040-8978/18/11/114003 J P J Chen and R D Arnal and A J Morgan and R J Bean and K R Beyerlein and H N Chapman and P J Bones and R P Millane and R A Kirian Chen, J.P.J. et …

https://www.bioxfel.org/resources/1209

De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure

27 Sep 2016 | BioXFEL Publications | Contributor(s): Jacques-Philippe Colletier, Michael R. Sawaya, Mari Gingery, Jose A. Rodriguez, Duilio Cascio, Aaron S. Brewster, Tara Michels-Clark, Robert H. Hice, Nicolas Coquelle, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, Daniel P. DePonte, Raymond G. Sierra, Hartawan Laksmono, Jason E. Koglin, Mark S. Hunter, Hyun-Woo Park, Monarin Uervirojnangkoorn, Dennis K. Bideshi, Axel T. Brunger, Brian A. Federici, Nicholas K. Sauter, David S. Eisenberg

http://dx.doi.org/10.1038/nature19825 Jacques-Philippe Colletier and Michael R. Sawaya and Mari Gingery and Jose A. Rodriguez and Duilio Cascio and Aaron S. Brewster and Tara Michels-Clark and Robert …

https://www.bioxfel.org/resources/1215

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

26 Sep 2016 | BioXFEL Publications | Contributor(s): Derek Mendez, Herschel Watkins, Shenglan Qiao, Kevin S. Raines, Thomas J. Lane, Gundolf Schenk, Garrett Charles Nelson, GANESH SUBRAMANIAN, Kensuke Tono, Yasumasa Joti, Makina Yabashi, Daniel Ratner, Sebastian Doniach

During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer …

https://www.bioxfel.org/resources/1206

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

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 …

https://www.bioxfel.org/resources/1202

Spectral Hole Burning in Cyanobacterial Photosystem I with P700 in Oxidized and Neutral States

23 Sep 2016 | BioXFEL Publications | Contributor(s): Nicoleta Herascu, Mark S. Hunter, Golia Shafiei, Mehdi Najafi, T. Wade Johnson, Petra Fromme, Valter Zazubovich

http://dx.doi.org/10.1021/acs.jpcb.6b07803 Nicoleta Herascu and Mark S. Hunter and Golia Shafiei and Mehdi Najafi and T. Wade Johnson and Petra Fromme and Valter Zazubovich Herascu, N. et al., 2016. …

https://www.bioxfel.org/resources/1224

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

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 …

https://www.bioxfel.org/resources/1222

Crystallographic Methods of Structural Biology

18 Sep 2016 | Courses | Contributor(s): Robert H Blessing, Edward Snell

The goal of the course is that students acquire sufficient knowledge and understanding of the basic principles of biomolecular crystal structure analysis that they will be able to comfortably, and …

https://www.bioxfel.org/resources/2014-crystallographic-methods-of-structural-biology

Establishing nonlinearity thresholds with ultraintense X-ray pulses

13 Sep 2016 | BioXFEL Publications | Contributor(s): Jakub Szlachetko, Joanna Hoszowska, Jean-Claude Dousse, Maarten Nachtegaal, Wojciech Błachucki, Yves Kayser, Jacinto Sà, Marc Messerschmidt, Sebastien Boutet, Garth J. Williams, Christian David, Grigory Smolentsev, Jeroen A. Van Bokhoven, Bruce D. Patterson, Thomas J. Penfold, Gregor Knopp, Marek Pajek, Rafael Abela, Christopher J. Milne

http://dx.doi.org/10.1038/srep33292 Jakub Szlachetko and Joanna Hoszowska and Jean-Claude Dousse and Maarten Nachtegaal and Wojciech Błachucki and Yves Kayser and Jacinto Sà and Marc Messerschmidt …

https://www.bioxfel.org/resources/1219

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 …

https://www.bioxfel.org/resources/1220

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex

09 Sep 2016 | BioXFEL Publications | Contributor(s): Philip J. Robinson, Michael J. Trnka, David Bushnell, Ralph E. Davis, Pierre-Jean Mattei, Alma L. Burlingame, Roger Kornberg

http://dx.doi.org/10.1016/j.cell.2016.08.050 Philip J. Robinson and Michael J. Trnka and David A. Bushnell and Ralph E. Davis and Pierre-Jean Mattei and Alma L. Burlingame and Roger D. Kornberg …

https://www.bioxfel.org/resources/1221

Ghost imaging with x rays

07 Sep 2016 | BioXFEL Publications | Contributor(s): Dilano Saldin

journal-article http://dx.doi.org/10.1103/physics.9.103 Saldin, D., 2016. Ghost imaging with x rays. Physics, 9. Available at: http://dx.doi.org/10.1103/physics.9.103. Dilano Saldin

https://www.bioxfel.org/resources/1294

Frontiers of free-electron laser science II

06 Sep 2016 | BioXFEL Publications | Contributor(s): Roger Falcone, Michael Dunne, Henry Chapman, Makina Yabashi, Kiyoshi Ueda

