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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: http://dx.doi.org/10.1002/wrna.1349. NSF-STC Biology with X-ray Lasers (NSF-1231306) journal-article

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

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

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

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 …

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. Biophysical Reviews, 8(2), pp.139–149. Available at: http://dx.doi.org/10.1007/s12551-016-0196-8. Joshua …

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. Neuropathology of Drug Addictions and Substance Misuse, pp.169–180. Available at: …

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 Tutorials".  ACA 2016 Workshop Site   Workshop format: The workshop will start with an introductory …

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 X-ray sources. TheCrystFELsoftware suite has been under development since 2009, just before the first …

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, A.H. et al., 2016. Measuring and modeling diffuse scattering in protein X-ray crystallography. …

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 Brent Segelke and Paul D. Hoeprich and Thomas Huser and Ted A. Laurence and Vladimir L. Motin and Brett …

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. Mor Kessans, S.A. et al., 2016. Immunological Characterization of Plant-Based HIV-1 Gag/Dgp41 …

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 al., 2016. Visualizing aerosol-particle injection for diffractive-imaging experiments. Optics …

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: http://dx.doi.org/10.1364/hilas.2016.hm3b.1. Matthias Fuchs

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. Available at: http://dx.doi.org/10.1038/ncomms10882. Peter A. Meyer and Stephanie Socias and Jason Key …

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 crystallography. Archives of Biochemistry and Biophysics, 602, pp.61–68. Available at: …

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. Hartin and M. Hemmer and R. Hobbs and Y. Hua and W.R. Huang and R. Letrun and N. Matlis and V. …

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 an Actuated Microfluidic Nanowell Device. Crystal Growth & Design. Available at: …

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. Olson and Hetal Patel and Petra Fromme and Kathryn F. Sykes Hansen, D.T. et al., 2016. Polyclonal …

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 of the new emerging X-ray free electron laser (XFEL) technology. Since the world's first XFEL …

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 (CalS11), an enzyme in calicheamicin biosynthesis. Structural Dynamics, 3(1), p.012004. Available …

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.

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 …

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. Available at: http://dx.doi.org/10.1016/j.bpj.2015.11.1166. Premila P. Samuel and William Ou and George …

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 Phase for Serial Femtosecond Crystallography. Biophysical Journal, 110(3), p.59a. Available at: …

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 Cryo-EM. Methods. Available at: http://dx.doi.org/10.1016/j.ymeth.2016.02.007. NSF-STC Biology with …

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 Chelsie E. Conrad and Raimund Fromme and Alexander Schaffer and Katerina Dörner and Daniel James and …

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 gradient insulator-based dielectrophoresis. Analyst. Available at: http://dx.doi.org/10.1039/c5an02430g. …

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 Omar N. Demerdash and Julie C. Mitchell and James A. Wells and James S. Fraser and Andrej Sali …

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 Lutman and Agostino Marinelli and Marc Messerschmidt and Kiyonobu Nagaya and Jim Turner and Kiyoshi Ueda …

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 focusing with high numerical aperture multilayer Laue lens. Available at: …

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 Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1–55. Available at: …

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 and Benjamin Erk and Lars Gumprecht and Lotte Holmegaard and Andreas Hartmann and Robert Hartmann …

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. Synapse, 70(5), pp.181–186. Available at: http://dx.doi.org/10.1002/syn.21892. Katherine M. Evely and …

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), pp.255–272. Available at: http://dx.doi.org/10.2174/0929866523666160120152937. NSF-STC Biology with …

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), pp.315–326. Available at: http://dx.doi.org/10.1016/j.bpj.2015.12.011. Maria L. Sushko and Dennis G. Thomas …

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 diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of …

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 Biochemistry and Biophysics. Available at: http://dx.doi.org/10.1016/j.abb.2016.01.004. journal-article

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 grown crystals at SACLA - developments and results . Acta Cryst Sect A Found Adv, 71(a1), …

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 P. Kalverda and Edward H. Snell and Hironori Niki and Arwen R. Pearson and Michael E. Webb Monteiro, …

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 Capotondi and Emanuele Pedersoli and Anton Barty and Henry N. Chapman and Philip J. Bones and Romain D. …

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 Chelsie E. Conrad and Raimund Fromme and Katerina Doerner and Matthias Frank and Daniel James and …

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 and Thomas R. Schneider Schneider, T.R. et al., 2015. Serial synchrotron crystallography …

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 or crystallization.

