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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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June 2016 Site Visit Agenda
21 Apr 2016 | Downloads
…
https://www.bioxfel.org/resources/918
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Protein Crystallization in an Actuated Microfluidic Nanowell Device
25 Feb 2016 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme, Alexandra Ros
http://dx.doi.org/10.1021/acs.cgd.5b01748 Bahige G. Abdallah and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2016. Protein Crystallization in …
https://www.bioxfel.org/resources/915
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Polyclonal Antibody Production for Membrane Proteins via Genetic Immunization
24 Feb 2016 | BioXFEL Publications | Contributor(s): Debra T. Hansen, Mark D. Robida, Felicia M. Craciunescu, Andrey V. Loskutov, Katerina Dörner, John-Charles Rodenberry, Xiao Wang, Tien L. Olson, Hetal Patel, Petra Fromme, Kathryn F. Sykes
http://dx.doi.org/10.1038/srep21925 Debra T. Hansen and Mark D. Robida and Felicia M. Craciunescu and Andrey V. Loskutov and Katerina Dörner and John-Charles Rodenberry and Xiao Wang and Tien L. …
https://www.bioxfel.org/resources/1099
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Reconstructing three-dimensional helical structure with an X-ray free electron laser
23 Feb 2016 | BioXFEL Publications | Contributor(s): M. Uddin
Recovery of three-dimensional structure from single-particle X-ray scattering of completely randomly oriented diffraction patterns as predicted a few decades ago has been realized owing to the advent …
https://www.bioxfel.org/resources/1295
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Loop dynamics of thymidine diphosphate-rhamnose 3′-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis
18 Feb 2016 | BioXFEL Publications | Contributor(s): Lu Han, Shanteri Singh, Jon S. Thorson, George Phillips
http://dx.doi.org/10.1063/1.4941368 Lu Han and Shanteri Singh and Jon S. Thorson and George N. Phillips Han, L. et al., 2016. Loop dynamics of thymidine diphosphate-rhamnose 3′-O-methyltransferase …
https://www.bioxfel.org/resources/929
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The Structural History of RNA Polymerase Transcription Machinery
18 Feb 2016 | Teaching Materials | Contributor(s): Roger Kornberg
Dr. Roger Kornberg, 2006 Nobel Laureate in Chemistry, discusses the structural history of the RNA polymerase II transcription machinery and how it played a role in his successful career.
https://www.bioxfel.org/resources/914
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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 …
https://www.bioxfel.org/resources/1077
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An in Vitro Investigation of Globin Folding and Expression
16 Feb 2016 | BioXFEL Publications | Contributor(s): Premila P. Samuel, William Ou, George Phillips, John S. Olson
http://dx.doi.org/10.1016/j.bpj.2015.11.1166 journal-article Samuel, P.P. et al., 2016. An in Vitro Investigation of Globin Folding and Expression. Biophysical Journal, 110(3), p.209a–210a. …
https://www.bioxfel.org/resources/1420
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Preparation and Delivery of Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography
16 Feb 2016 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Vadim Cherezov, Wei Liu
http://dx.doi.org/10.1016/j.bpj.2015.11.383 Andrii Ishchenko and Vadim Cherezov and Wei Liu Ishchenko, A., Cherezov, V. & Liu, W., 2016. Preparation and Delivery of Microcrystals in Lipidic Cubic …
https://www.bioxfel.org/resources/1078
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Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM
14 Feb 2016 | BioXFEL Publications | Contributor(s): Joachim Frank, Abbas Ourmazd
http://dx.doi.org/10.1016/j.ymeth.2016.02.007 Joachim Frank and Abbas Ourmazd Frank, J. & Ourmazd, A., 2016. Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in …