http://dx.doi.org/10.1088/0953-4075/49/18/180201 journal-article Falcone, R. et al., 2016. Frontiers of free-electron laser science II. Journal of Physics B: Atomic, Molecular and Optical Physics, …

https://www.bioxfel.org/resources/1472

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

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 …

https://www.bioxfel.org/resources/1382

The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction

29 Aug 2016 | BioXFEL Publications | Contributor(s): Ying Wu, Xiaohong Zhou, Christopher Barnes, Maria DeLucia, Aina E Cohen, Angela M Gronenborn, Jinwoo Ahn, Guillermo Calero

journal-article http://dx.doi.org/10.1038/nsmb.3284 NSF-STC Biology with X-ray Lasers (NSF-1231306) Wu, Y. et al., 2016. The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers …

https://www.bioxfel.org/resources/1276

Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 inStreptomyces globisporus

25 Aug 2016 | BioXFEL Publications | Contributor(s): Chin-Yuan Chang, Jeremy R. Lohman, Hongnan Cao, Kemin Tan, Jeffrey D. Rudolf, Ming Ma, Weijun Xu, Craig A. Bingman, Ragothaman M. Yennamalli, Lance Bigelow, Gyorgy Babnigg, Xiaohui Yan, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1021/acs.biochem.6b00713 Chin-Yuan Chang and Jeremy R. Lohman and Hongnan Cao and Kemin Tan and Jeffrey D. Rudolf and Ming Ma and Weijun Xu and Craig A. Bingman and Ragothaman M. …

https://www.bioxfel.org/resources/1230

Electron Crystallography, Charge-Density Mapping and Nanodiffraction

24 Aug 2016 | BioXFEL Publications | Contributor(s): John Spence

book-chapter http://dx.doi.org/10.1007/978-3-319-26651-0_5 Spence, J., 2016. Electron Crystallography, Charge-Density Mapping and Nanodiffraction. Transmission Electron Microscopy, pp.145–166. …

https://www.bioxfel.org/resources/1249

Serial Femtosecond Crystallography of Membrane Proteins

23 Aug 2016 | BioXFEL Publications | Contributor(s): Lan Zhu, Uwe Weierstall, Vadim Cherezov, Wei Liu

book-chapter http://dx.doi.org/10.1007/978-3-319-35072-1_11 NSF-STC Biology with X-ray Lasers (NSF-1231306) Zhu, L. et al., 2016. Serial Femtosecond Crystallography of Membrane Proteins. The Next …

https://www.bioxfel.org/resources/1250

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

22 Aug 2016 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Valerie Panneels, Garrett Charles Nelson, Cornelius Gati, Tetsunari Kimura, Christopher Milne, Despina Milathianaki, Minoru Kubo, Wenting Wu, Chelsie E Conrad, Jesse David Coe, Richard Bean, Yun Zhao, Petra Båth, Robert Dods, Rajiv Harimoorthy, Kenneth R. Beyerlein, Jan Rheinberger, Daniel James, Daniel DePonte, Chufeng Li, Leonardo Sala, Garth J. Williams, Mark S. Hunter, Jason E. Koglin, Peter Berntsen, Eriko Nango, So Iwata, Henry Chapman, Petra Fromme, Matthias Frank, Rafael Abela, Sébastien Boutet, Anton Barty, Thomas A. White, Uwe Weierstall, John Spence, Richard Neutze, Gebhard F.X. Schertler, Jörg Standfuss

http://dx.doi.org/10.1038/ncomms12314 Przemyslaw Nogly and Valerie Panneels and Garrett Nelson and Cornelius Gati and Tetsunari Kimura and Christopher Milne and Despina Milathianaki and Minoru Kubo …

https://www.bioxfel.org/resources/1243

An Introduction to X-Ray Diffraction Physics

10 Aug 2016 | Teaching Materials | Contributor(s): Blessing

These notes present basic principles of the physics that underlies X-ray analysis of the atomic structure of matter. In particular, classical electromagnetic wave theory of X-ray scattering by …

https://www.bioxfel.org/resources/diffraction-physics

Structure of the ent -Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase

04 Aug 2016 | BioXFEL Publications | Contributor(s): Jeffrey D. Rudolf, Liao-Bin Dong, Hongnan Cao, Catherine Hatzos-Skintges, Jerzy Osipiuk, Michael Endres, Chin-Yuan Chang, Ming Ma, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1021/jacs.6b04317 Jeffrey D. Rudolf and Liao-Bin Dong and Hongnan Cao and Catherine Hatzos-Skintges and Jerzy Osipiuk and Michael Endres and Chin-Yuan Chang and Ming Ma and …

https://www.bioxfel.org/resources/1228

Enhanced hydrogenation activity and diastereomeric interactions of methyl pyruvate co-adsorbed with R-1-(1-naphthyl)ethylamine on Pd(111)

