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

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

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

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

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

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

3rd BioXFEL International Conference

08 Sep 2015 | Downloads

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

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

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

Real-time observation of the initiation of RNA polymerase II transcription

02 Sep 2015 | BioXFEL Publications | Contributor(s): Furqan M. Fazal, Cong A. Meng, Kenji Murakami, Roger Kornberg, Steven M. Block

journal-article http://dx.doi.org/10.1038/nature14882 Fazal, F.M. et al., 2015. Real-time observation of the initiation of RNA polymerase II transcription. Nature, 525(7568), pp.274–277. Available at: http://dx.doi.org/10.1038/nature14882. Furqan M. Fazal and Cong A. Meng and Kenji Murakami and …

Anomalous nonlinear X-ray Compton scattering

31 Aug 2015 | BioXFEL Publications | Contributor(s): Matthias Fuchs, Mariano Trigo, Jian Chen, Shambhu Ghimire, Sharon Shwartz, Michael Kozina, Mason Jiang, Thomas Henighan, Crystal Bray, Georges Ndabashimiye, Philip H. Bucksbaum, Yiping Feng, Sven Herrmann, Gabriella A. Carini, Jack Pines, Philip Hart, Christopher Kenney, Serge Guillet, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, M. Marvin Seibert, Stefan Moeller, Jerome B. Hastings, David A. Reis

http://dx.doi.org/10.1038/nphys3452 Matthias Fuchs and Mariano Trigo and Jian Chen and Shambhu Ghimire and Sharon Shwartz and Michael Kozina and Mason Jiang and Thomas Henighan and Crystal Bray and Georges Ndabashimiye and Philip H. Bucksbaum and Yiping Feng and Sven Herrmann and Gabriella A. …

Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

26 Aug 2015 | BioXFEL Publications | Contributor(s): David Mavor, James Fraser, Ron Morganti

http://dx.doi.org/10.1101/025452 Ubiquitination is an essential post-translational regulatory process that can control protein stability, localization, and activity. Ubiquitin is essential for eukaryotic life and is highly conserved, varying in only 3 amino acid positions between yeast and humans. …

Toward steering a jet of particles into an x-ray beam with optically induced forces

25 Aug 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/10.1117/12.2191442 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. Toward steering a jet of particles into an x-ray beam with …

Biophysical Characterization of a Vaccine Candidate against HIV-1: The Transmembrane and Membrane Proximal Domains of HIV-1 gp41 as a Maltose Binding Protein Fusion

21 Aug 2015 | BioXFEL Publications | Contributor(s): Zhen Gong, Jose M. Martin-Garcia, Sasha M. Daskalova, Felicia M. Craciunescu, Lusheng Song, Katerina Dörner, Debra T. Hansen, Jay-How Yang, Joshua LaBaer, Brenda Hogue, Tsafrir S. Mor, Petra Fromme

http://dx.doi.org/10.1371/journal.pone.0136507 Zhen Gong and Jose M. Martin-Garcia and Sasha M. Daskalova and Felicia M. Craciunescu and Lusheng Song and Katerina Dörner and Debra T. Hansen and Jay-How Yang and Joshua LaBaer and Brenda G. Hogue and Tsafrir S. Mor and Petra Fromme Gong, Z. et al., …

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

20 Aug 2015 | BioXFEL Publications | Contributor(s): Robert M Lawrence, Chelsie E Conrad, Nadia Zatsepin, Thomas D. Grant, Haiguang Liu, Daniel James, Garrett Charles Nelson, GANESH SUBRAMANIAN, Andrew Aquila, Mark S. Hunter, Mengning Liang, Sébastien Boutet, Jesse David Coe, John Spence, Uwe Weierstall, Wei Liu, Petra Fromme, Vadim Cherezov, Brenda Hogue

http://dx.doi.org/10.1063/1.4929410 Robert M. Lawrence and Chelsie E. Conrad and Nadia A. Zatsepin and Thomas D. Grant and Haiguang Liu and Daniel James and Garrett Nelson and Ganesh Subramanian and Andrew Aquila and Mark S. Hunter and Mengning Liang and Sébastien Boutet and Jesse Coe and John C. …

Preface for Special Issue on Biology with X-ray Lasers 2

17 Aug 2015 | BioXFEL Publications | Contributor(s): Abbas Ourmazd

journal-article http://dx.doi.org/10.1063/1.4928768 Ourmazd, A., 2015. Preface for Special Issue on Biology with X-ray Lasers 2. Structural Dynamics, 2(4), p.041501. Available at: http://dx.doi.org/10.1063/1.4928768. Abbas Ourmazd

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

17 Aug 2015 | BioXFEL Publications | Contributor(s): Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James Fraser

http://dx.doi.org/10.1038/nmeth.3541 Benjamin A Barad and Nathaniel Echols and Ray Yu-Ruei Wang and Yifan Cheng and Frank DiMaio and Paul D Adams and James S Fraser Barad, B.A. et al., 2015. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy. Nat Meth, 12(10), …

2015 Single Particle Imaging Workshop

17 Aug 2015 | Workshops | Contributor(s): Russell Fung

How do you make a movie of a single particle jiggling and wiggling with atomic resolution and ultra-fast temporal resolution? How do you calculate the energy landscape or the kinetics/dynamics of a sequence of conformational changes? What do you do with millions and millions of snapshots, each for …

Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

04 Aug 2015 | BioXFEL Publications | Contributor(s): Raimund Fromme, Andrii Ishchenko, Markus Metz, Shatabdi Roy Chowdhury, Shibom Basu, Sébastien Boutet, Petra Fromme, Thomas A. White, Anton Barty, John Spence, Uwe Weierstall, Wei Liu, Vadim Cherezov

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 …

Structural Characterization of CalS8, a TDP-α-d-Glucose Dehydrogenase Involved in Calicheamicin Aminodideoxypentose Biosynthesis

03 Aug 2015 | BioXFEL Publications | Contributor(s): Shanteri Singh, Karolina Michalska, Lance Bigelow, Michael Endres, Madan K. Kharel, Gyorgy Babnigg, Ragothaman M. Yennamalli, Craig A. Bingman, Andrzej Joachimiak, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1074/jbc.m115.673459 Shanteri Singh and Karolina Michalska and Lance Bigelow and Michael Endres and Madan K. Kharel and Gyorgy Babnigg and Ragothaman M. Yennamalli and Craig A. Bingman and Andrzej Joachimiak and Jon S. Thorson and George N. Phillips Singh, S. et al., 2015. …

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

27 Jul 2015 | BioXFEL Publications | Contributor(s): Andrew H. Van Benschoten, Pavel V. Afonine, Thomas C. Terwilliger, Michael E. Wall, Colin J. Jackson, Nicholas K. Sauter, Paul D. Adams, Alexandre Urzhumtsev, James Fraser

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible …

From deep TLS validation to ensembles of atomic models built from elemental motions

27 Jul 2015 | BioXFEL Publications | Contributor(s): Alexandre Urzhumtsev, Pavel V. Afonine, Andrew H. Van Benschoten, James Fraser, Paul D. Adams

The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because theT,LandSmatrices describe a combination of …

SFX Indexing and Integration with CrystFEL

25 Jul 2015 | Teaching Materials

Dr. Thomas White discusses how to index and integrate serial crystallography images using the CrystFEL software package.

SFX Data Reduction and Preprocessing with Cheetah

25 Jul 2015 | Teaching Materials | Contributor(s): Nadia Zatsepin

Dr. Nadia Zatsepin discusses how to use the software program Cheetah to reduce raw SFX data from LCLS to a set of crystal "hits".

Recent Advances in SFX at BioXFEL

25 Jul 2015 | Teaching Materials | Contributor(s): John Spence

Dr. John Spence, Scientific Director for BioXFEL, discusses recent advances in the field of serial crystallography.

SFX Data Analysis Workshop at 2015 ACA

25 Jul 2015 | Workshops | Contributor(s): Nadia Zatsepin, Tom Grant, Cornelius Gati

Serial femtosecond crystallography has yielded several major and unique advances in structural biology previously unattainable with conventional technologies, including the potential for sub-picosecond time-resolved crystallographic studies, probing cyclic or even non-cyclic reactions. With the …

Apoglobin Stability Is the Major Factor Governing both Cell-free andin VivoExpression of Holomyoglobin

23 Jul 2015 | BioXFEL Publications | Contributor(s): Premila P. Samuel, Lucian P. Smith, George Phillips, John S. Olson

journal-article http://dx.doi.org/10.1074/jbc.m115.672204 Samuel, P.P. et al., 2015. Apoglobin Stability Is the Major Factor Governing both Cell-free andin VivoExpression of Holomyoglobin. Journal of Biological Chemistry, 290(39), pp.23479–23495. Available at: …

Cheetah documentation page 2

23 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Richard Kirian

Cheetah documentation Page 2. Click here for Page 1. Click here for a list of all keywords.  The official Cheetah website is http://www.desy.de/~barty/cheetah/   These pages will not reproduce all the content from the Cheetah site, but are meant as an addendum.   Running Cheetah …

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

22 Jul 2015 | BioXFEL Publications | Contributor(s): Yanyong Kang, X. Edward Zhou, Xiang Gao, Yuanzheng He, Wei Liu, Andrii Ishchenko, Anton Barty, Thomas A. White, Oleksandr Yefanov, Gye Won Han, Qingping Xu, Parker W. De Waal, Jiyuan Ke, M. H. Eileen Tan, Chenghai Zhang, Arne Moeller, Graham M. West, Bruce D. Pascal, Ned Van Eps, Lydia N. Caro, Sergey A. Vishnivetskiy, Regina J. Lee, Kelly M. Suino-Powell, Xin Gu, Kuntal Pal, Jinming Ma, Xiaoyong Zhi, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, Cornelius Gati, Nadia Zatsepin, Dingjie Wang, Daniel James, Shibom Basu, Shatabdi Roy-Chowdhury, Chelsie E Conrad, Jesse David Coe, Haiguang Liu, Stella Lisova, Christopher Kupitz, Ingo Grotjohann, Raimund Fromme, Yi Jiang, Minjia Tan, Huaiyu Yang, Jun Li, Meitian Wang, Zhong Zheng, Dianfan Li, Nicole Howe, Yingming Zhao, Jörg Standfuss, Kay Diederichs, Yuhui Dong, Clinton S. Potter, Bridget Carragher, Martin Caffrey, Hualiang Jiang, Henry Chapman, John Spence, Petra Fromme, Uwe Weierstall, Oliver P. Ernst, Vsevolod Katritch, Vsevolod V. Gurevich, Patrick R. Griffin, Wayne L. Hubbell, Raymond C. Stevens, Vadim Cherezov, Karsten Melcher, H. Eric Xu

http://dx.doi.org/10.1038/nature14656 Yanyong Kang and X. Edward Zhou and Xiang Gao and Yuanzheng He and Wei Liu and Andrii Ishchenko and Anton Barty and Thomas A. White and Oleksandr Yefanov and Gye Won Han and Qingping Xu and Parker W. de Waal and Jiyuan Ke and M. H. Eileen Tan and Chenghai Zhang …

Cheetah documentation

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

What is Cheetah and how do you use it?