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 …

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), pp.2644–2653. Available at: http://dx.doi.org/10.1016/j.bpj.2015.10.039. Julie L. Sutton and Lois Pollack

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 and Andrei V. Rode Eckerskorn, N. et al., 2015. Optically Induced Forces Imposed in an Optical …

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 News, 28(6), pp.25–30. Available at: http://dx.doi.org/10.1080/08940886.2015.1101324. NSF-STC Biology …

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 micro-injection molded nozzles for serial femtosecond crystallography sample delivery. Review of Scientific …

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 macromolecular structures, and diffuse scattering, which reports on correlations in charge density …

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 …

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 sources and XFELs.

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 and Daniel R. Noguera and Blake A. Simmons and Kenneth L. Sale and John Ralph and Timothy J. Donohue …

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 beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive …

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 and Aaron S Brewster and Iris D Young and Tara Michels-Clark and Andrew Aquila and Mengning Liang …

XFELs open a new era in structural chemical biology

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

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

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

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

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

BioXFEL Graduate Student Cross-Training Scholarship

11 Nov 2015 | Teaching Materials

BioXFEL is committed to providing our students with opportunities to diversify their skill sets and integrate themselves into our highly multidisciplinary Center. In addition to the workshops, conferences and online courses, we will now be offering our students the opportunity to train in another …

BioXFEL Scholar Application Form

10 Nov 2015 | Teaching Materials

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Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

10 Nov 2015 | Teaching Materials

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL …

Indexing ambiguity in SFX resolved using expectation maximization algorithm

10 Nov 2015 | Teaching Materials

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 …

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

05 Nov 2015 | BioXFEL Publications | Contributor(s): Kyle P. Eagen, Tom A. Hartl, Roger D. Kornberg

journal-article http://dx.doi.org/10.1016/j.cell.2015.10.026 Eagen, K.P., Hartl, T.A. & Kornberg, R.D., 2015. Stable Chromosome Condensation Revealed by Chromosome Conformation Capture. Cell, 163(4), pp.934–946. Available at: http://dx.doi.org/10.1016/j.cell.2015.10.026. Kyle P. Eagen and …

Chromatin-remodeling and the initiation of transcription

05 Nov 2015 | BioXFEL Publications | Contributor(s): Yahli Lorch, Roger Kornberg

http://dx.doi.org/10.1017/s0033583515000116 AbstractThe nucleosome serves as a general gene repressor by the occlusion of regulatory and promoter DNA sequences. Repression is relieved by the SWI/SNF-RSC family of chromatin-remodeling complexes. Research reviewed here has revealed the essential …

Introduction to XRayView Crystallographic Software

04 Nov 2015 | Teaching Materials

Dr. George Phillips introduces the basic concepts of crystallography focusing on the reciprocal lattice and Ewald sphere construction and using the XRayView software developed in his lab to help visualize these concepts.

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 …

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

02 Nov 2015 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Mercedes Alfonso-Prieto, Rahel Woldeyes, James Fraser, Michael L. Klein, Giacomo Fiorin, William F. DeGrado

http://dx.doi.org/10.1073/pnas.1518493112 Jessica L. Thomaston and Mercedes Alfonso-Prieto and Rahel A. Woldeyes and James S. Fraser and Michael L. Klein and Giacomo Fiorin and William F. DeGrado Thomaston, J.L. et al., 2015. High-resolution structures of the M2 channel from influenza A virus …

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

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

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

Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892

29 Oct 2015 | BioXFEL Publications | Contributor(s): Jeffrey D. Rudolf, Lance Bigelow, Changsoo Chang, Marianne E. Cuff, Jeremy R. Lohman, Chin-Yuan Chang, Ming Ma, Dong Yang, Shonda Clancy, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1021/acs.biochem.5b01008 Jeffrey D. Rudolf and Lance Bigelow and Changsoo Chang and Marianne E. Cuff and Jeremy R. Lohman and Chin-Yuan Chang and Ming Ma and Dong Yang and Shonda Clancy and Gyorgy Babnigg and Andrzej Joachimiak and George N. Phillips and Ben Shen Rudolf, J.D. …

