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Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both

24 Jun 2019 | BioXFEL Publications | Contributor(s): Helena Taberman, Charles S. Bury, Mark J. Van Der Woerd, Edward Snell, Elspeth F. Garman

http://dx.doi.org/10.1107/s1600577519005599 Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was …

Structural knowledge or X-ray damage? Dose-dependent case studies on xylose isomerase revealing structural perturbations

03 Jan 2020 | BioXFEL Publications | Contributor(s): Edward Snell, Helena Taberman, Charles S. Bury, Mark J. Van Der Woerd, Elspeth F. Garman

http://dx.doi.org/10.1107/s010876731909771x poster NSF-STC Biology with X-ray Lasers (NSF-1231306) Snell, E.H. et al., 1999. Structural knowledge or X-ray damage? Dose-dependent case studies on xylose isomerase revealing structural perturbations. Acta Crystallographica Section A Foundations and …

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

11 Jun 2015 | BioXFEL Publications | Contributor(s): Maike Bublitz, Karol Nass, Nikolaj D. Drachmann, Anders J. Markvardsen, Matthias J. Gutmann, Thomas R. M. Barends, Daniel Mattle, Robert L. Shoeman, R. Bruce Doak, Sébastien Boutet, Marc Messerschmidt, Marvin M. Seibert, Garth J. Williams, Lutz Foucar, Linda Reinhard, Oleg Sitsel, Jonas L. Gregersen, Johannes D. Clausen, Thomas Boesen, Kamil Gotfryd, Kai-Tuo Wang, Claus Olesen, Jesper V. Møller, Poul Nissen, Ilme Schlichting

Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly …

Structural Studies of the Human Kappa Opioid Receptor Active State Conformations

16 Feb 2016 | BioXFEL Publications | Contributor(s): Ming-Yue Lee, Nilkanth N Patel, Vsevolod Katritch, Raymond C. Stevens, Vadim Cherezov

http://dx.doi.org/10.1016/j.bpj.2015.11.275 Ming-Yue Lee and Nilkanth Patel and Vsevolod Katritch and Raymond C. Stevens and Vadim Cherezov Lee, M.-Y. et al., 2016. Structural Studies of the Human Kappa Opioid Receptor Active State Conformations. Biophysical Journal, 110(3), p.38a–39a. Available …

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

18 Sep 2014 | BioXFEL Publications | Contributor(s): Geoffrey K. Feld, Sahar El-Etr, Michele H. Corzett, Mark S. Hunter, Kamila Belhocine, Denise M. Monack, Matthias Frank, Brent W. Segelke, Amy Rasley

http://dx.doi.org/10.1074/jbc.m114.599381 journal-article Feld, G.K. et al., 2014. Structure and Function of REP34 Implicates Carboxypeptidase Activity inFrancisella tularensisHost Cell Invasion. Journal of Biological Chemistry, 289(44), pp.30668–30679. Available at: …

Structure and specificity of a permissive bacterial C-prenyltransferase

06 Feb 2017 | BioXFEL Publications | Contributor(s): Sherif I Elshahawi, Hongnan Cao, Khaled A Shaaban, Larissa V Ponomareva, Thangaiah Subramanian, Mark L Farman, H Peter Spielmann, George Phillips, Jon S Thorson, Shanteri Singh

journal-article http://dx.doi.org/10.1038/nchembio.2285 Elshahawi, S.I. et al., 2017. Structure and specificity of a permissive bacterial C-prenyltransferase. Nature Chemical Biology, 13(4), pp.366–368. Available at: http://dx.doi.org/10.1038/nchembio.2285. Sherif I Elshahawi and Hongnan Cao …

Structure and Substrate Specificity of a Eukaryotic Fucosidase fromFusarium graminearum

02 Aug 2014 | BioXFEL Publications | Contributor(s): Hongnan Cao, Jonathan D. Walton, Phil Brumm, George Phillips

http://dx.doi.org/10.1074/jbc.m114.583286 journal-article Cao, H. et al., 2014. Structure and Substrate Specificity of a Eukaryotic Fucosidase fromFusarium graminearum. Journal of Biological Chemistry, 289(37), pp.25624–25638. Available at: http://dx.doi.org/10.1074/jbc.m114.583286. Hongnan …

Structure determination based on continuous diffraction from macromolecular crystals

14 Sep 2017 | BioXFEL Publications | Contributor(s): Henry Chapman, Petra Fromme

http://dx.doi.org/10.1016/j.sbi.2017.07.008 journal-article Chapman, H.N. & Fromme, P., 2017. Structure determination based on continuous diffraction from macromolecular crystals. Current Opinion in Structural Biology, 45, pp.170–177. Available at: http://dx.doi.org/10.1016/j.sbi.2017.07.008. …

Structure Determination from Disordered Ensembles of Identical Particles

22 Mar 2013 | BioXFEL Publications | Contributor(s): Richard Kirian, Dilano Saldin

http://dx.doi.org/10.1080/08940886.2013.771070 journal-article Kirian, R.A. & Saldin, D.K., 2013. Structure Determination from Disordered Ensembles of Identical Particles. Synchrotron Radiation News, 26(2), pp.20–25. Available at: http://dx.doi.org/10.1080/08940886.2013.771070. Richard A. …

Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED

30 Jul 2020 | BioXFEL Publications | Contributor(s): Lan Zhu, Guanhong Bu, Liang Jing, Dan Shi, Ming-Yue Lee, Tamir Gonen, Wei Liu, Brent L. Nannenga

http://dx.doi.org/10.1016/j.str.2020.07.006 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zhu, L. et al., 2020. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure, 28(10), pp.1149–1159.e4. Available at: …

Structure Determination from Multiple-Scattering Electron Crystallography

22 Jul 2022 | BioXFEL Publications | Contributor(s): Jeffrey Donatelli, John Spence

http://dx.doi.org/10.1017/s1431927622010418 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Donatelli, J., & Spence, J. (2022). Structure Determination from Multiple-Scattering Electron Crystallography. Microscopy and Microanalysis, 28(S1), 2766–2767. …

Structure determination with weak anomalous signal

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

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

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 Robinson, P.J. et al., 2016. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. …

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

30 Oct 2014 | BioXFEL Publications | Contributor(s): R. Sophia Weerth, Karolina Michalska, Craig A. Bingman, Ragothaman M. Yennamalli, Hui Li, Robert Jedrzejczak, Fengbin Wang, Gyorgy Babnigg, Andrzej Joachimiak, Michael G. Thomas, George Phillips

http://dx.doi.org/10.1002/prot.24705 journal-article Weerth, R.S. et al., 2014. Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution. Proteins: Structure, Function, and Bioinformatics, 83(2), pp.383–388. Available at: …