04 Aug 2016 | BioXFEL Publications | Contributor(s): Mausumi Mahapatra, Luke Burkholder, Michael Garvey, Yun Bai, Dilano Saldin, Wilfred T. Tysoe

http://dx.doi.org/10.1038/ncomms12380 Mausumi Mahapatra and Luke Burkholder and Michael Garvey and Yun Bai and Dilano K. Saldin and Wilfred T. Tysoe Mahapatra, M. et al., 2016. Enhanced hydrogenation …

https://www.bioxfel.org/resources/1231

Succinyl-5-aminoimidazole-4-carboxamide-1-ribose 5′-Phosphate (SAICAR) Activates Pyruvate Kinase Isoform M2 (PKM2) in Its Dimeric Form

02 Aug 2016 | BioXFEL Publications | Contributor(s): Ming Yan, Srinivas Chakravarthy, Joshua M. Tokuda, Lois Pollack, Gregory D. Bowman, Young-Sam Lee

journal-article http://dx.doi.org/10.1021/acs.biochem.6b00658 Yan, M. et al., 2016. Succinyl-5-aminoimidazole-4-carboxamide-1-ribose 5′-Phosphate (SAICAR) Activates Pyruvate Kinase Isoform M2 …

https://www.bioxfel.org/resources/1264

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

29 Jul 2016 | BioXFEL Publications | Contributor(s): Anna Munke, Jakob Andreasson, Andrew Aquila, Salah Awel, Kartik Ayyer, Anton Barty, Richard J. Bean, Peter Berntsen, Johan Bielecki, Sébastien Boutet, Maximilian Bucher, Henry Chapman, Benedikt J. Daurer, Hasan Demirci, Veit Elser, Petra Fromme, Janos Hajdu, Max F. Hantke, Akifumi Higashiura, Brenda Hogue, Ahmad Hosseinizadeh, Yoonhee Kim, Richard Kirian, Hemanth K.N. Reddy, Ti-Yen Lan, Daniel S.D. Larsson, Haiguang Liu, N. Duane Loh, Filipe R.N.C. Maia, Adrian P. Mancuso, Kerstin Mühlig, Atsushi Nakagawa, Daewoong Nam, Garrett Charles Nelson, Carl Nettelblad, Kenta Okamoto, Abbas Ourmazd, Max Rose, Gijs Van Der Schot, Peter Schwander, M. Marvin Seibert, Jonas A. Sellberg, Raymond G. Sierra, Changyong Song, Martin Svenda, Nicusor Timneanu, Ivan A. Vartanyants, Daniel Westphal, Max Oliver Wiedorn, Garth J. Williams, Paulraj Lourdu Xavier, Chun Hong Yoon, James D Zook

http://dx.doi.org/10.1038/sdata.2016.64 Anna Munke and Jakob Andreasson and Andrew Aquila and Salah Awel and Kartik Ayyer and Anton Barty and Richard J. Bean and Peter Berntsen and Johan Bielecki and …

https://www.bioxfel.org/resources/1242

A data set from flash X-ray imaging of carboxysomes

29 Jul 2016 | BioXFEL Publications | Contributor(s): Max F. Hantke, Dirk Hasse, Tomas Ekeberg, Katja John, Martin Svenda, Duane Loh, Andrew V. Martin, Nicusor Timneanu, Daniel S.D. Larsson, Gijs Van Der Schot, Gunilla H. Carlsson, Margareta Ingelman, Jakob Andreasson, Daniel Westphal, Bianca Iwan, Charlotte Uetrecht, Johan Bielecki, Mengning Liang, Francesco Stellato, Daniel P. DePonte, Sadia Bari, Robert Hartmann, Nils Kimmel, Richard Kirian, M. Marvin Seibert, Kerstin Mühlig, Sebastian Schorb, Ken Ferguson, Christoph Bostedt, Sebastian Carron, John D. Bozek, Daniel Rolles, Artem Rudenko, Lutz Foucar, Sascha W. Epp, Henry Chapman, Anton Barty, Inger Andersson, Janos Hajdu, Filipe R.N.C. Maia

http://dx.doi.org/10.1038/sdata.2016.61 Max F. Hantke and Dirk Hasse and Tomas Ekeberg and Katja John and Martin Svenda and Duane Loh and Andrew V. Martin and Nicusor Timneanu and Daniel S.D. Larsson …

https://www.bioxfel.org/resources/1225

Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

29 Jul 2016 | BioXFEL Publications | Contributor(s): Tomas Ekeberg, Martin Svenda, M. Marvin Seibert, Chantal Abergel, Filipe R.N.C. Maia, Virginie Seltzer, Daniel P. DePonte, Andrew Aquila, Jakob Andreasson, Bianca Iwan, Olof Jönsson, Daniel Westphal, Duško Odić, Inger Andersson, Anton Barty, Meng Liang, Andrew V. Martin, Lars Gumprecht, Holger Fleckenstein, Saša Bajt, Miriam Barthelmess, Nicola Coppola, Jean-Michel Claverie, N. Duane Loh, Christoph Bostedt, John D. Bozek, Jacek Krzywinski, Marc Messerschmidt, Michael J. Bogan, Christina Y. Hampton, Raymond G. Sierra, Matthias Frank, Robert L. Shoeman, Lukas Lomb, Lutz Foucar, Sascha W. Epp, Daniel Rolles, Artem Rudenko, Robert Hartmann, Andreas Hartmann, Nils Kimmel, Peter Holl, Georg Weidenspointner, Benedikt Rudek, Benjamin Erk, Stephan Kassemeyer, Ilme Schlichting, Lothar Strüder, Joachim Ullrich, Carlo Schmidt, Faton Krasniqi, Günter Hauser, Christian Reich, Heike Soltau, Sebastian Schorb, Helmut Hirsemann, Cornelia Wunderer, Heinz Graafsma, Henry Chapman, Janos Hajdu