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

27 Oct 2015 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, James Fraser, Henry Van Den Bedem

http://dx.doi.org/10.1371/journal.pcbi.1004507 Daniel A. Keedy and James S. Fraser and Henry van den Bedem Keedy, D.A., Fraser, J.S. & van den Bedem, H., 2015. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit A. Shehu, ed. PLoS Comput Biol, 11(10), p.e1004507. …

Accurate determination of segmented X-ray detector geometry

22 Oct 2015 | BioXFEL Publications | Contributor(s): Oleksandr Yefanov, Valerio Mariani, Cornelius Gati, Thomas A. White, Henry Chapman, Anton Barty

http://dx.doi.org/10.1364/oe.23.028459 Oleksandr Yefanov and Valerio Mariani and Cornelius Gati and Thomas A. White and Henry N. Chapman and Anton Barty Yefanov, O. et al., 2015. Accurate determination of segmented X-ray detector geometry. Optics Express, 23(22), p.28459. Available at: …

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 …

Overview of Serial Femtosecond Crystallography

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

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

Virus Crystallography

14 Oct 2015 | Teaching Materials | Contributor(s): Robert M Lawrence

Dr. Rob Lawrence describes the unique problems associated with crystallization of virus particles and different methods to overcome them.

When Your Crystals Bite

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

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

Optimizing crystallization hits - small to large and large to small

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

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

Practical Considerations for Crystallographic Data Analysis

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

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

Applications of TEM for Evaluation and Optimization of Crystal Growth

14 Oct 2015 | Teaching Materials | Contributor(s): Guillermo Calero

Dr. Guillero Calero discusses using transmission electron microscopy to characterize, evaluate and subsequently optimize the growth of crystals.

What is the outcome of your crystallization experiment

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

Joe Luft discusses the detection of hits in crystallization screening experiments for both macro and nanocrystals.

Strategies to sample crystallization space

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

Joe Luft discusses crystallization screening strategies to maximize the likelihood of success.

Fundamentals of Crystal Growth

14 Oct 2015 | Teaching Materials | Contributor(s): Edward Snell, Eaton E Lattman

Dr. Ed Lattman discusses the foundations of crystallography and theoretical and practical considerations including X-ray radiation and production and crystallization nucleation, growth and optimization.

2015 HWI Crystallization Workshop

13 Oct 2015 | Workshops | Contributor(s): Tom Grant, Bill Bauer, Edward Snell

Crystallization is the major bottleneck to 3D structure determination using X-ray crystallography. In this workshop we will discuss many tenets of successful crystallization for both conventional and serial crystallography. Many topics will be covered including fundamentals of crystal growth, …

Using XFELs to measure the solution structures of biomolecules

13 Oct 2015 | Teaching Materials

Dr. Lois Pollack presents an introduction to small and wide angle X-ray solution scattering techniques and describes the advances made possible by XFELs.

Single Particle Reconstruction

13 Oct 2015 | Teaching Materials

Dr. Dilano Saldin discusses recent advances in algorithms for single particle reconstruction from solution scattering data at XFELs.

Extraction of fast changes in the structure of a disordered ensemble of photoexcited biomolecules

13 Oct 2015 | Teaching Materials

Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation. We show here that quantities extractable from multiple …

Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells

13 Oct 2015 | Teaching Materials

X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the `diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that …

Post-refinement method for snapshot serial crystallography

13 Oct 2015 | Teaching Materials

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

Mapping the continuous reciprocal space intensity of X-ray serial crystallography

13 Oct 2015 | Teaching Materials

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by …

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

13 Oct 2015 | Teaching Materials

We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast …

Double-focusing mixing jet for XFEL study of chemical kinetics

13 Oct 2015 | Teaching Materials

Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

High-resolution structure of viruses from random diffraction snapshots

13 Oct 2015 | Teaching Materials

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the …

Deducing fast electron density changes in uncrystallized biomolecules

13 Oct 2015 | Teaching Materials

We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a …

Serial femtosecond crystallography of G-protein coupled receptors

13 Oct 2015 | Teaching Materials

G protein–coupled receptors (GPCRs) are eukaryotic membrane proteins that have a central role in cellular communication and have become key drug targets. To overcome the difficulties of growing GPCRs crystals, Liu et al. (p. 1521) used an x-ray free-electron laser to determine a …

Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

09 Oct 2015 | Teaching Materials

Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even …

3D Single Particle Structure Recovery

07 Oct 2015 | Teaching Materials | Contributor(s): Ahmad Hosseinizadeh

Dr. Ahmad Hosseinizadeh discuss different pathways to recovering the structure of single particles from XFEL snapshots.

Energy Landscapes

07 Oct 2015 | Teaching Materials | Contributor(s): Ali Dashti

Energy landscapes and continuous conformational mapping of molecular machines.

Manifold Embedding

07 Oct 2015 | Teaching Materials | Contributor(s): Peter Schwander

From single particle snapshots to movies of molecular machines and energy landscapes.

Angular Momentum Decomposition

07 Oct 2015 | Teaching Materials | Contributor(s): Dilano Saldin

Dr. Dilano Saldin discusses using angular momentum decomposition in the analysis of single and multi-particle imaging with XFELs.

Imaging of Objects by Coherent Diffraction of X-Ray FEL Pulses

03 Oct 2015 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

http://dx.doi.org/10.1007/978-3-319-04507-8_27-1 Richard A. Kirian and Henry N. Chapman Kirian, R.A. & Chapman, H.N., 2015. Imaging of Objects by Coherent Diffraction of X-Ray FEL Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1–55. Available at: …

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

30 Sep 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, Lillian R Kenner, Matthew Warkentin, Rahel Woldeyes, Jesse B Hopkins, Michael Thompson, Aaron S Brewster, Andrew H Van Benschoten, Elizabeth L Baxter, Monarin Uervirojnangkoorn, Scott E McPhillips, Jinhu Song, Roberto Alonso-Mori, James Holton, William I Weis, Axel T Brunger, S Michael Soltis, Henrik Lemke, Ana Gonzalez, Nicholas K Sauter, Aina E Cohen, Henry Van Den Bedem, Robert E Thorne, James Fraser

Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which …

Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

29 Sep 2015 | BioXFEL Publications | Contributor(s): Jeremy R. Lohman, Ming Ma, Jerzy Osipiuk, Boguslaw Nocek, Youngchang Kim, Changsoo Chang, Marianne Cuff, Jamey Mack, Lance Bigelow, Hui Li, Michael Endres, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1073/pnas.1515460112 Jeremy R. Lohman and Ming Ma and Jerzy Osipiuk and Boguslaw Nocek and Youngchang Kim and Changsoo Chang and Marianne Cuff and Jamey Mack and Lance Bigelow and Hui Li and Michael Endres and Gyorgy Babnigg and Andrzej Joachimiak and George N. Phillips and Ben …

Structural Basis for Ligand Recognition and Functional Selectivity at Angiotensin Receptor

29 Sep 2015 | BioXFEL Publications | Contributor(s): Haitao Zhang, Hamiyet Unal, Russell Desnoyer, Gye Won Han, Nilkanth N Patel, Vsevolod Katritch, Sadashiva S. Karnik, Vadim Cherezov, Raymond C. Stevens

http://dx.doi.org/10.1074/jbc.m115.689000 Haitao Zhang and Hamiyet Unal and Russell Desnoyer and Gye Won Han and Nilkanth Patel and Vsevolod Katritch and Sadashiva S. Karnik and Vadim Cherezov and Raymond C. Stevens Zhang, H. et al., 2015. Structural Basis for Ligand Recognition and Functional …

Towards phasing using high X-ray intensity

29 Sep 2015 | BioXFEL Publications | Contributor(s): Lorenzo Galli, Sang-Kil Son, Thomas R. M. Barends, Thomas A. White, Anton Barty, Sabine Botha, Sébastien Boutet, Carl Caleman, R. Bruce Doak, Max H. Nanao, Karol Nass, Robert L. Shoeman, Nicusor Timneanu, Robin Santra, Ilme Schlichting, Henry Chapman

X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a …