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

14 Apr 2015 | BioXFEL Publications | Contributor(s): R. Sophia Weerth, Karolina Michalska, Craig A. Bingman, Ragothaman M. Yennamalli, Hui Li, Robert Jedrzejczak, Fengbin Wang, Gyorgy Babnigg, Andrzej Joachimiak, Michael G. Thomas, George Phillips

http://dx.doi.org/10.1002/prot.24798 R. Sophia Weerth and Karolina Michalska and Craig A. Bingman and Ragothaman M. Yennamalli and Hui Li and Robert Jedrzejczak and Fengbin Wang and Gyorgy Babnigg and Andrzej Joachimiak and Michael G. Thomas and George N. Phillips Sophia Weerth, R. et al., 2015. …

Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

19 Dec 2013 | BioXFEL Publications | Contributor(s): Linda C. Johansson, David Arnlund, Gergely Katona, Thomas A. White, Anton Barty, Daniel P. DePonte, Robert L. Shoeman, Cecilia Wickstrand, Amit Sharma, Garth J. Williams, Andrew Aquila, Michael J. Bogan, Carl Caleman, Jan Davidsson, R Bruce Doak, Matthias Frank, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Mark S. Hunter, Stephan Kassemeyer, Richard Kirian, Christopher Kupitz, Mengning Liang, Lukas Lomb, Erik Malmerberg, Andrew V. Martin, Marc Messerschmidt, Karol Nass, Lars Redecke, M Marvin Seibert, Jennie Sjöhamn, Jan Steinbrener, Francesco Stellato, Dingjie Wang, Weixaio Y. Wahlgren, Uwe Weierstall, Sebastian Westenhoff, Nadia Zatsepin, Sébastien Boutet, John Spence, Ilme Schlichting, Henry Chapman, Petra Fromme, Richard Neutze

http://dx.doi.org/10.1038/ncomms3911 Linda C. Johansson and David Arnlund and Gergely Katona and Thomas A. White and Anton Barty and Daniel P. DePonte and Robert L. Shoeman and Cecilia Wickstrand and Amit Sharma and Garth J. Williams and Andrew Aquila and Michael J. Bogan and Carl Caleman and Jan …

Structure of an RNA polymerase II preinitiation complex

20 Oct 2015 | BioXFEL Publications | Contributor(s): Kenji Murakami, Kuang-Lei Tsai, Nir Kalisman, David Bushnell, Francisco J. Asturias, Roger Kornberg

journal-article http://dx.doi.org/10.1073/pnas.1518255112 Murakami, K. et al., 2015. Structure of an RNA polymerase II preinitiation complex. Proceedings of the National Academy of Sciences, 112(44), pp.13543–13548. Available at: http://dx.doi.org/10.1073/pnas.1518255112. Kenji Murakami and …

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. Available at: http://dx.doi.org/10.1038/nature20605. Yi Zheng and Ling Qin and Natalia V. Ortiz …

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

21 Jun 2017 | BioXFEL Publications | Contributor(s): Yi Zheng, Gye Won Han, Ruben Abagyan, Beili Wu, Raymond C. Stevens, Vadim Cherezov, Irina Kufareva, Tracy M. Handel

http://dx.doi.org/10.1016/j.immuni.2017.05.002 journal-article Zheng, Y. et al., 2017. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity, 46(6), pp.1005–1017.e5. Available at: …

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

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

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

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 Roberto Alonso-Mori and Thomas Kroll and Tara Michels-Clark and Hartawan Laksmono and Raymond G. Sierra …

Structure of RNA 3′-phosphate cyclase bound to substrate RNA

27 Aug 2014 | BioXFEL Publications | Contributor(s): Kevin K. Desai, Craig A. Bingman, Chin L. Cheng, George Phillips, Ronald T. Raines

http://dx.doi.org/10.1261/rna.045823.114 journal-article Desai, K.K. et al., 2014. Structure of RNA 3′-phosphate cyclase bound to substrate RNA. RNA, 20(10), pp.1560–1566. Available at: http://dx.doi.org/10.1261/rna.045823.114. Kevin K. Desai and Craig A. Bingman and Chin L. Cheng and George …

Structure of the 30S ribosomal decoding complex at ambient temperature

12 Feb 2018 | BioXFEL Publications | Contributor(s): E. Han Dao, Frederic Poitevin, Raymond G. Sierra, Cornelius Gati, Yashas Rao, Halil Ibrahim Ciftci, Fulya Akşit, Alex McGurk, Trevor Obrinski, Paul Mgbam, Brandon Hayes, Casper De Lichtenberg, Fatima Pardo-Avila, Nicholas Corsepius, Lindsey Zhang, Matt Seaberg, Mark S. Hunter, Mengling Liang, Jason E. Koglin, Soichi Wakatsuki, Hasan Demirci

http://dx.doi.org/10.1101/262972 The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on …

Structure of the 30S ribosomal decoding complex at ambient temperature

23 Aug 2018 | BioXFEL Publications | Contributor(s): E. Han Dao, Frédéric Poitevin, Raymond G. Sierra, Cornelius Gati, Yashas Rao, Halil Ibrahim Ciftci, Fulya Akşit, Alex McGurk, Trevor Obrinski, Paul Mgbam, Brandon Hayes, Casper De Lichtenberg, Fatima Pardo-Avila, Nicholas Corsepius, Lindsey Zhang, Matthew H. Seaberg, Mark S. Hunter, Mengling Liang, Jason E. Koglin, Soichi Wakatsuki, Hasan Demirci

http://dx.doi.org/10.1261/rna.067660.118 The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly …

Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

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

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

Structure of the Bifunctional Acyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double-Hot-Dog Fold

15 Jan 2013 | BioXFEL Publications | Contributor(s): Jeremy R. Lohman, Craig A. Bingman, George Phillips, Ben Shen

http://dx.doi.org/10.1021/bi301652y journal-article Lohman, J.R. et al., 2013. Structure of the Bifunctional Acyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double-Hot-Dog Fold. Biochemistry, 52(5), pp.902–911. Available at: …

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 Gyorgy Babnigg and Andrzej Joachimiak and George N. Phillips and Ben Shen Rudolf, J.D. et al., 2016. …