Cheetah documentation - all keywords

21 Jul 2015 | Series | Contributor(s): Richard Kirian, Nadia Zatsepin

List of all Cheetah's keywords

Crystallography with an XFEL

21 Jul 2015 | Seminars | Contributor(s): Marc Messerschmidt

Dr. Marc Messerschmidt discusses the design and operation of the X-ray free electron laser at the LCLS. Be sure to grab the attached MP3 audio file to follow along. Topics discussed include: - XFEL fundamentals - LCLS machine capabilities and energy spectrum - Beamlines and instrumentation for …

Data Analysis Scripts

21 Jul 2015 | Downloads

A repository of useful scripts for the analysis of XFEL data. 

Zatsepin_IUCr2015_SFX_software.pdf

21 Jul 2015 | PDF

Zatsepin_IUCr2015_SFX_software.pdf

1. Before your beamtime

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

Advice for preparing for an LCLS beamtime, especially for data analysts.

2. During your beamtime

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

Important tasks for data analysts during the LCLS beamtime.  Explanation of LCLS eLog.

3. Accessing your data

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

Where is your LCLS data? How long will it be there? 

5. Data reduction and hit finding

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Richard A Kirian

LCLS data reduction and hit finding. Running Cheetah at LCLS. Tuning hit finding parameters and understanding Cheetah's output.

9. Indexing, merging, evaluation crystal diffraction data: CrystFEL

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

Indexing, merging, evaluation serial crystallography data

7. Working with LCLS data remotely

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

Working with LCLS data remotely

4. Detectors and geometry

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

CXI detectors and geometry

6. Live data monitoring and interactive hit finding refinement: OnDA

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

OnDA - live data monitoring and interactive hit finding refinement

8. Managing and copying LCLS data

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

LCLS data management and transfer.

Introduction to serial femtosecond crystallography data analysis

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Tom Grant

Introduction to serial femtosecond crystallography (SFX) with X-ray free electron lasers.  Presentation on software for SFX. 

LCLS serial femtosecond crystallography data analysis instructions

21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

SFX data analysis at LCLS Overview.

Confirmation of TTC8 as a disease gene for nonsyndromic autosomal recessive retinitis pigmentosa (RP51)

21 Jul 2015 | BioXFEL Publications | Contributor(s): S. Goyal, M. Jäger, P.N. Robinson, V. Vanita

http://dx.doi.org/10.1111/cge.12644 S. Goyal and M. Jäger and P.N. Robinson and V. Vanita Goyal, S. et al., 2015. Confirmation of TTC8 as a disease gene for nonsyndromic autosomal recessive retinitis pigmentosa (RP51) . Clinical Genetics, 89(4), pp.454–460. Available at: …

Inside Cover: One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites (ChemBioChem 11/2015)

20 Jul 2015 | BioXFEL Publications | Contributor(s): Marcus Fischer, Brian K. Shoichet, James Fraser

http://dx.doi.org/10.1002/cbic.201590029 Marcus Fischer and Brian K. Shoichet and James S. Fraser Fischer, M., Shoichet, B.K. & Fraser, J.S., 2015. Inside Cover: One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites (ChemBioChem 11/2015). ChemBioChem, …

Imprinting a Focused X-Ray Laser Beam to Measure Its Full Spatial Characteristics

15 Jul 2015 | BioXFEL Publications | Contributor(s): J. Chalupský, P. Boháček, T. Burian, V. Hájková, S. P. Hau-Riege, P. A. Heimann, L. Juha, M. Messerschmidt, S. P. Moeller, B. Nagler, M. Rowen, W. F. Schlotter, M. L. Swiggers, J. J. Turner, J. Krzywinski

http://dx.doi.org/10.1103/physrevapplied.4.014004 J. Chalupský and P. Boháček and T. Burian and V. Hájková and S. P. Hau-Riege and P. A. Heimann and L. Juha and M. Messerschmidt and S. P. Moeller and B. Nagler and M. Rowen and W. F. Schlotter and M. L. Swiggers and J. J. Turner and …

Anomalous Behavior of the Homogeneous Ice Nucleation Rate in “No-Man’s Land”

03 Jul 2015 | BioXFEL Publications | Contributor(s): Hartawan Laksmono, Trevor A. McQueen, Jonas A. Sellberg, N. Duane Loh, Congcong Huang, Daniel Schlesinger, Raymond G. Sierra, Christina Y. Hampton, Dennis Nordlund, Martin Beye, Andrew V. Martin, Anton Barty, M. Marvin Seibert, Marc Messerschmidt, Garth J. Williams, Sébastien Boutet, Katrin Amann-Winkel, Thomas Loerting, Lars G. M. Pettersson, Michael J. Bogan, Anders Nilsson

http://dx.doi.org/10.1021/acs.jpclett.5b01164 Hartawan Laksmono and Trevor A. McQueen and Jonas A. Sellberg and N. Duane Loh and Congcong Huang and Daniel Schlesinger and Raymond G. Sierra and Christina Y. Hampton and Dennis Nordlund and Martin Beye and Andrew V. Martin and Anton Barty and M. …