http://dx.doi.org/10.1038/sdata.2016.60 Tomas Ekeberg and Martin Svenda and M. Marvin Seibert and Chantal Abergel and Filipe R.N.C. Maia and Virginie Seltzer and Daniel P. DePonte and Andrew Aquila …

https://www.bioxfel.org/resources/1241

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

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 …

https://www.bioxfel.org/resources/1226

Serial femtosecond crystallography datasets from G protein-coupled receptors

29 Jul 2016 | BioXFEL Publications | Contributor(s): Thomas A. White, Anton Barty, Wei Liu, Andrii Ishchenko, Haitao Zhang, Cornelius Gati, Nadia Zatsepin, Shibom Basu, Dominik Oberthür, Markus Metz, Kenneth R. Beyerlein, Chun Hong Yoon, Oleksandr M. Yefanov, Daniel James, Dingjie Wang, Marc Messerschmidt, Jason E. Koglin, Sébastien Boutet, Uwe Weierstall, Vadim Cherezov

http://dx.doi.org/10.1038/sdata.2016.57 Thomas A. White and Anton Barty and Wei Liu and Andrii Ishchenko and Haitao Zhang and Cornelius Gati and Nadia A. Zatsepin and Shibom Basu and Dominik …

https://www.bioxfel.org/resources/1240

Full inactivation of alphaviruses in single particle and crystallized forms

26 Jul 2016 | BioXFEL Publications | Contributor(s): Robert M Lawrence, James D Zook, Brenda Hogue

http://dx.doi.org/10.1016/j.jviromet.2016.07.020 Robert M. Lawrence and James D. Zook and Brenda G. Hogue Lawrence, R.M., Zook, J.D. & Hogue, B.G., 2016. Full inactivation of alphaviruses in single …

https://www.bioxfel.org/resources/1181

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. …

https://www.bioxfel.org/resources/1180

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

15 Jul 2016 | BioXFEL Publications | Contributor(s): Hongxing He, Hengrui Fang, Mitchell Miller, George Phillips, Wu-Pei Su

An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein …

https://www.bioxfel.org/resources/1229

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027

13 Jul 2016 | BioXFEL Publications | Contributor(s): Tingting Huang, Chin-Yuan Chang, Jeremy R Lohman, Jeffrey D Rudolf, Youngchang Kim, Changsoo Chang, Dong Yang, Ming Ma, Xiaohui Yan, Ivana Crnovcic, Lance Bigelow, Shonda Clancy, Craig A Bingman, Ragothaman M Yennamalli, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1038/ja.2016.88 Tingting Huang and Chin-Yuan Chang and Jeremy R Lohman and Jeffrey D Rudolf and Youngchang Kim and Changsoo Chang and Dong Yang and Ming Ma and Xiaohui Yan and …

https://www.bioxfel.org/resources/1216

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

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, …

https://www.bioxfel.org/resources/1362

Special issue on imaging the dynamic structure of matter

30 Jun 2016 | BioXFEL Publications | Contributor(s): Heinrich Schwoerer, Henry Chapman, Bradley J Siwick, R J Dwayne Miller

http://dx.doi.org/10.1088/0953-4075/49/15/150201 journal-article Schwoerer, H. et al., 2016. Special issue on imaging the dynamic structure of matter. Journal of Physics B: Atomic, Molecular and …

https://www.bioxfel.org/resources/1623

Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways

28 Jun 2016 | BioXFEL Publications | Contributor(s): Tyler D. Huber, Fengbin Wang, Shanteri Singh, Brooke R. Johnson, Jianjun Zhang, Manjula Sunkara, Steven G. Van Lanen, Andrew J. Morris, George Phillips, Jon S. Thorson

http://dx.doi.org/10.1021/acschembio.6b00348 journal-article Huber, T.D. et al., 2016. Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways. ACS Chemical Biology, 11(9), …

https://www.bioxfel.org/resources/1403

Imaging enzyme kinetics at atomic resolution

28 Jun 2016 | BioXFEL Publications | Contributor(s): John Spence, Eaton E Lattman

http://dx.doi.org/10.1107/s2052252516010204 John Spence and Eaton Lattman Spence, J. & Lattman, E., 2016. Imaging enzyme kinetics at atomic resolution. IUCrJ, 3(4), pp.228–229. Available at: …

https://www.bioxfel.org/resources/1207

Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals

24 Jun 2016 | BioXFEL Publications | Contributor(s): Ximeng Y. Dow, Christopher M. Dettmar, Emma L. DeWalt, Justin A. Newman, Alexander R. Dow, Shatabdi Roy-Chowdhury, Jesse David Coe, Christopher Kupitz, Petra Fromme, Garth J. Simpson