Structure of the full-length glucagon class B G-protein-coupled receptor

17 May 2017 | BioXFEL Publications | Contributor(s): Haonan Zhang, Anna Qiao, Dehua Yang, Linlin Yang, Antao Dai, Chris De Graaf, Steffen Reedtz-Runge, Venkatasubramanian Dharmarajan, Hui Zhang, Gye Won Han, Thomas D. Grant, Raymond G. Sierra, Uwe Weierstall, Garrett Charles Nelson, Wei Liu, Yanhong Wu, Limin Ma, Xiaoqing Cai, Guangyao Lin, Xiaoai Wu, Zhi Geng, Yuhui Dong, Gaojie Song, Patrick R. Griffin, Jesper Lau, Vadim Cherezov, Huaiyu Yang, Michael A. Hanson, Raymond C. Stevens, Qiang Zhao, Hualiang Jiang, Ming-Wei Wang, Beili Wu

http://dx.doi.org/10.1038/nature22363 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zhang, Haonan et al., 2017. Structure of the full-length glucagon class B G-protein-coupled receptor. Nature. Available at: http://dx.doi.org/10.1038/nature22363. Haonan Zhang and Anna Qiao and …

Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor

04 Jan 2018 | BioXFEL Publications | Contributor(s): Tao Che, Susruta Majumdar, Saheem A. Zaidi, Pauline Ondachi, John D. McCorvy, Sheng Wang, Philip D. Mosier, Rajendra Uprety, Eyal Vardy, Brian E. Krumm, Gye Won Han, Ming-Yue Lee, Els Pardon, Jan Steyaert, Xi-Ping Huang, Ryan T. Strachan, Alexandra R. Tribo, Gavril W. Pasternak, F. Ivy Carroll, Raymond C. Stevens, Vadim Cherezov, Vsevolod Katritch, Daniel Wacker, Bryan L. Roth

http://dx.doi.org/10.1016/j.cell.2017.12.011 journal-article Che, T. et al., 2018. Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor. Cell, 172(1-2), pp.55–67.e15. Available at: http://dx.doi.org/10.1016/j.cell.2017.12.011. Tao Che and Susruta Majumdar and Saheem …

Structure of the toxic core of α-synuclein from invisible crystals

08 Sep 2015 | BioXFEL Publications | Contributor(s): Jose A. Rodriguez, Magdalena I. Ivanova, Michael R. Sawaya, Duilio Cascio, Francis E. Reyes, Dan Shi, Smriti Sangwan, Elizabeth L. Guenther, Lisa M. Johnson, Meng Zhang, Lin Jiang, Mark A. Arbing, Brent L. Nannenga, Johan Hattne, Julian Whitelegge, Aaron S. Brewster, Marc Messerschmidt, Sébastien Boutet, Nicholas K. Sauter, Tamir Gonen, David S. Eisenberg

http://dx.doi.org/10.1038/nature15368 Jose A. Rodriguez and Magdalena I. Ivanova and Michael R. Sawaya and Duilio Cascio and Francis E. Reyes and Dan Shi and Smriti Sangwan and Elizabeth L. Guenther and Lisa M. Johnson and Meng Zhang and Lin Jiang and Mark A. Arbing and Brent L. Nannenga and Johan …

Structure Refinement in Phenix

08 Apr 2015 | Teaching Materials

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

Structure Validation in Phenix

08 Apr 2015 | Teaching Materials

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

Structure, Dynamics, and Specificity of Endoglucanase D from Clostridium cellulovorans

08 Jun 2013 | BioXFEL Publications | Contributor(s): Christopher M. Bianchetti, Phillip Brumm, Robert W. Smith, Kevin Dyer, Greg L. Hura, Thomas J. Rutkoski, George Phillips

journal-article http://dx.doi.org/10.1016/j.jmb.2013.05.030 Bianchetti, C.M. et al., 2013. Structure, Dynamics, and Specificity of Endoglucanase D from Clostridium cellulovorans. Journal of Molecular Biology, 425(22), pp.4267–4285. Available at: http://dx.doi.org/10.1016/j.jmb.2013.05.030. …

Structure-based discovery of potent and selective melatonin receptor agonists

02 Mar 2020 | BioXFEL Publications | Contributor(s): Nilkanth N Patel, Xi Ping Huang, Jessica M Grandner, Linda C Johansson, Benjamin Stauch, John D McCorvy, Yongfeng Liu, Bryan Roth, Vsevolod Katritch

http://dx.doi.org/10.7554/elife.53779 Melatonin receptors MT1 and MT2 are involved in synchronizing circadian rhythms and are important targets for treating sleep and mood disorders, type-2 diabetes and cancer. Here, we performed large scale structure-based virtual screening for new ligand …

Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs

09 Oct 2019 | BioXFEL Publications | Contributor(s): Aleksandra Luginina, Anastasiia Gusach, Egor Marin, Alexey Mishin, Rebecca Brouillette, Petr Popov, Anna Shiriaeva, Élie Besserer-Offroy, Jean-Michel Longpré, Elizaveta Lyapina, Andrii Ishchenko, Nilkanth N Patel, Vitaly Polovinkin, Nadezhda Safronova, Andrey Bogorodskiy, Evelina Edelweiss, Hao Hu, Uwe Weierstall, Wei Liu, Alexander Batyuk, Valentin Gordeliy, Gye Won Han, Philippe Sarret, Vsevolod Katritch, Valentin Borshchevskiy, Vadim Cherezov

http://dx.doi.org/10.1126/sciadv.aax2518 The G protein–coupled cysteinyl leukotriene receptor CysLT1R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT1R antagonists are widely …

Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals

12 Nov 2018 | BioXFEL Publications | Contributor(s): Cecilia M. Casadei, Karol Nass, Anton Barty, Mark S. Hunter, Celestino Padeste, Ching-Ju Tsai, Sébastien Boutet, Marc Messerschmidt, Leonardo Sala, Garth J. Williams, Dmitry Ozerov, Matthew Coleman, Xiao-Dan Li, Matthias Frank, Bill Pedrini

http://dx.doi.org/10.1107/s2052252518014641 Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional …

Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19

31 Jul 2014 | BioXFEL Publications | Contributor(s): Sherif I. Elshahawi, Theresa A. Ramelot, Jayaraman Seetharaman, Jing Chen, Shanteri Singh, Yunhuang Yang, Kari Pederson, Madan K. Kharel, Rong Xiao, Scott Lew, Ragothaman M. Yennamalli, Mitchell Miller, Fengbin Wang, Liang Tong, Gaetano T. Montelione, Michael A. Kennedy, Craig A. Bingman, Haining Zhu, George Phillips, Jon S. Thorson

http://dx.doi.org/10.1021/cb500327m Sherif I. Elshahawi and Theresa A. Ramelot and Jayaraman Seetharaman and Jing Chen and Shanteri Singh and Yunhuang Yang and Kari Pederson and Madan K. Kharel and Rong Xiao and Scott Lew and Ragothaman M. Yennamalli and Mitchell D. Miller and Fengbin Wang and …