https://www.bioxfel.org/resources/913
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Macromolecular diffractive imaging using imperfect crystals
10 Feb 2016 | BioXFEL Publications | Contributor(s): Kartik Ayyer, Oleksandr M. Yefanov, Dominik Oberthür, Shatabdi Roy-Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse David Coe, Chelsie E Conrad, Raimund Fromme, Alexander Schaffer, Katerina Dörner, Daniel James, Christopher Kupitz, Markus Metz, Garrett Charles Nelson, Paulraj Lourdu Xavier, Kenneth R. Beyerlein, Marius Schmidt, Iosifina Sarrou, John Spence, Uwe Weierstall, Thomas A. White, Jay-How Yang, Yun Zhao, Mengning Liang, Andrew Aquila, Mark S. Hunter, Joseph S. Robinson, Jason E. Koglin, Sébastien Boutet, Petra Fromme, Anton Barty, Henry Chapman
http://dx.doi.org/10.1038/nature16949 Kartik Ayyer and Oleksandr M. Yefanov and Dominik Oberthür and Shatabdi Roy-Chowdhury and Lorenzo Galli and Valerio Mariani and Shibom Basu and Jesse Coe and …
https://www.bioxfel.org/resources/912
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Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis
08 Feb 2016 | BioXFEL Publications | Contributor(s): Jie Ding, Robert M Lawrence, Paul V. Jones, Brenda Hogue, Mark A. Hayes
http://dx.doi.org/10.1039/c5an02430g Jie Ding and Robert M. Lawrence and Paul V. Jones and Brenda G. Hogue and Mark A. Hayes Ding, J. et al., 2016. Concentration of Sindbis virus with optimized …
https://www.bioxfel.org/resources/911
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CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites
05 Feb 2016 | BioXFEL Publications | Contributor(s): Peter Cimermancic, Patrick Weinkam, T. Justin Rettenmaier, Leon Bichmann, Daniel A. Keedy, Rahel Woldeyes, Dina Schneidman-Duhovny, Omar N. Demerdash, Julie C. Mitchell, James A. Wells, James Fraser, Andrej Sali
http://dx.doi.org/10.1016/j.jmb.2016.01.029 Peter Cimermancic and Patrick Weinkam and T. Justin Rettenmaier and Leon Bichmann and Daniel A. Keedy and Rahel A. Woldeyes and Dina Schneidman-Duhovny and …
https://www.bioxfel.org/resources/910
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Transient lattice contraction in the solid-to-plasma transition
29 Jan 2016 | BioXFEL Publications | Contributor(s): Ken R. Ferguson, Maximilian Bucher, Tais Gorkhover, Sébastien Boutet, Hironobu Fukuzawa, Jason E. Koglin, Yoshiaki Kumagai, Alberto Lutman, Agostino Marinelli, Marc Messerschmidt, Kiyonobu Nagaya, Jim Turner, Kiyoshi Ueda, Garth J. Williams, Philip H. Bucksbaum, Christoph Bostedt
http://dx.doi.org/10.1126/sciadv.1500837 Ken R. Ferguson and Maximilian Bucher and Tais Gorkhover and Sébastien Boutet and Hironobu Fukuzawa and Jason E. Koglin and Yoshiaki Kumagai and Alberto …
https://www.bioxfel.org/resources/909
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One dimensional focusing with high numerical aperture multilayer Laue lens
28 Jan 2016 | BioXFEL Publications | Contributor(s): Saša Bajt, Mauro Prasciolu, Andrew J. Morgan, Henry Chapman, Jacek Krzywinski, Andrzej Andrejczuk
http://dx.doi.org/10.1063/1.4937543 Saša Bajt and Mauro Prasciolu and Andrew J. Morgan and Henry N. Chapman and Jacek Krzywinski and Andrzej Andrejczuk Bajt, S. et al., 2016. One dimensional …
https://www.bioxfel.org/resources/928
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Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses
28 Jan 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman
http://dx.doi.org/10.1007/978-3-319-04507-8_27-2 Richard A. Kirian and Henry N. Chapman Kirian, R.A. & Chapman, H.N., 2015. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser …
https://www.bioxfel.org/resources/1070
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Femtosecond and nanometre visualization of structural dynamics in superheated nanoparticles