Second harmonic generation correlation spectroscopy (SHG-CS) is demonstrated as a new approach to protein nanocrystal characterization. A novel line-scanning approach was performed to enable …

https://www.bioxfel.org/resources/1204

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

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 …

https://www.bioxfel.org/resources/1296

Extracting water and ion distributions from solution x-ray scattering experiments

03 Jun 2016 | BioXFEL Publications | Contributor(s): Hung T. Nguyen, Suzette A. Pabit, Lois Pollack, David Case

http://dx.doi.org/10.1063/1.4953037 journal-article Nguyen, H.T. et al., 2016. Extracting water and ion distributions from solution x-ray scattering experiments. The Journal of Chemical Physics, …

https://www.bioxfel.org/resources/1383

Toward Analysis of Proteins in Single Cells: A Quantitative Approach Employing Isobaric Tags with MALDI Mass Spectrometry Realized with a Microfluidic Platform

03 Jun 2016 | BioXFEL Publications | Contributor(s): Mian Yang, Randall Nelson, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.5b03419 journal-article Yang, M., Nelson, R. & Ros, A., 2016. Toward Analysis of Proteins in Single Cells: A Quantitative Approach Employing Isobaric Tags …

https://www.bioxfel.org/resources/1405

The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

01 Jun 2016 | BioXFEL Publications | Contributor(s): Che-Hsiung Hsu, Sangho Park, David E. Mortenson, B. Lachele Foley, Xiaocong Wang, Robert J. Woods, David Case, Evan T. Powers, Chi-Huey Wong, H. Jane Dyson, Jeffery W. Kelly

http://dx.doi.org/10.1021/jacs.6b02879 journal-article Hsu, C.-H. et al., 2016. The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate. Journal of the …

https://www.bioxfel.org/resources/2020

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

25 May 2016 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Andrea Katz, Igor S. Tolokh, Aleksander Drozdetski, Nathan Baker, Alexey V. Onufriev, Lois Pollack

http://dx.doi.org/10.1063/1.4950814 journal-article Pabit, S.A. et al., 2016. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular …

https://www.bioxfel.org/resources/1384

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

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 …

https://www.bioxfel.org/resources/1208

Liquid explosions induced by X-ray laser pulses

24 May 2016 | BioXFEL Publications | Contributor(s): Claudiu A. Stan, Despina Milathianaki, Hartawan Laksmono, Raymond G. Sierra, Trevor A. McQueen, Marc Messerschmidt, Garth J. Williams, Jason E. Koglin, Thomas J. Lane, Matt J. Hayes, Serge A. H. Guillet, Mengning Liang, Andrew L. Aquila, Philip R. Willmott, Joseph S. Robinson, Karl L. Gumerlock, Sabine Botha, Karol Nass, Ilme Schlichting, Robert L. Shoeman, Howard A. Stone, Sébastien Boutet

http://dx.doi.org/10.1038/nphys3779 Claudiu A. Stan and Despina Milathianaki and Hartawan Laksmono and Raymond G. Sierra and Trevor A. McQueen and Marc Messerschmidt and Garth J. Williams and Jason …

https://www.bioxfel.org/resources/1211

Preprints for the life sciences

20 May 2016 | BioXFEL Publications | Contributor(s): J. M. Berg, N. Bhalla, P. E. Bourne, M. Chalfie, D. G. Drubin, J. S. Fraser, C. W. Greider, M. Hendricks, C. Jones, R. Kiley, S. King, M. W. Kirschner, H. M. Krumholz, R. Lehmann, M. Leptin, B. Pulverer, B. Rosenzweig, J. E. Spiro, M. Stebbins, C. Strasser, S. Swaminathan, P. Turner, R. D. Vale, K. VijayRaghavan, C. Wolberger

http://dx.doi.org/10.1126/science.aaf9133 journal-article Berg, J.M. et al., 2016. Preprints for the life sciences. Science, 352(6288), pp.899–901. Available at: …

https://www.bioxfel.org/resources/1457

Expression and purification of an engineered human endothelin receptor B in a monomeric form

19 May 2016 | BioXFEL Publications | Contributor(s): A. V. Mishin, A. P. Luginina, A. P. Potapenko, V. I. Borshchevskiy, V. Katritch, E. Edelweiss, I. S. Okhrimenko, V. I. Gordeliy, V. G. Cherezov

journal-article http://dx.doi.org/10.1134/s1607672916020216 Mishin, A.V. et al., 2016. Expression and purification of an engineered human endothelin receptor B in a monomeric form. Doklady …

https://www.bioxfel.org/resources/1300

Three-dimensional-printed gas dynamic virtual nozzles for x-ray laser sample delivery