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. D. Coe and M. O. Wiedorn and J. Knoska and D. Oberthuer and R. A. Tuckey and P. Yu and M. Dyba and …

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

19 Dec 2017 | 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/10.1107/s0108767317099081 journal-article Stagno, J.R. et al., 2017. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a92–a92. Available at: …

Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation

28 Mar 2013 | BioXFEL Publications | Contributor(s): Kevin K. Desai, Craig A. Bingman, George Phillips, Ronald T. Raines

http://dx.doi.org/10.1021/bi4002375 journal-article Desai, K.K. et al., 2013. Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation. Biochemistry, 52(15), pp.2518–2525. Available at: http://dx.doi.org/10.1021/bi4002375. Kevin K. Desai and Craig A. …

Sub-Femtosecond Free-Electron Laser Pulses

07 May 2015 | BioXFEL Publications | Contributor(s): W. Helml, A. R. Maier, W. Schweinberger, I. Grguraš, P. Radcliffe, G. Doumy, C. Roedig, J. Gagnon, M. Messerschmidt, S. Schorb, C. Bostedt, F. Grüner, L. F. DiMauro, D. Cubaynes, J. D. Bozek, Th. Tschentscher, J. T. Costello, M. Meyer, R. Coffee, S. Düsterer, A. L. Cavalieri, R. Kienberger

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

Subcongenic Analyses Reveal Complex Interactions between Distal Chromosome 4 Genes Controlling Diabetogenic B Cells and CD4 T Cells in Nonobese Diabetic Mice

26 Jun 2012 | BioXFEL Publications | Contributor(s): J. Stolp, Y.-G. Chen, S. L. Cox, V. Henck, W. Zhang, S.-W. Tsaih, H. Chapman, T. Stearns, D. V. Serreze, P. A. Silveira

http://dx.doi.org/10.4049/jimmunol.1200120 journal-article Stolp, J. et al., 2012. Subcongenic Analyses Reveal Complex Interactions between Distal Chromosome 4 Genes Controlling Diabetogenic B Cells and CD4 T Cells in Nonobese Diabetic Mice. The Journal of Immunology, 189(3), pp.1406–1417. …

Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser

22 Sep 2020 | BioXFEL Publications | Contributor(s): T. Burian, J. Chalupský, V. Hájková, M. Toufarová, V. Vorlíček, S. Hau-Riege, J. Krzywinski, J.D. Bozek, C. Bostedt, A.T. Graf, U.F. Jastrow, S. Kreis, R.A. London, M. Messerschmidt, S. Moeller, R. Sobierajski, K. Tiedtke, M. De Grazia, T. Auguste, B. Carré, S. Guizard, H. Merdji, N. Medvedev, L. Juha

http://dx.doi.org/10.1103/physrevapplied.14.034057 journal-article Burian, T. et al., 2020. Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser. Physical Review Applied, 14(3). Available at: http://dx.doi.org/10.1103/physrevapplied.14.034057. T. …

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 GPCRs. Trends in Pharmacological Sciences, 37(12), pp.1055–1069. Available at: …

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 (PKM2) in Its Dimeric Form. Biochemistry, 55(33), pp.4731–4736. Available at: …

Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA synthesis

10 May 2024 | BioXFEL Publications | Contributor(s): Caleb Chang, Grace Zhou, Christie Lee Luo, Sarah Eleraky, Madeline Moradi, Yang Gao

http://dx.doi.org/10.1016/j.jbc.2024.107361 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chang, C., Zhou, G., Lee Luo, C., Eleraky, S., Moradi, M., & Gao, Y. (2024). Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA …

Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography

01 Feb 2018 | BioXFEL Publications | Contributor(s): Dan Bi Lee, Jong-Min Kim, Jong Hyeon Seok, Ji-Hye Lee, Jae Deok Jo, Ji Young Mun, Chelsie E Conrad, Jesse David Coe, Garrett Charles Nelson, Brenda Hogue, Thomas A. White, Nadia Zatsepin, Uwe Weierstall, Anton Barty, Henry Chapman, Petra Fromme, John Spence, Mi Sook Chung, Chang-Hyun Oh, Kyung Hyun Kim

http://dx.doi.org/10.1038/s41598-018-20899-9 journal-article Lee, D.B. et al., 2018. Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography. Scientific Reports, 8(1). Available at: http://dx.doi.org/10.1038/s41598-018-20899-9. Dan Bi Lee …

Suppression of lipopolysaccharide-induced inflammatory responses in RAW 264.7 murine macrophages by aqueous extract of Clinopodium vulgare L. (Lamiaceae)

20 Sep 2009 | BioXFEL Publications | Contributor(s): David R. Burk, Patti Senechal-Willis, Linda C. Lopez, Brenda Hogue, Sasha M. Daskalova

http://dx.doi.org/10.1016/j.jep.2009.09.026 journal-article Burk, D.R. et al., 2009. Suppression of lipopolysaccharide-induced inflammatory responses in RAW 264.7 murine macrophages by aqueous extract of Clinopodium vulgare L. (Lamiaceae). Journal of Ethnopharmacology, 126(3), pp.397–405. …

Surface coatings for microfluidic biomedical devices

16 Aug 2021 | BioXFEL Publications | Contributor(s): M. Sonker, B.G. Abdallah, A. Ros

http://dx.doi.org/10.1016/b978-0-12-819971-8.00003-2 book-chapter Sonker, M., Abdallah, B.G. & Ros, A., 2021. Surface coatings for microfluidic biomedical devices. Microfluidic Devices for Biomedical Applications, pp.79–123. Available at: http://dx.doi.org/10.1016/b978-0-12-819971-8.00003-2. …

Surface coatings for microfluidic-based biomedical devices

01 Nov 2013 | BioXFEL Publications | Contributor(s): B.G. Abdallah, A. Ros

http://dx.doi.org/10.1533/9780857097040.1.63 book-chapter Abdallah, B.G. & Ros, A., 2013. Surface coatings for microfluidic-based biomedical devices. Microfluidic Devices for Biomedical Applications, pp.63–99. Available at: http://dx.doi.org/10.1533/9780857097040.1.63. B.G. Abdallah and A. Ros