25 Jan 2016 | BioXFEL Publications | Contributor(s): Tais Gorkhover, Sebastian Schorb, Ryan Coffee, Marcus Adolph, Lutz Foucar, Daniela Rupp, Andrew Aquila, John D. Bozek, Sascha W. Epp, Benjamin Erk, Lars Gumprecht, Lotte Holmegaard, Andreas Hartmann, Robert Hartmann, Günter Hauser, Peter Holl, Andre Hömke, Per Johnsson, Nils Kimmel, Kai-Uwe Kühnel, Marc Messerschmidt, Christian Reich, Arnaud Rouzée, Benedikt Rudek, Carlo Schmidt, Joachim Schulz, Heike Soltau, Stephan Stern, Georg Weidenspointner, Bill White, Jochen Küpper, Lothar Strüder, Ilme Schlichting, Joachim Ullrich, Daniel Rolles, Artem Rudenko, Thomas Möller, Christoph Bostedt
http://dx.doi.org/10.1038/nphoton.2015.264 Tais Gorkhover and Sebastian Schorb and Ryan Coffee and Marcus Adolph and Lutz Foucar and Daniela Rupp and Andrew Aquila and John D. Bozek and Sascha W. Epp …
https://www.bioxfel.org/resources/908
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Melatonin receptor activation increases glutamatergic synaptic transmission in the rat medial lateral habenula
22 Jan 2016 | BioXFEL Publications | Contributor(s): Katherine M. Evely, Randall L. Hudson, Margarita L. Dubocovich, Samir Haj-dahmane
http://dx.doi.org/10.1002/syn.21892 journal-article Evely, K.M. et al., 2016. Melatonin receptor activation increases glutamatergic synaptic transmission in the rat medial lateral habenula. …
https://www.bioxfel.org/resources/1667
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Serial femtosecond crystallography opens new avenues for Structural Biology
20 Jan 2016 | BioXFEL Publications | Contributor(s): Jesse David Coe, Petra Fromme
http://dx.doi.org/10.2174/0929866523666160120152937 Jesse Coe and Petra Fromme Coe, J. & Fromme, P., 2016. Serial femtosecond crystallography opens new avenues for Structural Biology. PPL, 23(3), …
https://www.bioxfel.org/resources/981
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The Role of Correlation and Solvation in Ion Interactions with B-DNA
19 Jan 2016 | BioXFEL Publications | Contributor(s): Maria L. Sushko, Dennis G. Thomas, Suzette A. Pabit, Lois Pollack, Alexey V. Onufriev, Nathan A. Baker
journal-article http://dx.doi.org/10.1016/j.bpj.2015.12.011 Sushko, M.L. et al., 2016. The Role of Correlation and Solvation in Ion Interactions with B-DNA. Biophysical Journal, 110(2), …
https://www.bioxfel.org/resources/1306
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In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells
11 Jan 2016 | BioXFEL Publications | Contributor(s): Arjen J. Jakobi, Daniel M. Passon, Kèvin Knoops, Francesco Stellato, Mengning Liang, Thomas A. White, Thomas Seine, Marc Messerschmidt, Henry Chapman, Matthias Wilmanns
The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray …
https://www.bioxfel.org/resources/907
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Computational crystallization
11 Jan 2016 | BioXFEL Publications | Contributor(s): Irem Altan, Patrick Charbonneau, Edward Snell
http://dx.doi.org/10.1016/j.abb.2016.01.004 Irem Altan and Patrick Charbonneau and Edward H. Snell Altan, I., Charbonneau, P. & Snell, E.H., 2016. Computational crystallization. Archives of …
https://www.bioxfel.org/resources/1076
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Serial femtosecond crystallography on in vivo grown crystals at SACLA - developments and results
05 Jan 2016 | BioXFEL Publications | Contributor(s): Leonard M. G. Chavas, Sasa Bajt, Lars Gumprecht, Henry Chapman
http://dx.doi.org/10.1107/s2053273315097831 Leonard M. G. Chavas and Sasa Bajt and Lars Gumprecht and Henry N. Chapman Chavas, L.M.G. et al., 2015. Serial femtosecond crystallography on in vivo …
https://www.bioxfel.org/resources/959
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Towards a generalised approach for the time-resolved crystallographic study of enzymes
05 Jan 2016 | BioXFEL Publications | Contributor(s): Diana C. F. Monteiro, Vijay Patel, Christopher P. Bartlett, Shingo Nozaki, Thomas D. Grant, James A. Gowdy, Gary S. Thompson, Arnout P. Kalverda, Edward Snell, Hironori Niki, Arwen R. Pearson, Michael E. Webb