18 May 2016 | BioXFEL Publications | Contributor(s): Garrett Charles Nelson, Richard Kirian, Uwe Weierstall, Nadia Zatsepin, Tomáš Faragó, Tilo Baumbach, Fabian Wilde, Fabian B. P. Niesler, Benjamin Zimmer, Izumi Ishigami, Masahide Hikita, Saša Bajt, Syun-Ru Yeh, Denis L. Rousseau, Henry Chapman, John Spence, Michael Heymann

http://dx.doi.org/10.1364/oe.24.011515 Garrett Nelson and Richard A. Kirian and Uwe Weierstall and Nadia A. Zatsepin and Tomáš Faragó and Tilo Baumbach and Fabian Wilde and Fabian B. P. Niesler …

https://www.bioxfel.org/resources/1106

Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses

12 May 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

http://dx.doi.org/10.1007/978-3-319-14394-1_27 Richard A. Kirian and Henry N. Chapman Kirian, R.A. & Chapman, H.N., 2016. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser …

https://www.bioxfel.org/resources/1218

Characterization of protein nanocrystals based on the reversibility of crystallization

10 May 2016 | BioXFEL Publications | Contributor(s): Katerina Dörner, Jose M. Martin-Garcia, Christopher Kupitz, Zhen Gong, T. Conn Mallet, Liqing Chen, Rebekka M. Wachter, Petra Fromme

http://dx.doi.org/10.1021/acs.cgd.6b00384 Katerina Dörner and Jose M. Martin-Garcia and Christopher Kupitz and Zhen Gong and T. Conn Mallet and Liqing Chen and Rebekka M. Wachter and Petra Fromme …

https://www.bioxfel.org/resources/923

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

05 May 2016 | BioXFEL Publications | Contributor(s): K. Pande, C. D. M. Hutchison, G. Groenhof, A. Aquila, J. S. Robinson, J. Tenboer, S. Basu, S. Boutet, D. P. DePonte, M. Liang, T. A. White, N. A. Zatsepin, O. Yefanov, D. Morozov, D. Oberthuer, C. Gati, G. Subramanian, D. James, Y. Zhao, J. Koralek, J. Brayshaw, C. Kupitz, C. Conrad, S. Roy-Chowdhury, J. D. Coe, M. Metz, P. L. Xavier, T. D. Grant, J. E. Koglin, G. Ketawala, R. Fromme, V.  rajer, R. Henning, J. C. H. Spence, A. Ourmazd, P. Schwander, U. Weierstall, M. Frank, P. Fromme, A. Barty, H. N. Chapman, K. Moffat, J. J. Van Thor, M. Schmidt

http://dx.doi.org/10.1126/science.aad5081 K. Pande and C. D. M. Hutchison and G. Groenhof and A. Aquila and J. S. Robinson and J. Tenboer and S. Basu and S. Boutet and D. P. DePonte and M. Liang and …

https://www.bioxfel.org/resources/921

Deterministic Absolute Negative Mobility for Micro- and Submicrometer Particles Induced in a Microfluidic Device

05 May 2016 | BioXFEL Publications | Contributor(s): Jinghui Luo, Katherine A. Muratore, Edgar A. Arriaga, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.6b00837 Jinghui Luo and Katherine A. Muratore and Edgar A. Arriaga and Alexandra Ros Luo, J. et al., 2016. Deterministic Absolute Negative Mobility for Micro- …

https://www.bioxfel.org/resources/1217

Review: Serial femtosecond crystallography: A revolution in structural biology

01 May 2016 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Chelsie E Conrad, Jesse David Coe, Shatabdi Roy-Chowdhury, Petra Fromme

http://dx.doi.org/10.1016/j.abb.2016.03.036 Jose M. Martin-Garcia and Chelsie E. Conrad and Jesse Coe and Shatabdi Roy-Chowdhury and Petra Fromme Martin-Garcia, J.M. et al., 2016. Serial femtosecond …

https://www.bioxfel.org/resources/922

Photocycle Populations with Femtosecond Excitation of Crystalline Photoactive Yellow Protein

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 …

https://www.bioxfel.org/resources/919

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

29 Apr 2016 | BioXFEL Publications | Contributor(s): Hongnan Cao, Kemin Tan, Fengbin Wang, Lance Bigelow, Ragothaman M. Yennamalli, Robert Jedrzejczak, Gyorgy Babnigg, Craig A. Bingman, Andrzej Joachimiak, Madan K. Kharel, Shanteri Singh, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1063/1.4948539 journal-article Cao, H. et al., 2016. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking …

https://www.bioxfel.org/resources/1385

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

27 Apr 2016 | BioXFEL Publications | Contributor(s): Ray Yu-Ruei Wang, Yifan Song, Benjamin Barad, Yifan Cheng, James Fraser, Frank DiMaio

http://dx.doi.org/10.1101/050286 Cryo-EM has revealed many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5 Angstrom), providing biological phenomena with molecular …

https://www.bioxfel.org/resources/1366

Dynamics from noisy data with extreme timing uncertainty

26 Apr 2016 | BioXFEL Publications | Contributor(s): R. Fung, A. Ourmazd, A. M. Hanna, O. Vendrell, S. Ramakrishna, T. Seideman, R. Santra

http://dx.doi.org/10.1038/nature17627 R. Fung and A. Ourmazd and A. M. Hanna and O. Vendrell and S. Ramakrishna and T. Seideman and R. Santra and A. Ourmazd Fung, R. et al., 2016. Dynamics from noisy …

https://www.bioxfel.org/resources/920

Transmission electron microscopy for the evaluation and optimization of crystal growth