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

19 Mar 2021 | BioXFEL Publications | Contributor(s): Saminathan Ramakrishnan, Jason R. Stagno, Chelsie E Conrad, Jienyu Ding, Ping Yu, Yuba R. Bhandari, Yun-Tzai Lee, Gary Pauly, Oleksandr Yefanov, Max Oliver Wiedorn, Juraj Knoska, Dominik Oberthür, Thomas A. White, Anton Barty, Valerio Mariani, Chufeng Li, Wolfgang Brehm, William F. Heinz, Valentin Magidson, Stephen Lockett, Mark S. Hunter, Sébastien Boutet, Nadia Zatsepin, Xiaobing Zuo, Thomas D. Grant, Suraj Pandey, Marius Schmidt, John Spence, Henry Chapman, Yun-Xing Wang

http://dx.doi.org/10.1038/s41467-021-21838-5 AbstractTime-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in …

Synchrotron topographic evaluation of strain around craters generated by irradiation with X-ray pulses from free electron laser with different intensities

11 Sep 2015 | BioXFEL Publications | Contributor(s): W. Wierzchowski, K. Wieteska, R. Sobierajski, D. Klinger, J. Pełka, D. Żymierska, C. Paulmann, S.P. Hau-Riege, R.A. London, A. Graf, T. Burian, J. Chalupský, J. Gaudin, J. Krzywinski, S. Moeller, M. Messerschmidt, J. Bozek, Ch. Bostedt

http://dx.doi.org/10.1016/j.nimb.2015.07.115 W. Wierzchowski and K. Wieteska and R. Sobierajski and D. Klinger and J. Pełka and D. Żymierska and C. Paulmann and S.P. Hau-Riege and R.A. London and A. Graf and T. Burian and J. Chalupský and J. Gaudin and J. Krzywinski and S. Moeller and M. …

Synthesis and biochemical characterization of EGF receptor in a water-soluble membrane model system

06 Jun 2017 | BioXFEL Publications | Contributor(s): Tiffany M. Scharadin, Wei He, Yianni Yiannakou, Alexey A. Tomilov, Matthew Saldana, Gino A. Cortopassi, Kermit L. Carraway, Matthew Coleman, Paul T. Henderson

http://dx.doi.org/10.1371/journal.pone.0177761 journal-article Scharadin, T.M. et al., 2017. Synthesis and biochemical characterization of EGF receptor in a water-soluble membrane model system L. Buday, ed. PLOS ONE, 12(6), p.e0177761. Available at: …

Synthesis and structural studies of 16‐ferrocenemethyl‐estra‐1,3,5(10)‐triene‐3,17β‐diol and its interaction with human serum albumin by fluorescence spectroscopy and in silico docking approaches

06 Feb 2020 | BioXFEL Publications | Contributor(s): José A. Carmona‐Negrón, José M. Liboy‐Lugo, Alberto Santana, Enrique Meléndez

http://dx.doi.org/10.1002/aoc.5483 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carmona‐Negrón, J.A. et al., 2020. Synthesis and structural studies of 16‐ferrocenemethyl‐estra‐1,3,5(10)‐triene‐3,17β‐diol and its interaction with human serum albumin by …

Synthesis of Novel Heterocyclic Ferrocenyl Chalcones and Their Biological Evaluation

11 Sep 2023 | BioXFEL Publications | Contributor(s): Ámbar M. Alsina-Sánchez, Sebastián Montalvo-Vázquez, Nilmary Grafals-Ruiz, Carmen Acosta, Emily M. Ormé, Israel Rodriguez, Sara M. Delgado-Rivera, Arthur Tinoco, Suranganie Dharmawardhane, Ingrid C. Montes-González

http://dx.doi.org/10.1021/acsomega.3c01830 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Alsina-Sánchez, Á. M., Montalvo-Vázquez, S., Grafals-Ruiz, N., Acosta, C., Ormé, E. M., Rodríguez, I., Delgado-Rivera, S. M., Tinoco, A. D., Dharmawardhane, S., & Montes-González, I. C. …

Synthesis of two fluorescent GTPγS molecules and their biological relevance

10 Mar 2017 | BioXFEL Publications | Contributor(s): Denise J. Trans, Ruoli Bai, J. Bennet Addison, Ruiwu Liu, Ernest Hamel, Matthew Coleman, Paul T. Henderson

http://dx.doi.org/10.1080/15257770.2016.1231320 journal-article Trans, D.J. et al., 2017. Synthesis of two fluorescent GTPγS molecules and their biological relevance. Nucleosides, Nucleotides and Nucleic Acids, 36(6), pp.379–391. Available at: http://dx.doi.org/10.1080/15257770.2016.1231320. …

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, 16(5), pp.3348–3351. Available at: http://dx.doi.org/10.1021/acs.nanolett.6b00981. Maia Azubel and …

Synthesis, structure, docking and cytotoxic studies of ferrocene–hormone conjugates for hormone-dependent breast cancer application

22 Nov 2018 | BioXFEL Publications | Contributor(s): José A. Carmona-Negrón, Alberto Santana, Arnold L. Rheingold, Enrique Meléndez

http://dx.doi.org/10.1039/c8dt01856a Ferrocene–estrogen conjugates can be recognized by ERα, suggesting that estrogens could serve as vectors to target specifically breast cancer cell lines. journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carmona-Negrón, J.A. et al., 2019. …

Synthetic group A streptogramin antibiotics that overcome Vat resistance

23 Sep 2020 | BioXFEL Publications | Contributor(s): Qi Li, Jenna Pellegrino, D. John Lee, Arthur A. Tran, Hector Chaires, Ruoxi Wang, Jesslyn E. Park, Kaijie Ji, David Chow, Na Zhang, Axel F. Brilot, Justin T. Biel, Gydo Van Zundert, Kenneth Borrelli, Dean Shinabarger, Cindy Wolfe, Beverly Murray, Matthew P. Jacobson, Estelle Mühle, Olivier Chesneau, James Fraser, Ian B. Seiple

http://dx.doi.org/10.1038/s41586-020-2761-3 journal-article Li, Q. et al., 2020. Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature, 586(7827), pp.145–150. Available at: http://dx.doi.org/10.1038/s41586-020-2761-3. Qi Li and Jenna Pellegrino and D. John Lee and …

T box RNA decodes both the information content and geometry of tRNA to affect gene expression