http://dx.doi.org/10.1107/s205327331509957x Diana C. F. Monteiro and Vijay Patel and Christopher P. Bartlett and Shingo Nozaki and Thomas D. Grant and James A. Gowdy and Gary S. Thompson and Arnout …
https://www.bioxfel.org/resources/960
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Phase retrieval for randomly terminated finite crystals
05 Jan 2016 | BioXFEL Publications | Contributor(s): Joe Chen, Rick A. Kirian, Richard J. Bean, Kenneth R. Beyerlein, Miriam Barthelmess, Chun Hong Yoon, Fenglin Wang, Flavio Capotondi, Emanuele Pedersoli, Anton Barty, Henry Chapman, Philip J. Bones, Romain D. Arnal, Rick P. Millane, John Spence
http://dx.doi.org/10.1107/s2053273315099714 Joe P. J. Chen and Rick A. Kirian and Richard J. Bean and Kenneth R. Beyerlein and Miriam Barthelmess and Chun Hong Yoon and Fenglin Wang and Flavio …
https://www.bioxfel.org/resources/961
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Improving resolution in serial crystallography
05 Jan 2016 | BioXFEL Publications | Contributor(s): Kartik Ayyer, Oleksandr M. Yefanov, Dominik Oberthuer, Shatabdi Roy Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse David Coe, Chelsie E Conrad, Raimund Fromme, Katerina Doerner, Matthias Frank, Daniel James, Christopher Kupitz, Markus Metz, Garrett Charles Nelson, Xavier L. Paulraj, Kenneth Beyerlein, Marius Schmidt, Iosifina Sarrou, John Spence, Uwe Weierstall, Thomas A. White, Jayhow Yang, Nadia Zatsepin, Yun Zhao, Mengning Liang, Andrew Aquila, Mark S. Hunter, Joseph S. Robinson, Jason E. Koglin, Sébastien Boutet, Petra Fromme, Anton Barty, Henry Chapman
http://dx.doi.org/10.1107/s2053273315099738 Kartik Ayyer and Oleksandr M. Yefanov and Dominik Oberthuer and Shatabdi Chowdhury and Lorenzo Galli and Valerio Mariani and Shibom Basu and Jesse Coe and …
https://www.bioxfel.org/resources/962
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Serial synchrotron crystallography experiments at EMBL beamline P14 at PETRA III
05 Jan 2016 | BioXFEL Publications | Contributor(s): Thomas R. Schneider, Gleb Bourenkov, Cornelius Gati, Henry Chapman, Lars Redecke, Ulrich Zander, José A. Marquez, Florent Cipriani
http://dx.doi.org/10.1107/s2053273315099805 Thomas R. Schneider and Gleb Bourenkov and Cornelius Gati and Henry N. Chapman and Lars Redecke and Ulrich Zander and José A. Marquez and Florent Cipriani …
https://www.bioxfel.org/resources/963
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Interview with Dilano Saldin
05 Jan 2016 | Teaching Materials
Combining data from new facilities with mathematical methods, Professor Dilano Saldin is in pursuit of a technique to determine the structure of molecules without the need for purification …
https://www.bioxfel.org/resources/868
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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 …
https://www.bioxfel.org/resources/881
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Tuning RNA Flexibility with Helix Length and Junction Sequence
15 Dec 2015 | BioXFEL Publications | Contributor(s): Julie L. Sutton, Lois Pollack
http://dx.doi.org/10.1016/j.bpj.2015.10.039 journal-article Sutton, J.L. & Pollack, L., 2015. Tuning RNA Flexibility with Helix Length and Junction Sequence. Biophysical Journal, 109(12), …
https://www.bioxfel.org/resources/1421
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Optically Induced Forces Imposed in an Optical Funnel on a Stream of Particles in Air or Vacuum
11 Dec 2015 | BioXFEL Publications | Contributor(s): Niko Eckerskorn, Richard Bowman, Richard Kirian, Salah Awel, Max Oliver Wiedorn, Jochen Küpper, Miles J. Padgett, Henry Chapman, Andrei V. Rode
http://dx.doi.org/10.1103/physrevapplied.4.064001 Niko Eckerskorn and Richard Bowman and Richard A. Kirian and Salah Awel and Max Wiedorn and Jochen Küpper and Miles J. Padgett and Henry N. Chapman …
https://www.bioxfel.org/resources/872
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Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources
09 Dec 2015 | BioXFEL Publications | Contributor(s): Marius Schmidt
http://dx.doi.org/10.1080/08940886.2015.1101324 Marius Schmidt Schmidt, M., 2015. Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources. Synchrotron Radiation …
https://www.bioxfel.org/resources/886
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Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery
09 Dec 2015 | BioXFEL Publications | Contributor(s): K. R. Beyerlein, L. Adriano, M. Heymann, R. Kirian, J. Knoška, F. Wilde, H. N. Chapman, S. Bajt
http://dx.doi.org/10.1063/1.4936843 K. R. Beyerlein and L. Adriano and M. Heymann and R. Kirian and J. Knoška and F. Wilde and H. N. Chapman and S. Bajt Beyerlein, K.R. et al., 2015. Ceramic …
https://www.bioxfel.org/resources/927
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Measuring and modeling diffuse scattering in protein X-ray crystallography
07 Dec 2015 | BioXFEL Publications | Contributor(s): Andrew H Van Benschoten, Lin Liu, Ana Gonzalez, Aaron S Brewster, Nicholas K Sauter, James Fraser, Michael Wall
X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive …
https://www.bioxfel.org/resources/944
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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 …
https://www.bioxfel.org/resources/1223
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Multitemperature data and diffuse scattering in X-ray crystallography
07 Dec 2015 | Teaching Materials | Contributor(s): James Fraser
Dr. James Fraser will discuss recent advances in mapping the structural basis of protein conformational dynamics using multitemperature data and diffuse scattering from both conventional synchrotron …
https://www.bioxfel.org/resources/865
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Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin
04 Dec 2015 | BioXFEL Publications | Contributor(s): Kate E. Helmich, Jose Henrique Pereira, Daniel L. Gall, Richard A. Heins, Ryan P. McAndrew, Craig Bingman, Kai Deng, Keefe C. Holland, Daniel R. Noguera, Blake A. Simmons, Kenneth L. Sale, John Ralph, Timothy J. Donohue, Paul D. Adams, George Phillips
http://dx.doi.org/10.1074/jbc.m115.694307 Kate E. Helmich and Jose Henrique Pereira and Daniel L. Gall and Richard A. Heins and Ryan P. McAndrew and Craig Bingman and Kai Deng and Keefe C. Holland …
https://www.bioxfel.org/resources/935
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High-density grids for efficient data collection from multiple crystals
03 Dec 2015 | BioXFEL Publications | Contributor(s): Elizabeth L. Baxter, Laura Aguila, Roberto Alonso-Mori, Christopher Barnes, Christopher A. Bonagura, Winnie Brehmer, Axel T. Brunger, Guillermo Calero, Tom T. Caradoc-Davies, Ruchira Chatterjee, William F. Degrado, James Fraser, Mohamed Ibrahim, Jan Kern, Brian K. Kobilka, Andrew C. Kruse, Karl M. Larsson, Heinrik T. Lemke, Artem Y. Lyubimov, Aashish Manglik, Scott E. McPhillips, Erik Norgren, Siew S. Pang, S. M. Soltis, Jinhu Song, Jessica Thomaston, Yingssu Tsai, William I. Weis, Rahel Woldeyes, Vittal Yachandra, Junko Yano, Athina Zouni, Aina E. Cohen
Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron …
https://www.bioxfel.org/resources/893
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Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II
30 Nov 2015 | BioXFEL Publications | Contributor(s): Raymond G Sierra, Cornelius Gati, Hartawan Laksmono, E Han Dao, Sheraz Gul, Franklin Fuller, Jan Kern, Ruchira Chatterjee, Mohamed Ibrahim, Aaron S Brewster, Iris Diane Young, Tara Michels-Clark, Andrew Aquila, Mengning Liang, Mark S. Hunter, Jason E Koglin, Sébastien Boutet, Elia A Junco, Brandon Hayes, Michael J Bogan, Christina Y Hampton, Elisabetta V Puglisi, Nicholas K Sauter, Claudiu A Stan, Athina Zouni, Junko Yano, Vittal K Yachandra, S Michael Soltis, Joseph D Puglisi, Hasan Demirci
http://dx.doi.org/10.1038/nmeth.3667 Raymond G Sierra and Cornelius Gati and Hartawan Laksmono and E Han Dao and Sheraz Gul and Franklin Fuller and Jan Kern and Ruchira Chatterjee and Mohamed Ibrahim …
https://www.bioxfel.org/resources/1095