26 Apr 2016 | BioXFEL Publications | Contributor(s): Hilary P. Stevenson, Guowu Lin, Christopher Barnes, Ieva Sutkeviciute, Troy Krzysiak, Simon C. Weiss, Shelley Reynolds, Ying Wu, Veeranagu Nagarajan, Alexander M. Makhov, Robert M Lawrence, Emily Lamm, Lisa Clark, Timothy J. Gardella, Brenda Hogue, Craig M. Ogata, Jinwoo Ahn, Angela M. Gronenborn, James F. Conway, Jean-Pierre Vilardaga, Aina E. Cohen, Guillermo Calero

The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) …

https://www.bioxfel.org/resources/1334

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

25 Apr 2016 | BioXFEL Publications | Contributor(s): David Mavor, Kyle Barlow, Samuel Thompson, Benjamin A Barad, Alain R Bonny, Clinton L Cario, Garrett Gaskins, Zairan Liu, Laura Deming, Seth D Axen, Elena Caceres, Weilin Chen, Adolfo Cuesta, Rachel E Gate, Evan M Green, Kaitlin R Hulce, Weiyue Ji, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Steven M Moss, Marco Mravic, Ryan K Muir, Stefan Niekamp, Chimno I Nnadi, Eugene Palovcak, Erin M Poss, Tyler D Ross, Eugenia C Salcedo, Stephanie K See, Meena Subramaniam, Allison W Wong, Jennifer Li, Kurt S Thorn, Shane Ó Conchúir, Benjamin P Roscoe, Eric D Chow, Joseph L DeRisi, Tanja Kortemme, Daniel N Bolon, James Fraser

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to …

https://www.bioxfel.org/resources/1201

Multi-shell model of ion-induced nucleic acid condensation

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. …

https://www.bioxfel.org/resources/1386

June 2016 Site Visit Agenda

21 Apr 2016 | Downloads

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https://www.bioxfel.org/resources/918

SAXS studies of RNA: structures, dynamics, and interactions with partners

12 Apr 2016 | BioXFEL Publications | Contributor(s): Yujie Chen, Lois Pollack

http://dx.doi.org/10.1002/wrna.1349 Yujie Chen and Lois Pollack Chen, Y. & Pollack, L., 2016. SAXS studies of RNA: structures, dynamics, and interactions with partners. WIREs RNA. Available at: …

https://www.bioxfel.org/resources/917

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 …

https://www.bioxfel.org/resources/1097

Synthesis of Water-Soluble, Thiolate-Protected Gold Nanoparticles Uniform in Size

04 Apr 2016 | BioXFEL Publications | Contributor(s): Maia Azubel, Roger Kornberg

journal-article http://dx.doi.org/10.1021/acs.nanolett.6b00981 Azubel, M. & Kornberg, R.D., 2016. Synthesis of Water-Soluble, Thiolate-Protected Gold Nanoparticles Uniform in Size. Nano Letters, …

https://www.bioxfel.org/resources/1266

Protein–DNA and ion–DNA interactions revealed through contrast variation SAXS

02 Apr 2016 | BioXFEL Publications | Contributor(s): Joshua M. Tokuda, Suzette A. Pabit, Lois Pollack

http://dx.doi.org/10.1007/s12551-016-0196-8 journal-article Tokuda, J.M., Pabit, S.A. & Pollack, L., 2016. Protein–DNA and ion–DNA interactions revealed through contrast variation SAXS. …

https://www.bioxfel.org/resources/1430

Melatonin Receptors as Modulators of Methamphetamine-Mediated Behaviors

01 Apr 2016 | BioXFEL Publications | Contributor(s): Shannon J. Clough, Anthony J. Hutchinson, Margarita L. Dubocovich

http://dx.doi.org/10.1016/b978-0-12-800212-4.00016-9 book-chapter Clough, S.J., Hutchinson, A.J. & Dubocovich, M.L., 2016. Melatonin Receptors as Modulators of Methamphetamine-Mediated Behaviors. …

https://www.bioxfel.org/resources/1666

2016 Serial Crystallography Data Analysis Workshop at ACA Annual Meeting.

31 Mar 2016 | Workshops

We are running a serial femtosecond crystallography data analysis workshop at ACA 2016 in Denver, CO, focused on "Serial Crystallography Data Analysis with Cheetah and CrystFEL: Concepts and …

https://www.bioxfel.org/resources/2016-data-analysis-workshop

Recent developments in CrystFEL

29 Mar 2016 | BioXFEL Publications | Contributor(s): Thomas A. White, Valerio Mariani, Wolfgang Brehm, Oleksandr Yefanov, Anton Barty, Kenneth R. Beyerlein, Fedor Chervinskii, Lorenzo Galli, Cornelius Gati, Takanori Nakane, Alexandra Tolstikova, Keitaro Yamashita, Chun Hong Yoon, Kay Diederichs, Henry Chapman