15 Apr 2013 | BioXFEL Publications | Contributor(s): J. C. Grigg, Y. Chen, F. J. Grundy, T. M. Henkin, L. Pollack, A. Ke

http://dx.doi.org/10.1073/pnas.1222214110 journal-article Grigg, J.C. et al., 2013. T box RNA decodes both the information content and geometry of tRNA to affect gene expression. Proceedings of the National Academy of Sciences, 110(18), pp.7240–7245. Available at: …

Tabletop source for intense hard X-rays: toward a compact XFEL

28 Oct 2014 | Seminars

Dr. William Graves ASU Biophysics Seminar Series Today x-ray science is pursued either at major facilities housed in national labs, where the large synchrotrons and x-ray free-electron lasers (XFELs) produce an x-ray brilliance of at least 1020 photons/(sec mm2 mrad2 0.1%), or else it is pursued …

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy

09 Jul 2014 | BioXFEL Publications | Contributor(s): Jan Kern, Rosalie Tran, Roberto Alonso-Mori, Sergey Koroidov, Nathaniel Echols, Johan Hattne, Mohamed Ibrahim, Sheraz Gul, Hartawan Laksmono, Raymond G. Sierra, Richard J. Gildea, Guangye Han, Julia Hellmich, Benedikt Lassalle-Kaiser, Ruchira Chatterjee, Aaron S. Brewster, Claudiu A. Stan, Carina Glöckner, Alyssa Lampe, Dörte DiFiore, Despina Milathianaki, Alan R. Fry, M. Marvin Seibert, Jason E. Koglin, Erik Gallo, Jens Uhlig, Dimosthenis Sokaras, Tsu-Chien Weng, Petrus H. Zwart, David Skinner, Michael J. Bogan, Marc Messerschmidt, Pieter Glatzel, Garth J. Williams, Sébastien Boutet, Paul D. Adams, Athina Zouni, Johannes Messinger, Nicholas K. Sauter, Uwe Bergmann, Junko Yano, Vittal K. Yachandra

journal-article http://dx.doi.org/10.1038/ncomms5371 Kern, J. et al., 2014. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications, 5. Available at: http://dx.doi.org/10.1038/ncomms5371. Jan Kern and Rosalie Tran and Roberto …

Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma.

25 May 2020 | BioXFEL Publications | Contributor(s): Wei Wu, Ross A. Okimoto, Collin Michael Blakely, James Fraser, Trever G. Bivona

http://dx.doi.org/10.1200/jco.2020.38.15_suppl.9526 9526 Background: Lung cancer remains the leading cause of death from cancer around the world. Several oncogenic drivers have been identified from large cancer genome projects focused mainly on profiling early-stage lung cancers. Targeted …

Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

16 Sep 2019 | BioXFEL Publications | Contributor(s): Michael Thompson, Benjamin A. Barad, Alexander M. Wolff, Hyun Sun Cho, Friedrich Schotte, Daniel M. C. Schwarz, Philip Anfinrud, James Fraser

http://dx.doi.org/10.1038/s41557-019-0329-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Thompson, M.C. et al., 2019. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nature Chemistry, 11(11), pp.1058–1066. Available at: …

Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme:

22 Nov 2018 | BioXFEL Publications | Contributor(s): Michael Thompson, Benjamin A Barad, Alexander M Wolff, Hyun Sun Cho, Friedrich Schotte, Daniel M.C. Schwarz, Philip Anfinrud, James Fraser

http://dx.doi.org/10.1101/476432 Correlated motions of proteins and their bound solvent molecules are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved methods hold promise for addressing this challenge but have …

Temporal and Spatial Temperature Measurement in Insulator-Based Dielectrophoretic Devices

03 Jun 2014 | BioXFEL Publications | Contributor(s): Asuka Nakano, Jinghui Luo, Alexandra Ros

http://dx.doi.org/10.1021/ac501083h journal-article Nakano, A., Luo, J. & Ros, A., 2014. Temporal and Spatial Temperature Measurement in Insulator-Based Dielectrophoretic Devices. Analytical Chemistry, 86(13), pp.6516–6524. Available at: http://dx.doi.org/10.1021/ac501083h. Asuka Nakano and …

Ternary structure reveals mechanism of a membrane diacylglycerol kinase

17 Dec 2015 | BioXFEL Publications | Contributor(s): Dianfan Li, Phillip J. Stansfeld, Mark S. P. Sansom, Aaron Keogh, Lutz Vogeley, Nicole Howe, Joseph A. Lyons, David Aragao, Petra Fromme, Raimund Fromme, Shibom Basu, Ingo Grotjohann, Christopher Kupitz, Kimberley Rendek, Uwe Weierstall, Nadia Zatsepin, Vadim Cherezov, Wei Liu, Sateesh Bandaru, Niall J. English, Cornelius Gati, Anton Barty, Oleksandr Yefanov, Henry Chapman, Kay Diederichs, Marc Messerschmidt, Sébastien Boutet, Garth J. Williams, M. Marvin Seibert, Martin Caffrey

http://dx.doi.org/10.1038/ncomms10140 Dianfan Li and Phillip J. Stansfeld and Mark S. P. Sansom and Aaron Keogh and Lutz Vogeley and Nicole Howe and Joseph A. Lyons and David Aragao and Petra Fromme and Raimund Fromme and Shibom Basu and Ingo Grotjohann and Christopher Kupitz and Kimberley Rendek …

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

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

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

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

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

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

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

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

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

The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome

16 Mar 2018 | BioXFEL Publications | Contributor(s): Joshua M Tokuda, Ren Ren, Robert F Levendosky, Rebecca J Tay, Ming Yan, Lois Pollack, Gregory D Bowman

http://dx.doi.org/10.1093/nar/gky206 journal-article Tokuda, J.M. et al., 2018. The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Research, 46(10), pp.4978–4990. Available at: http://dx.doi.org/10.1093/nar/gky206. Joshua M Tokuda and …

The Catalytic Cycle of Water Oxidation in Crystallized Photosystem II Complexes: Performance and Requirements for Formation of Intermediates

04 Jan 2019 | BioXFEL Publications | Contributor(s): Gennady Ananyev, Shatabdi Roy-Chowdhury, Colin Gates, Petra Fromme, G. Charles Dismukes

http://dx.doi.org/10.1021/acscatal.8b04513 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ananyev, G. et al., 2019. The Catalytic Cycle of Water Oxidation in Crystallized Photosystem II Complexes: Performance and Requirements for Formation of Intermediates. ACS Catalysis, …