Covariance mapping of two-photon double core hole states in C2H2and C2H6produced by an x-ray free electron laser

02 Jul 2015 | BioXFEL Publications | Contributor(s): M Mucke, V Zhaunerchyk, L J Frasinski, R J Squibb, M Siano, J H D Eland, P Linusson, P Salén, P V D Meulen, R D Thomas, M Larsson, L Foucar, J Ullrich, K Motomura, S Mondal, K Ueda, T Osipov, L Fang, B F Murphy, N Berrah, C Bostedt, J D Bozek, S Schorb, M Messerschmidt, J M Glownia, J P Cryan, R N Coffee, O Takahashi, S Wada, M N Piancastelli, R Richter, K C Prince, R Feifel

http://dx.doi.org/10.1088/1367-2630/17/7/073002 M Mucke and V Zhaunerchyk and L J Frasinski and R J Squibb and M Siano and J H D Eland and P Linusson and P Salén and P v d Meulen and R D Thomas and M Larsson and L Foucar and J Ullrich and K Motomura and S Mondal and K Ueda and T Osipov and L Fang …

Corrigendum: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

30 Jun 2015 | BioXFEL Publications | Contributor(s): Johan Hattne, Nathaniel Echols, Rosalie Tran, Jan Kern, Richard J Gildea, Aaron S Brewster, Roberto Alonso-Mori, Carina Glöckner, Julia Hellmich, Hartawan Laksmono, Raymond G Sierra, Benedikt Lassalle-Kaiser, Alyssa Lampe, Guangye Han, Sheraz Gul, Dörte DiFiore, Despina Milathianaki, Alan R Fry, Alan Miahnahri, William E White, Donald W Schafer, M Marvin Seibert, Jason E Koglin, Dimosthenis Sokaras, Tsu-Chien Weng, Jonas Sellberg, Matthew J Latimer, Pieter Glatzel, Petrus H Zwart, Ralf W Grosse-Kunstleve, Michael J Bogan, Marc Messerschmidt, Garth J Williams, Sébastien Boutet, Johannes Messinger, Athina Zouni, Junko Yano, Uwe Bergmann, Vittal K Yachandra, Paul D Adams, Nicholas K Sauter

http://dx.doi.org/10.1038/nmeth0715-692d Johan Hattne and Nathaniel Echols and Rosalie Tran and Jan Kern and Richard J Gildea and Aaron S Brewster and Roberto Alonso-Mori and Carina Glöckner and Julia Hellmich and Hartawan Laksmono and Raymond G Sierra and Benedikt Lassalle-Kaiser and Alyssa Lampe …

Time-resolved structural studies with serial crystallography: A new light on retinal proteins

29 Jun 2015 | BioXFEL Publications | Contributor(s): Valérie Panneels, Wenting Wu, Ching-Ju Tsai, Przemek Nogly, Jan Rheinberger, Kathrin Jaeger, Gregor Cicchetti, Cornelius Gati, Leonhard M. Kick, Leonardo Sala, Guido Capitani, Chris Milne, Celestino Padeste, Bill Pedrini, Xiao-Dan Li, Jörg Standfuss, Rafael Abela, Gebhard F.X. Schertler

journal-article http://dx.doi.org/10.1063/1.4922774 NSF-STC Biology with X-ray Lasers (NSF-1231306) Panneels, V. et al., 2015. Time-resolved structural studies with serial crystallography: A new light on retinal proteins. Structural Dynamics, 2(4), p.041718. Available at: …

A novel inert crystal delivery medium for serial femtosecond crystallography

29 Jun 2015 | BioXFEL Publications | Contributor(s): Chelsie E Conrad, Shibom Basu, Daniel James, Dingjie Wang, Alexander Schaffer, Shatabdi Roy-Chowdhury, Nadia Zatsepin, Andrew Aquila, Jesse David Coe, Cornelius Gati, Mark S. Hunter, Jason E. Koglin, Christopher Kupitz, Garrett Charles Nelson, GANESH SUBRAMANIAN, Thomas A. White, Yun Zhao, James D Zook, Sébastien Boutet, Vadim Cherezov, John Spence, Raimund Fromme, Uwe Weierstall, Petra Fromme

Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from …

Towards time-resolved serial crystallography in a microfluidic device

26 Jun 2015 | BioXFEL Publications | Contributor(s): Ashtamurthy S. Pawate, Vukica Šrajer, Jeremy Schieferstein, Sudipto Guha, Robert Henning, Irina Kosheleva, Marius Schmidt, Zhong Ren, Paul J. A. Kenis, Sarah Perry

Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction …

Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

26 Jun 2015 | BioXFEL Publications | Contributor(s): Wenting Wu, Przemyslaw Nogly, Jan Rheinberger, Leonhard M. Kick, Cornelius Gati, Garrett Charles Nelson, Xavier Deupi, Jörg Standfuss, Gebhard F.X. Schertler, Valérie Panneels

Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the …

Low- Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography

26 Jun 2015 | BioXFEL Publications | Contributor(s): Geoffrey K. Feld, Michael Heymann, W. Henry Benner, Tommaso Pardini, Ching-Ju Tsai, Sébastien Boutet, Matthew Coleman, Mark S. Hunter, Xiaodan Li, Marc Messerschmidt, Achini Opathalage, Bill Pedrini, Garth J. Williams, Bryan A. Krantz, Seth Fraden, Stefan Hau-Riege, James E. Evans, Brent W. Segelke, Matthias Frank

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target …

Structural and evolutionary relationships of ketosynthase domains from modular polyketide synthases

25 Jun 2015 | BioXFEL Publications | Contributor(s): JR Lohman, A Joachimiak, GN Phillips Jr, B Shen

journal-article http://dx.doi.org/10.1055/s-0035-1556231 Lohman, J. et al., 2015. Structural and evolutionary relationships of ketosynthase domains from modular polyketide synthases. Planta Medica, 81(11). Available at: http://dx.doi.org/10.1055/s-0035-1556231. JR Lohman and A Joachimiak and GN …

Simple convergent-nozzle aerosol injector for single-particle diffractive imaging with X-ray free-electron lasers

19 Jun 2015 | BioXFEL Publications | Contributor(s): R. A. Kirian, S. Awel, N. Eckerskorn, H. Fleckenstein, M. Wiedorn, L. Adriano, S. Bajt, M. Barthelmess, R. Bean, K. R. Beyerlein, L. M. G. Chavas, M. Domaracky, M. Heymann, D. A. Horke, J. Knoska, M. Metz, A. Morgan, D. Oberthuer, N. Roth, T. Sato, P. L. Xavier, O. Yefanov, A. V. Rode, J. Küpper, H. N. Chapman

http://dx.doi.org/10.1063/1.4922648 R. A. Kirian and S. Awel and N. Eckerskorn and H. Fleckenstein and M. Wiedorn and L. Adriano and S. Bajt and M. Barthelmess and R. Bean and K. R. Beyerlein and L. M. G. Chavas and M. Domaracky and M. Heymann and D. A. Horke and J. Knoska and M. Metz and A. Morgan …

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

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

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

Use of triple correlations for the sign determinations of expansion coefficients of symmetric approximations to the diffraction volumes of regular viruses

18 Jun 2015 | BioXFEL Publications | Contributor(s): H. C. Poon, D. K. Saldin

http://dx.doi.org/10.1063/1.4922476 H. C. Poon and D. K. Saldin Poon, H.C. & Saldin, D.K., 2015. Use of triple correlations for the sign determinations of expansion coefficients of symmetric approximations to the diffraction volumes of regular viruses. Structural Dynamics, 2(4), p.041716. Available …

Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements

16 Jun 2015 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, Suzette A. Pabit, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2015.05.006 journal-article Meisburger, S.P., Pabit, S.A. & Pollack, L., 2015. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements. Biophysical Journal, 108(12), pp.2886–2895. Available at: …

Uncoupling Promoter Opening from Start-Site Scanning

13 Jun 2015 | BioXFEL Publications | Contributor(s): Kenji Murakami, Pierre-Jean Mattei, Ralph E. Davis, Huiyan Jin, Craig D. Kaplan, Roger D. Kornberg

journal-article http://dx.doi.org/10.1016/j.molcel.2015.05.021 Murakami, K. et al., 2015. Uncoupling Promoter Opening from Start-Site Scanning. Molecular Cell, 59(1), pp.133–138. Available at: http://dx.doi.org/10.1016/j.molcel.2015.05.021. Kenji Murakami and Pierre-Jean Mattei and Ralph E. …

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

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

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

Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis

10 Jun 2015 | BioXFEL Publications | Contributor(s): Shanteri Singh, Youngchang Kim, Fengbin Wang, Lance Bigelow, Michael Endres, Madan K. Kharel, Gyorgy Babnigg, Craig A. Bingman, Andrzej Joachimiak, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1002/prot.24844 Shanteri Singh and Youngchang Kim and Fengbin Wang and Lance Bigelow and Michael Endres and Madan K. Kharel and Gyorgy Babnigg and Craig A. Bingman and Andrzej Joachimiak and Jon S. Thorson and George N. Phillips Singh, S. et al., 2015. Structural …

Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile α Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors

04 Jun 2015 | BioXFEL Publications | Contributor(s): Ying Wu, Leonardus M. I. Koharudin, Jennifer Mehrens, Maria DeLucia, Chang-Hyeok Byeon, In-Ja L. Byeon, Guillermo Calero, Jinwoo Ahn, Angela M. Gronenborn

journal-article http://dx.doi.org/10.1074/jbc.m115.665513 Wu, Y. et al., 2015. Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile α Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors. Journal of Biological …

Imaging transient melting of a nanocrystal using an X-ray laser

02 Jun 2015 | BioXFEL Publications | Contributor(s): Jesse N. Clark, Loren Beitra, Gang Xiong, David M. Fritz, Henrik T. Lemke, Diling Zhu, Matthieu Chollet, Garth J. Williams, Marc Messerschmidt, Brian Abbey, Ross J. Harder, Alexander M. Korsunsky, Justin S. Wark, David A. Reis, Ian K. Robinson

http://dx.doi.org/10.1073/pnas.1417678112 Jesse N. Clark and Loren Beitra and Gang Xiong and David M. Fritz and Henrik T. Lemke and Diling Zhu and Matthieu Chollet and Garth J. Williams and Marc M. Messerschmidt and Brian Abbey and Ross J. Harder and Alexander M. Korsunsky and Justin S. Wark and …