CrystFELis a suite of programs for processing data from `serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other …

https://www.bioxfel.org/resources/950

Measuring and modeling diffuse scattering in protein X-ray crystallography

28 Mar 2016 | BioXFEL Publications | Contributor(s): Andrew H. Van Benschoten, Lin Liu, Ana Gonzalez, Aaron S. Brewster, Nicholas K. Sauter, James Fraser, Michael E. Wall

http://dx.doi.org/10.1073/pnas.1524048113 Andrew H. Van Benschoten and Lin Liu and Ana Gonzalez and Aaron S. Brewster and Nicholas K. Sauter and James S. Fraser and Michael E. Wall Van Benschoten, …

https://www.bioxfel.org/resources/932

Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles

25 Mar 2016 | BioXFEL Publications | Contributor(s): Matthew Coleman, Jenny A. Cappuccio, Craig D. Blanchette, Tingjuan Gao, Erin S. Arroyo, Angela K. Hinz, Feliza A. Bourguet, Brent W. Segelke, Paul D. Hoeprich, Thomas Huser, Ted A. Laurence, Vladimir L. Motin, Brett A. Chromy

http://dx.doi.org/10.1371/journal.pone.0150166 Matthew A. Coleman and Jenny A. Cappuccio and Craig D. Blanchette and Tingjuan Gao and Erin S. Arroyo and Angela K. Hinz and Feliza A. Bourguet and …

https://www.bioxfel.org/resources/978

Immunological Characterization of Plant-Based HIV-1 Gag/Dgp41 Virus-Like Particles

17 Mar 2016 | BioXFEL Publications | Contributor(s): Sarah A. Kessans, Mark D. Linhart, Lydia R. Meador, Jacquelyn Kilbourne, Brenda Hogue, Petra Fromme, Nobuyuki Matoba, Tsafrir S. Mor

http://dx.doi.org/10.1371/journal.pone.0151842 Sarah A. Kessans and Mark D. Linhart and Lydia R. Meador and Jacquelyn Kilbourne and Brenda G. Hogue and Petra Fromme and Nobuyuki Matoba and Tsafrir S. …

https://www.bioxfel.org/resources/979

Visualizing aerosol-particle injection for diffractive-imaging experiments

16 Mar 2016 | BioXFEL Publications | Contributor(s): Salah Awel, Richard Kirian, Niko Eckerskorn, Max Oliver Wiedorn, Daniel A. Horke, Andrei V. Rode, Jochen Küpper, Henry Chapman

http://dx.doi.org/10.1364/oe.24.006507 Salah Awel and Richard A. Kirian and Niko Eckerskorn and Max Wiedorn and Daniel A. Horke and Andrei V. Rode and Jochen Küpper and Henry N. Chapman Awel, S. et …

https://www.bioxfel.org/resources/972

Anomalous Nonlinear X-ray Compton Scattering

14 Mar 2016 | BioXFEL Publications | Contributor(s): Matthias Fuchs

proceedings-article http://dx.doi.org/10.1364/hilas.2016.hm3b.1 Fuchs, M., 2016. Anomalous Nonlinear X-ray Compton Scattering. High-Brightness Sources and Light-Driven Interactions. Available at: …

https://www.bioxfel.org/resources/1303

Data publication with the structural biology data grid supports live analysis

07 Mar 2016 | BioXFEL Publications | Contributor(s): Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabby Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James Fraser, Filipe R. N C. Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercè Crosas, Piotr Sliz

journal-article http://dx.doi.org/10.1038/ncomms10882 Meyer, P.A. et al., 2016. Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, p.10882. …

https://www.bioxfel.org/resources/1314

Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography

02 Mar 2016 | BioXFEL Publications | Contributor(s): Christopher Barnes, Elena G. Kovaleva, Xiaofeng Fu, Hilary P. Stevenson, Aaron S. Brewster, Daniel P. DePonte, Elizabeth L. Baxter, Aina E. Cohen, Guillermo Calero

journal-article http://dx.doi.org/10.1016/j.abb.2016.02.011 Barnes, C.O. et al., 2016. Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond …

https://www.bioxfel.org/resources/1251

AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy

28 Feb 2016 | BioXFEL Publications | Contributor(s): F.X. Kärtner, F. Ahr, A.-L. Calendron, H. Çankaya, S. Carbajo, G. Chang, G. Cirmi, K. Dörner, U. Dorda, A. Fallahi, A. Hartin, M. Hemmer, R. Hobbs, Y. Hua, W.R. Huang, R. Letrun, N. Matlis, V. Mazalova, O.D. Mücke, E. Nanni, W. Putnam, K. Ravi, F. Reichert, I. Sarrou, X. Wu, A. Yahaghi, H. Ye, L. Zapata, D. Zhang, C. Zhou, R.J.D. Miller, K.K. Berggren, H. Graafsma, A. Meents, R.W. Assmann, H.N. Chapman, P. Fromme

http://dx.doi.org/10.1016/j.nima.2016.02.080 F.X. Kärtner and F. Ahr and A.-L. Calendron and H. Çankaya and S. Carbajo and G. Chang and G. Cirmi and K. Dörner and U. Dorda and A. Fallahi and A. …

https://www.bioxfel.org/resources/1081