The Coherent X-ray Imaging Data Bank

31 Dec 2010 | Publications | Contributor(s): F. R. N. C. Maia

www.cxidb.org The Coherent X-ray Imaging Data Bank (CXIDB) is a database offering scientists access to data from Coherent X-ray Imaging (CXI) experiments, including serial femtosecond crystallography and single particle imaging. www.cxidb.org The Coherent X-ray Imaging Data Bank Filipe R …

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

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

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

The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins

26 Nov 2013 | BioXFEL Publications | Contributor(s): Jeremy R. Lohman, Ming Ma, Marianne E. Cuff, Lance Bigelow, Jessica Bearden, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1002/prot.24485 journal-article Lohman, J.R. et al., 2013. The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins. Proteins: Structure, Function, and Bioinformatics, 82(7), pp.1210–1218. Available at: …

The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina

16 Dec 2021 | BioXFEL Publications | Contributor(s): Abigael Kosgei, Mitchell Miller, Minakshi Bhardwaj, Weijun Xu, Jon S. Thorson, Steven G. Van Lanen, George Phillips

http://dx.doi.org/10.1107/s2053230x21012322 Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique …

The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region

14 Dec 2022 | BioXFEL Publications | Contributor(s): Baris Cakilkaya, Ibrahim Halil Kavakli, Hasan Demirci

http://dx.doi.org/10.1016/j.jbc.2022.102794 journal-article Cakilkaya, B., Kavakli, I. H., & DeMirci, H. (2023). The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region. Journal of Biological Chemistry, 299(1), 102794. …

The crystal structure ofAbsH3: A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway

27 Aug 2020 | BioXFEL Publications | Contributor(s): Jonathan Clinger, Xiachang Wang, Wenlong Cai, Yanyan Zhu, Mitchell Miller, Chang‐Guo Zhan, Steven G. Van Lanen, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1002/prot.25994 journal-article Clinger, J.A. et al., 2020. The crystal structure ofAbsH3: A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway. Proteins: Structure, Function, and Bioinformatics, 89(1), pp.132–137. Available …

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 human UNG2 toward destruction. Nature Structural & Molecular Biology, 23(10), pp.933–940. Available …

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 American Chemical Society, 138(24), pp.7636–7648. Available at: …

The detection and subsequent volume optimization of biological nanocrystals

15 May 2015 | BioXFEL Publications | Contributor(s): Joseph Luft, Jennifer R. Wolfley, Eleanor Cook Franks, Angela M. Lauricella, Ellen J. Gualtieri, Edward Snell, Rong Xiao, John K. Everett, Gaetano T. Montelione

http://dx.doi.org/10.1063/1.4921199 Joseph R. Luft and Jennifer R. Wolfley and Eleanor Cook Franks and Angela M. Lauricella and Ellen J. Gualtieri and Edward H. Snell and Rong Xiao and John K. Everett and Gaetano T. Montelione Luft, J.R. et al., 2015. The detection and subsequent volume …

The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern

17 Jun 2013 | BioXFEL Publications | Contributor(s): A.V. Martin, A.J. Morgan, T. Ekeberg, N.D. Loh, F.R.N.C. Maia, F. Wang, J.C.H. Spence, H.N. Chapman

http://dx.doi.org/10.1364/oe.21.015102 journal-article Martin, A.V. et al., 2013. The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern. Optics Express, 21(13), p.15102. Available at: http://dx.doi.org/10.1364/oe.21.015102. A.V. Martin and A.J. …

The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR–Ligand Interactions

07 Dec 2015 | BioXFEL Publications | Contributor(s): Alexander Heifetz, Ewa I. Chudyk, Laura Gleave, Matteo Aldeghi, Vadim Cherezov, Dmitri G. Fedorov, Philip C. Biggin, Mike J. Bodkin

http://dx.doi.org/10.1021/acs.jcim.5b00644 Alexander Heifetz and Ewa I. Chudyk and Laura Gleave and Matteo Aldeghi and Vadim Cherezov and Dmitri G. Fedorov and Philip C. Biggin and Mike J. Bodkin Heifetz, A. et al., 2016. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical …

The Gamification of XFEL Education Using XFEL Crystal Blaster

06 May 2022 | BioXFEL Publications | Contributor(s): Fiacre Kabayiza, Sarah Woodruff, William J. Bauer

http://dx.doi.org/10.3390/cryst12050671 Novel groundbreaking techniques, such as serial femtosecond crystallography (SFX), which utilizes X-ray free-electron lasers (XFELs), have led to impressive advances in the field of structural biology. However, educating the next generation of scientists on …

The ideal crystal for structural biology

21 Oct 2021 | BioXFEL Publications | Contributor(s): Edward Snell, Diana Monteiro, Sarah EJ Bowman

http://dx.doi.org/10.1107/s0108767321098901 journal-article Snell, E., Monteiro, D., & Bowman, S. (2021). The ideal crystal for structural biology. Acta Crystallographica Section A Foundations and Advances, 77(a1), a109–a109. https://doi.org/10.1107/s0108767321098901 Edward Snell and Diana …

The impact of base stacking on the conformations and electrostatics of single-stranded DNA

17 Feb 2017 | BioXFEL Publications | Contributor(s): Alex Plumridge, Steve P. Meisburger, Kurt Andresen, Lois Pollack

http://dx.doi.org/10.1093/nar/gkx140 journal-article Plumridge, A. et al., 2017. The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Research. Available at: http://dx.doi.org/10.1093/nar/gkx140. Alex Plumridge and Steve P. Meisburger and Kurt …

The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor

03 Nov 2015 | BioXFEL Publications | Contributor(s): Rebecca L. Miller, Aaron A. Thompson, Claudio Trapella, Remo Guerrini, Davide Malfacini, Nilkanth N Patel, Gye Won Han, Vadim Cherezov, Girolamo Caló, Vsevolod Katritch, Raymond C. Stevens

http://dx.doi.org/10.1016/j.str.2015.07.024 Rebecca L. Miller and Aaron A. Thompson and Claudio Trapella and Remo Guerrini and Davide Malfacini and Nilkanth Patel and Gye Won Han and Vadim Cherezov and Girolamo Caló and Vsevolod Katritch and Raymond C. Stevens Miller, R.L. et al., 2015. The …

The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm

23 Sep 2014 | BioXFEL Publications | Contributor(s): Haiguang Liu, John Spence

Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will …

The influence of promiscuous metals on metalloprotein structure: complementary techniques to separate the good, the bad and the ugly