Extended asymmetric-cut multilayer X-ray gratings

01 Jun 2015 | BioXFEL Publications | Contributor(s): Mauro Prasciolu, Anton Haase, Frank Scholze, Henry Chapman, Saša Bajt

http://dx.doi.org/10.1364/oe.23.015195 Mauro Prasciolu and Anton Haase and Frank Scholze and Henry N. Chapman and Saša Bajt Prasciolu, M. et al., 2015. Extended asymmetric-cut multilayer X-ray gratings. Optics Express, 23(12), p.15195. Available at: http://dx.doi.org/10.1364/oe.23.015195. …

High numerical aperture multilayer Laue lenses

01 Jun 2015 | BioXFEL Publications | Contributor(s): Andrew J. Morgan, Mauro Prasciolu, Andrzej Andrejczuk, Jacek Krzywinski, Alke Meents, David Pennicard, Heinz Graafsma, Anton Barty, Richard J. Bean, Miriam Barthelmess, Dominik Oberthuer, Oleksandr Yefanov, Andrew Aquila, Henry Chapman, Saša Bajt

http://dx.doi.org/10.1038/srep09892 Andrew J. Morgan and Mauro Prasciolu and Andrzej Andrejczuk and Jacek Krzywinski and Alke Meents and David Pennicard and Heinz Graafsma and Anton Barty and Richard J. Bean and Miriam Barthelmess and Dominik Oberthuer and Oleksandr Yefanov and Andrew Aquila and …

Structural Basis for the Stereochemical Control of Amine Installation in Nucleotide Sugar Aminotransferases

29 May 2015 | BioXFEL Publications | Contributor(s): Fengbin Wang, Shanteri Singh, Weijun Xu, Kate E. Helmich, Mitchell Miller, Hongnan Cao, Craig A. Bingman, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1021/acschembio.5b00244 Fengbin Wang and Shanteri Singh and Weijun Xu and Kate E. Helmich and Mitchell D. Miller and Hongnan Cao and Craig A. Bingman and Jon S. Thorson and George N. Phillips Wang, F. et al., 2015. Structural Basis for the Stereochemical Control of Amine …

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites

28 May 2015 | BioXFEL Publications | Contributor(s): Marcus Fischer, Brian K. Shoichet, James Fraser

http://dx.doi.org/10.1002/cbic.201500196 Marcus Fischer and Brian K. Shoichet and James S. Fraser Fischer, M., Shoichet, B.K. & Fraser, J.S., 2015. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. ChemBioChem, 16(11), pp.1560–1564. Available …

Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme's Conformational Freedom and Disorder

22 May 2015 | BioXFEL Publications | Contributor(s): Eynat Dellus-Gur, Mikael Elias, Emilia Caselli, Fabio Prati, Merijn L.M. Salverda, J. Arjan G.M. De Visser, James Fraser, Dan S. Tawfik

journal-article http://dx.doi.org/10.1016/j.jmb.2015.05.011 Dellus-Gur, E. et al., 2015. Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme’s Conformational Freedom and Disorder. Journal of Molecular Biology, 427(14), pp.2396–2409. Available at: …

NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins

21 May 2015 | BioXFEL Publications | Contributor(s): James D Zook, Gina Mo, Nicholas J. Sisco, Felicia M. Craciunescu, Debra T. Hansen, Bobby Baravati, Brian R. Cherry, Kathryn Sykes, Rebekka Wachter, Wade D. Van Horn, Petra Fromme

http://dx.doi.org/10.1016/j.str.2015.03.025 James Zook and Gina Mo and Nicholas J. Sisco and Felicia M. Craciunescu and Debra T. Hansen and Bobby Baravati and Brian R. Cherry and Kathryn Sykes and Rebekka Wachter and Wade D. Van Horn and Petra Fromme Zook, J. et al., 2015. NMR Structure of …

The detection and subsequent volume optimization of biological nanocrystals

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

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

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity

14 May 2015 | BioXFEL Publications | Contributor(s): Joshua R. Kane, David J. Stanley, Judd F. Hultquist, Jeffrey R. Johnson, Nicole Mietrach, Jennifer M. Binning, Stefán R. Jónsson, Sarah Barelier, Billy W. Newton, Tasha L. Johnson, Kathleen E. Franks-Skiba, Ming Li, William L. Brown, Hörður I. Gunnarsson, Adalbjorg Adalbjornsdóttir, James S. Fraser, Reuben S. Harris, Valgerður Andrésdóttir, John D. Gross, Nevan J. Krogan

journal-article http://dx.doi.org/10.1016/j.celrep.2015.04.038 Kane, J.R. et al., 2015. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Reports, 11(8), pp.1236–1250. Available at: …

Possibilities for serial femtosecond crystallography sample delivery at future light sourcesa)

14 May 2015 | BioXFEL Publications | Contributor(s): L. M. G. Chavas, L. Gumprecht, H. N. Chapman

http://dx.doi.org/10.1063/1.4921220 L. M. G. Chavas and L. Gumprecht and H. N. Chapman Chavas, L.M.G., Gumprecht, L. & Chapman, H.N., 2015. Possibilities for serial femtosecond crystallography sample delivery at future light sourcesa). Structural Dynamics, 2(4), p.041709. Available at: …

Purification and biochemical characterization of the ATP synthase from Heliobacterium modesticaldum

12 May 2015 | BioXFEL Publications | Contributor(s): Jay-How Yang, Iosifina Sarrou, Jose M. Martin-Garcia, Shangji Zhang, Kevin E. Redding, Petra Fromme

http://dx.doi.org/10.1016/j.pep.2015.05.006 Jay-How Yang and Iosifina Sarrou and Jose M. Martin-Garcia and Shangji Zhang and Kevin E. Redding and Petra Fromme Yang, J.-H. et al., 2015. Purification and biochemical characterization of the ATP synthase from Heliobacterium modesticaldum. Protein …

Sub-Femtosecond Free-Electron Laser Pulses

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

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

2D Crystallography

06 May 2015 | Teaching Materials

Dr. Mattias Frank discusses new possibilities in the field of 2D crystallography made possible by XFEL sources.

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

05 May 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, James Fraser, Henry Van Den Bedem

Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated …

Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges

30 Apr 2015 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, A. Dashti, P. Schwander, R. Fung, A. Ourmazd

http://dx.doi.org/10.1063/1.4919740 A. Hosseinizadeh and A. Dashti and P. Schwander and R. Fung and A. Ourmazd Hosseinizadeh, A. et al., 2015. Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges. Structural Dynamics, 2(4), p.041601. Available at: …

Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

29 Apr 2015 | BioXFEL Publications | Contributor(s): L. Galli, S.-K. Son, M. Klinge, S. Bajt, A. Barty, R. Bean, C. Betzel, K. R. Beyerlein, C. Caleman, R. B. Doak, M. Duszenko, H. Fleckenstein, C. Gati, B. Hunt, R. A. Kirian, M. Liang, M. H. Nanao, K. Nass, D. Oberthür, L. Redecke, R. Shoeman, F. Stellato, C. H. Yoon, T. A. White, O. Yefanov, J. Spence, H. N. Chapman

http://dx.doi.org/10.1063/1.4919398 L. Galli and S.-K. Son and M. Klinge and S. Bajt and A. Barty and R. Bean and C. Betzel and K. R. Beyerlein and C. Caleman and R. B. Doak and M. Duszenko and H. Fleckenstein and C. Gati and B. Hunt and R. A. Kirian and M. Liang and M. H. Nanao and K. Nass and D. …

Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with AMP

28 Apr 2015 | BioXFEL Publications | Contributor(s): Do Jin Kim, Eduard Bitto, Craig A. Bingman, Hyun-Jung Kim, Byung Woo Han, George Phillips

http://dx.doi.org/10.1002/prot.24821 Do Jin Kim and Eduard Bitto and Craig A. Bingman and Hyun-Jung Kim and Byung Woo Han and George N. Phillips Kim, D.J. et al., 2015. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in …

Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

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

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

Structure determination with weak anomalous signal

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

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

LucY: A Versatile New Fluorescent Reporter Protein

23 Apr 2015 | BioXFEL Publications | Contributor(s): Michele E. Auldridge, Hongnan Cao, Saurabh Sen, Laura P. Franz, Craig A. Bingman, Ragothaman M. Yennamalli, George Phillips, David Mead, Eric J. Steinmetz

http://dx.doi.org/10.1371/journal.pone.0124272 Michele E. Auldridge and Hongnan Cao and Saurabh Sen and Laura P. Franz and Craig A. Bingman and Ragothaman M. Yennamalli and George N. Phillips and David Mead and Eric J. Steinmetz Auldridge, M.E. et al., 2015. LucY: A Versatile New Fluorescent …

The Structure of the PanD/PanZ Protein Complex Reveals Negative Feedback Regulation of Pantothenate Biosynthesis by Coenzyme A

23 Apr 2015 | 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 H. Snell, Hironori Niki, Arwen R. Pearson, Michael E. Webb

http://dx.doi.org/10.1016/j.chembiol.2015.03.017 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. …

2015 Serial Crystallography Data Analysis Workshop at ACA Annual Meeting.

23 Apr 2015 | Workshops | Contributor(s): Nadia Zatsepin, Tom Grant

We are running a serial femtosecond crystallography data analysis workshop at ACA 2015 in Philadelphia, PA, focused on "Serial Crystallography Data Analysis with Cheetah and CrystFEL: Concepts and Tutorials".  www.amercrystalassn.org/2015-wk.02   Workshop format: The workshop will start with an …

The linac coherent light source single particle imaging road map

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

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

Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data

21 Apr 2015 | BioXFEL Publications | Contributor(s): Thomas Barends, Thomas A. White, Anton Barty, Lutz Foucar, Marc Messerschmidt, Roberto Alonso-Mori, Sabine Botha, Henry Chapman, R. Bruce Doak, Lorenzo Galli, Cornelius Gati, Matthias Gutmann, Jason Koglin, Anders Markvardsen, Karol Nass, Dominik Oberthur, Robert L. Shoeman, Ilme Schlichting, Sébastien Boutet

Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo …

framesorter

20 Apr 2015 | Downloads

Framesorter is a script for parsing the output from Cheetah  

Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser

18 Apr 2015 | BioXFEL Publications | Contributor(s): Jesse David Coe, Christopher Kupitz, Shibom Basu, Chelsie E Conrad, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme

http://dx.doi.org/10.1016/bs.mie.2015.01.011 Jesse Coe and Christopher Kupitz and Shibom Basu and Chelsie E. Conrad and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme Coe, J. et al., 2015. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free …

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

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

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

High-Resolution NMR Spectroscopy Reveals Structure of Lipoprotein flpp3

18 Apr 2015 | BioXFEL Publications | Contributor(s): James D Zook, Nicholas Sisco, Gina Mo, Debra Hansen, Felicia Craciunescu, Brian Cherry, Kathryn Sykes, Wade Van Horn, Petra Fromme

http://dx.doi.org/10.1016/j.bpj.2013.11.1142 journal-article Zook, J.D. et al., 2014. High-Resolution NMR Spectroscopy Reveals Structure of Lipoprotein flpp3. Biophysical Journal, 106(2), p.193a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.1142. James D. Zook and Nicholas Sisco and …

Fast Binding Kinetics of RNA Aptamers Measured using a Novel Microfluidic Mixer

18 Apr 2015 | BioXFEL Publications | Contributor(s): Alexander L. Van Slyke, Juan Wang, Avtar Singh, Lois Pollack, Warren R. Zipfel

http://dx.doi.org/10.1016/j.bpj.2013.11.4364 journal-article Van Slyke, A.L. et al., 2014. Fast Binding Kinetics of RNA Aptamers Measured using a Novel Microfluidic Mixer. Biophysical Journal, 106(2), p.796a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.4364. Alexander L. Van Slyke and …

Detection of Protein Nanocrystals Based on the Reversibility of Crystallization

18 Apr 2015 | BioXFEL Publications | Contributor(s): Katerina Dörner, Jose Martin Garcia, Christopher Kupitz, Rebekka M. Wachter, Petra Fromme

http://dx.doi.org/10.1016/j.bpj.2013.11.2597 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Dörner, K. et al., 2014. Detection of Protein Nanocrystals Based on the Reversibility of Crystallization. Biophysical Journal, 106(2), p.458a. Available at: …

Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

18 Apr 2015 | BioXFEL Publications | Contributor(s): Michael E. Wall, Thomas C. Terwilliger, James Fraser, Paul D. Adams, Nicholas K. Sauter, Andrew VanBenschoten

http://dx.doi.org/10.1016/j.bpj.2013.11.2171 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins. Biophysical Journal, 106(2), p.384a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.2171. Michael E. Wall and Thomas C. Terwilliger …

Sequence Analysis and Biophysical Characterization Reveals the Presence of a Long Disordered Region in the CapA Membrane Protein from F. Tularensis

18 Apr 2015 | BioXFEL Publications | Contributor(s): Jose M. Martin, Debra T. Hansen, Andrrey Loskutov, Mark D. Robida, Felicia M. Craciunescu, Kathryn Sykes, Rebekka M. Wachter, Petra Fromme, James P. Allen

http://dx.doi.org/10.1016/j.bpj.2013.11.3806 journal-article Martin, J.M. et al., 2014. Sequence Analysis and Biophysical Characterization Reveals the Presence of a Long Disordered Region in the CapA Membrane Protein from F. Tularensis. Biophysical Journal, 106(2), p.688a. Available at: …

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

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

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

Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.

15 Apr 2015 | Publications

Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for …

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

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

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

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

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

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

Mentoring Manual

14 Apr 2015 | Teaching Materials

This manual was written by the members of the Institute for Broadening Participation and their affiliates. "Each section of this manual is devoted to the perspective and experience of each of the distinct roles in program-based mentoring environments, and organized according to the major …

Simulations on time-resolved structure determination of uncrystallized biomolecules in the presence of shot noise

10 Apr 2015 | BioXFEL Publications | Contributor(s): K. Pande, M. Schmidt, P. Schwander, D. K. Saldin

http://dx.doi.org/10.1063/1.4916980 K. Pande and M. Schmidt and P. Schwander and D. K. Saldin Pande, K. et al., 2015. Simulations on time-resolved structure determination of uncrystallized biomolecules in the presence of shot noise. Structural Dynamics, 2(2), p.024103. Available at: …

Characterization and use of the spent beam for serial operation of LCLS

10 Apr 2015 | BioXFEL Publications | Contributor(s): Sébastien Boutet, Lutz Foucar, Thomas R. M. Barends, Sabine Botha, R. Bruce Doak, Jason E. Koglin, Marc Messerschmidt, Karol Nass, Ilme Schlichting, M. Marvin Seibert, Robert L. Shoeman, Garth J. Williams

X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort …

Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source

09 Apr 2015 | BioXFEL Publications | Contributor(s): Y. Feng, R. Alonso-Mori, T. R. M. Barends, V. D. Blank, S. Botha, M. Chollet, D. S. Damiani, R. B. Doak, J. M. Glownia, J. M. Koglin, H. T. Lemke, M. Messerschmidt, K. Nass, S. Nelson, I. Schlichting, R. L. Shoeman, Yu. V. Shvyd'ko, M. Sikorski, S. Song, S. Stoupin, S. Terentyev, G. J. Williams, D. Zhu, A. Robert, S. Boutet

Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, …