19 Dec 2017 | BioXFEL Publications | Contributor(s): Edward Snell, M. Elizabeth Snell, Oliver B. Zeldin, Geoffrey W. Grime, Elspeth F. Garman

http://dx.doi.org/10.1107/s0108767317097677 journal-article Snell, E.H. et al., 2017. The influence of promiscuous metals on metalloprotein structure: complementary techniques to separate the good, the bad and the ugly. Acta Crystallographica Section A Foundations and Advances, 73(a1), …

The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly

04 Feb 2020 | BioXFEL Publications | Contributor(s): Premila P. Samuel, Mark A. White, William C. Ou, David Case, George Phillips, John S. Olson

http://dx.doi.org/10.1016/j.bpj.2020.01.031 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Samuel, P.P. et al., 2020. The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly. Biophysical Journal, 118(6), pp.1381–1400. Available at: …

The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules

26 Feb 2021 | BioXFEL Publications | Contributor(s): Laura Lemel, Katarzyna Nieścierowicz, M. Dolores García-Fernández, Leonardo Darré, Thierry Durroux, Marta Busnelli, Mylène Pezet, Fabrice Rébeillé, Juliette Jouhet, Bernard Mouillac, Carmen Domene, Bice Chini, Vadim Cherezov, Christophe J. Moreau

http://dx.doi.org/10.1016/j.jlr.2021.100059 journal-article Lemel, L. et al., 2021. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules. Journal of Lipid Research, 62, p.100059. Available at: …

The linac coherent light source single particle imaging road map

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

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

The lipid phase preference of the adenosine A2A receptor depends on its ligand binding state

30 Apr 2019 | BioXFEL Publications | Contributor(s): M. Gertrude Gutierrez, Jacob Deyell, Kate L. White, Lucia C. Dalle Ore, Vadim Cherezov, Raymond C. Stevens, Noah Malmstadt

http://dx.doi.org/10.1039/c8cc10130b As cholesterol fraction increases, ligand-bound receptor occupies more vesicle surface area, demonstrating co-localization with the cholesterol-rich phase. journal-article Gutierrez, M.G. et al., 2019. The lipid phase preference of the adenosine A2A receptor …

The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source

22 Feb 2019 | BioXFEL Publications | Contributor(s): Raymond G. Sierra, Alexander Batyuk, Zhibin Sun, Andrew Aquila, Mark S. Hunter, Thomas J. Lane, Mengning Liang, Chun Hong Yoon, Roberto Alonso-Mori, Rebecca Armenta, Jean-Charles Castagna, Michael Hollenbeck, Ted O. Osier, Matt Hayes, Jeff Aldrich, Robin Curtis, Jason E. Koglin, Theodore Rendahl, Evan Rodriguez, Sergio Carbajo, Serge Guillet, Rob Paul, Philip Hart, Kazutaka Nakahara, Gabriella Carini, Hasan Demirci, E. Han Dao, Brandon Hayes, Yashas P. Rao, Matthieu Chollet, Yiping Feng, Franklin D. Fuller, Christopher Kupitz, Takahiro Sato, Matthew H. Seaberg, Sanghoon Song, Tim B. Van Driel, Hasan Yavas, Diling Zhu, Aina E. Cohen, Soichi Wakatsuki, Sébastien Boutet

http://dx.doi.org/10.1107/s1600577519001577 The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, …

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

27 May 2022 | BioXFEL Publications | Contributor(s): Galen J. Correy, Daniel W. Kneller, Gwyndalyn Phillips, Swati Pant, Silvia Russi, Aina E. Cohen, George Meigs, James Holton, Stefan Gahbauer, Michael Thompson, Alan Ashworth, Leighton Coates, Andrey Kovalevsky, Flora Meilleur, James Fraser

http://dx.doi.org/10.1126/sciadv.abo5083 The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of …

The mythical metal – insights on the accuracy of metal identification in structural biology

26 Sep 2023 | BioXFEL Publications | Contributor(s): Edward Snell, Elspeth F. Garman, Geoff W. Grime, Aina E. Cohen, Sarah EJ Bowman

http://dx.doi.org/10.1107/s2053273323097188 journal-article Snell, E. H., Garman, E. F., Grime, G. W., Cohen, A. E., & Bowman, S. E. J. (2023). The mythical metal – insights on the accuracy of metal identification in structural biology. Acta Crystallographica Section A Foundations and Advances, …

The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies

22 Oct 2021 | BioXFEL Publications | Contributor(s): Serdar Durdagi, Timucin Avsar, Muge Didem Orhan, Muge Serhatli, Bertan Koray Balcioglu, Hasan Umit Ozturk, Alisan Kayabolen, Yuksel Cetin, Seyma Aydinlik, Tugba Bagci-Onder, Saban Tekin, Hasan Demirci, Mustafa Guzel, Atilla Akdemir, Seyma Calis, Lalehan Oktay, Ilayda Tolu, Yasar Enes Butun, Ece Erdemoglu, Alpsu Olkan, Nurettin Tokay, Şeyma Işık, Aysenur Ozcan, Elif Acar, Sehriban Buyukkilic, Yesim Yumak

http://dx.doi.org/10.1016/j.ymthe.2021.10.014 journal-article Durdagi, S., Avsar, T., Orhan, M. D., Serhatli, M., Balcioglu, B. K., Ozturk, H. U., Kayabolen, A., Cetin, Y., Aydinlik, S., Bagci-Onder, T., Tekin, S., Demirci, H., Guzel, M., Akdemir, A., Calis, S., Oktay, L., Tolu, I., Butun, Y. E., …

The phase problem for two-dimensional crystals. II. Simulations

03 Sep 2018 | BioXFEL Publications | Contributor(s): Romain D. Arnal, Yun Zhao, Alok K. Mitra, John Spence, Rick P. Millane

http://dx.doi.org/10.1107/s2053273318008707 Phasing of diffraction data from two-dimensional crystals using only minimal molecular envelope information is investigated by simulation. Two-dimensional crystals are an attractive target for studying membrane proteins using X-ray free-electron lasers, …

The Pixel Anomaly Detection Tool: a user-friendly GUI for classifying detector frames using machine-learning approaches

12 Feb 2024 | BioXFEL Publications | Contributor(s): Gihan Kaushylal Ketawala, Caitlin M. Reiter, Petra Fromme, Sabine Botha

http://dx.doi.org/10.1107/s1600576724000116 Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, …

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

30 Mar 2020 | BioXFEL Publications | Contributor(s): Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert William Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit Groenhof, Emina Stojkovic, Janne A Ihalainen, Marius Schmidt, Sebastian Westenhoff

http://dx.doi.org/10.7554/elife.53514 Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial …