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Double-focusing mixing jet for XFEL study of chemical kinetics

06 Oct 2014 | BioXFEL Publications | Contributor(s): Dingjie Wang, Uwe Weierstall, Lois Pollack, John Spence

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 …

Probing the Nature of Charge Transfer at Nano–Bio Interfaces: Peptides on Metal Oxide Nanoparticles

03 Oct 2014 | BioXFEL Publications | Contributor(s): Pilarisetty Tarakeshwar, Julio L. Palma, Gregory P. Holland, Petra Fromme, Jeffery L. Yarger, Vladimiro Mujica

journal-article http://dx.doi.org/10.1021/jz501854x Tarakeshwar, P. et al., 2014. Probing the Nature of Charge Transfer at Nano–Bio Interfaces: Peptides on Metal Oxide Nanoparticles. The Journal of Physical Chemistry Letters, 5(20), pp.3555–3559. Available at: …

Crystallographic Methods - X-ray Diffraction Physics - Part IX

03 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VIII

01 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

29 Sep 2014 | BioXFEL Publications | Contributor(s): Hung T. Nguyen, Suzette A. Pabit, Steve P. Meisburger, Lois Pollack, David Case

http://dx.doi.org/10.1063/1.4896220 journal-article Nguyen, H.T. et al., 2014. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. The Journal of Chemical Physics, 141(22), p.22D508. Available at: http://dx.doi.org/10.1063/1.4896220. Hung T. …

Crystallographic Methods - X-ray Diffraction Physics - Part VII

28 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VI

25 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine

25 Sep 2014 | BioXFEL Publications | Contributor(s): Brianna B. Williams, Andrew H. Van Benschoten, Peter Cimermancic, Mohamed S. Donia, Michael Zimmermann, Mao Taketani, Atsushi Ishihara, Purna C. Kashyap, James S. Fraser, Michael A. Fischbach

http://dx.doi.org/10.1016/j.chom.2014.09.001 journal-article Williams, B.B. et al., 2014. Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine. Cell Host & Microbe, 16(4), pp.495–503. Available at: …

Microfluidic Platforms for Bimolecular and Nanocrystal Separation

23 Sep 2014 | Seminars | Contributor(s): Alexandra Ros

Dr. Alexandra Ros Analytical and bioanalytical applications of microfluidic devices or so called Lab-on-a-Chip Systems have been an extensive field of research over the past two decades. In many instances, integration of (bio)chemical analyses onto microfluidic platforms has been inspired by …

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

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

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

Crystallographic Methods - X-ray Diffraction Physics - Part V

22 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - Geometrical Crystallography - Part I

19 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

Crystallographic Methods - X-ray Diffraction Physics - Part IV

18 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

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

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

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

Crystallographic Methods - X-ray Diffraction Physics - Part III

15 Sep 2014 | Teaching Materials

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part II

11 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

11 Sep 2014 | Publications

Authors: Kupitz, C., Basu, S., Grotjohann, I., Fromme, R., Zatsepin, N. A., Rendek, K. N., Hunter, M. S., Shoeman, R. L., White, T. A., Wang, D., James, D., Yang, J. H., Cobb, D. E., Reeder, B., Sierra, R. G., Liu, H., Barty, A., Aquila, A. L., Deponte, D., Kirian, R. A., Bari, S., Bergkamp, J. J., …

Crystallographic Methods - X-ray Diffraction Physics - Part I

08 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Silicon single crystal as back-reflector for high-intensity hard x-rays

05 Sep 2014 | BioXFEL Publications | Contributor(s): Tom Pardini, Sébastien Boutet, Joseph Bradley, Tilo Doeppner, Luke B. Fletcher, Dennis F. Gardner, Randy M. Hill, Mark S. Hunter, Jacek Krzywinski, Marc Messerschmidt, Arthur E. Pak, Florian Quirin, Klaus Sokolowski-Tinten, Garth J. Williams, Stefan Hau-Riege

http://dx.doi.org/10.1117/12.2061087 proceedings-article Pardini, T. et al., 2014. Silicon single crystal as back-reflector for high-intensity hard x-rays S. P. Hau-Riege, S. P. Moeller, & M. Yabashi, eds. X-Ray Free-Electron Lasers: Beam Diagnostics, Beamline Instrumentation, and Applications …

Crystallographic Methods - Geometrical Crystallography - Part II

04 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

Psana Tutorial

03 Sep 2014 | Teaching Materials

Chris O'Grady (SLAC) Psana is the main analysis tool developed by LCLS, upon which some other tools are based. It uses a combination of C++ and python. I will discuss recent psana developments and future plans. Recent developments include the ability to express complex analysis ideas with simple …

Cheetah Tutorial

03 Sep 2014 | Teaching Materials

Anton Barty (CFEL)

CASS and SFX SAD Tutorial

03 Sep 2014 | Teaching Materials

Karol Nass (MPI) Extraction of diffraction images of the lysozyme Gadolinium derivative (Barends et al. Science 2013) from the raw LCLS format to HDF5 format. Integration of CrystFEL analysis with CASS start-up scripts. Ab initio SAD phasing of SFX data.

CrystFEL Tutorial

03 Sep 2014 | Teaching Materials

Tom White (CFEL)

cctbx.xfel Tutorial

03 Sep 2014 | Teaching Materials

Nick Sauter (LBNL) Aaron Brewster (LBNL) Oliver Zeldin (Stanford)

Data Analysis and Sample Delivery

29 Aug 2014 | Teaching Materials

John Spence (ASU/LBNL) How XFEL MX differs from MX and why we do it.

Free Electron Lasers and Crystallography

29 Aug 2014 | Teaching Materials

Paul Adams (LBNL) BioXFEL in the greater context of crystallography

SFX Data Reduction and Preprocessing

29 Aug 2014 | Teaching Materials

Anton Barty (CFEL) Photons, detectors and data streams: how to get at the data and what it records. Data reduction and pre-processing: how it works and how to optimize it.

Rapid Data Quality Feedback and Online Monitoring using CASS

29 Aug 2014 | Teaching Materials

Karol Nass (MPI) Description of the layout of CASS software suite and its functionality on the LCLS online and offline data streams. Real time monitoring of the SFX experiment: hit rate, resolution, pixel saturation, 2D powder pattern. Rapid offline processing of the raw LCLS data: crystal hit …

Introduction to CrystFEL

29 Aug 2014 | Teaching Materials

Tom White (CFEL) CrystFEL is a suite of programs that deal with viewing, indexing, integrating and merging serial crystallography data, evaluating its quality and simulating patterns. At the core of CrystFEL is an automated, high throughput processing pipeline which indexes and integrates each …

How good are my data?

29 Aug 2014 | Teaching Materials

Nick Sauter (LBNL) A design goal of the data reduction package cctbx.xfel is to discover and apply the numerous systematic corrections necessary to correctly model XFEL diffraction images. Numerous challenges must be addressed to interpret serial femtosecond diffraction, including an inaccurate …

Practical considerations during processing of serial crystallographic XFEL data

29 Aug 2014 | Teaching Materials

Aaron Brewster (LBNL) Fundamental differences exist between processing rotational data collected at a synchrotron source and data collected during a serial crystallographic XFEL experiment. Practical techniques will be described to enable the user to get the most out of their data using the …

From cctbx to cctbx.xfel and beyond

29 Aug 2014 | Teaching Materials

Johan Hattne (HHMI) Algorithms to process X-ray diffraction images into accurate atomic models of macromolecules have undergone steady refinement over the past decades. As methods by which crystallographic diffraction patters are obtained are further developed, these techniques continue to provide …

Handling sample heterogeneity in serial crystallography

29 Aug 2014 | Teaching Materials

Oliver Zeldin (Stanford) Serial crystallography data is made up of images obtained from a population of slightly in-homogenous crystals. We will discuss clustering and filtering approaches to (1) characterizing sample heterogeneity in unmerged data, and (2) identifying optimal sub-sets of images …

Winning the Battle of Signal vs. Noise

29 Aug 2014 | Teaching Materials

James Holton (UCSF/LBNL) I will review the major sources of error that contribute to macromolecular crystallography (MX) data with a particular focus on MX data from X-ray Free Electron Lasers. The absolute limits will be defined, and the potential of new and future technologies for overcoming …

Clustering and main sources of variance of SFX data

29 Aug 2014 | Teaching Materials

Wolfgang Brehm (University of Konstanz) Clustering approaches and variance analysis are explained using the example of the indexing ambiguity in serial crystallography. Recently published algorithms for detwinning and advancements thereof will be shown. Variance analysis can lead to a more …

BioXFEL Expert Panel Discussion

29 Aug 2014 | Teaching Materials

Expert Panel Discussion including: Anton Barty, Michael Rossman, James Holton, Tom White, Wolfgang Brehm, Oliver Zeldin, John Spence, Karol Nass, Nick Sauter, Aaron Brewster, Johan Hattne

Spectral encoding method for measuring the relative arrival time between x-ray/optical pulses

28 Aug 2014 | BioXFEL Publications | Contributor(s): M. R. Bionta, N. Hartmann, M. Weaver, D. French, D. J. Nicholson, J. P. Cryan, J. M. Glownia, K. Baker, C. Bostedt, M. Chollet, Y. Ding, D. M. Fritz, A. R. Fry, D. J. Kane, J. Krzywinski, H. T. Lemke, M. Messerschmidt, S. Schorb, D. Zhu, W. E. White, R. N. Coffee

journal-article http://dx.doi.org/10.1063/1.4893657 Bionta, M.R. et al., 2014. Spectral encoding method for measuring the relative arrival time between x-ray/optical pulses. Review of Scientific Instruments, 85(8), p.083116. Available at: http://dx.doi.org/10.1063/1.4893657. M. R. Bionta and N. …

Biochemical Characterization and Crystal Structures of a Fungal Family 3  -Glucosidase, Cel3A from Hypocrea jecorina

27 Aug 2014 | BioXFEL Publications | Contributor(s): Saeid Karkehabadi, Kate E. Helmich, Thijs Kaper, Henrik Hansson, Nils-Egil Mikkelsen, Mikael Gudmundsson, Kathleen Piens, Meredith Fujdala, Goutami Banerjee, John S. Scott-Craig, Jonathan D. Walton, George Phillips, Mats Sandgren

http://dx.doi.org/10.1074/jbc.m114.587766 journal-article Karkehabadi, S. et al., 2014. Biochemical Characterization and Crystal Structures of a Fungal Family 3  -Glucosidase, Cel3A from Hypocrea jecorina. Journal of Biological Chemistry, 289(45), pp.31624–31637. Available at: …

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

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

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

2014 Data Analysis Workshop

26 Aug 2014 | Workshops | Contributor(s): Tom Grant, Nadia Zatsepin

Video and interactive web presentations with PDF slides available for download. Description Serial crystallography is a rapidly growing field with a correspondingly rapidly growing user base. One of the main bottlenecks in serial crystallography is the ability to efficiently filter and analyze …

Crystallographic Methods - Introduction and Overview

25 Aug 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Introduction     Protein structural elements: 1° aa sequence,  2° α-helix, β strand, β sheet, loop, 3° domain fold,  4° domain assembly; Overview of biomacromolecular crystallography

Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source

25 Aug 2014 | BioXFEL Publications | Contributor(s): K. Tiedtke, A. A. Sorokin, U. Jastrow, P. Juranić, S. Kreis, N. Gerken, M. Richter, U. Arp, Y. Feng, D. Nordlund, R. Soufli, M. Fernández-Perea, L. Juha, P. Heimann, B. Nagler, H. J. Lee, S. Mack, M. Cammarata, O. Krupin, M. Messerschmidt, M. Holmes, M. Rowen, W. Schlotter, S. Moeller, J. J. Turner

journal-article http://dx.doi.org/10.1364/oe.22.021214 Tiedtke, K. et al., 2014. Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source. Optics Express, 22(18), p.21214. Available at: http://dx.doi.org/10.1364/oe.22.021214. K. Tiedtke and A. A. Sorokin and U. Jastrow …

Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41

23 Aug 2014 | BioXFEL Publications | Contributor(s): Zhen Gong, Sarah A. Kessans, Lusheng Song, Katerina Dörner, Ho-Hsien Lee, Lydia R Meador, Joshua LaBaer, Brenda Hogue, Tsafrir S. Mor, Petra Fromme

http://dx.doi.org/10.1002/pro.2540 journal-article Gong, Z. et al., 2014. Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41. Protein Science, 23(11), pp.1607–1618. Available at: …

Electron microscopy of gold nanoparticles at atomic resolution

21 Aug 2014 | BioXFEL Publications | Contributor(s): M. Azubel, J. Koivisto, S. Malola, D. Bushnell, G. L. Hura, A. L. Koh, H. Tsunoyama, T. Tsukuda, M. Pettersson, H. Hakkinen, R. D. Kornberg

http://dx.doi.org/10.1126/science.1251959 journal-article Azubel, M. et al., 2014. Electron microscopy of gold nanoparticles at atomic resolution. Science, 345(6199), pp.909–912. Available at: http://dx.doi.org/10.1126/science.1251959. M. Azubel and J. Koivisto and S. Malola and D. Bushnell …

Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

19 Aug 2014 | BioXFEL Publications | Contributor(s): Ho-Hsien Lee, Irene Cherni, HongQi Yu, Raimund Fromme, Jeffrey D. Doran, Ingo Grotjohann, Michele Mittman, Shibom Basu, Arpan Deb, Katerina Dörner, Andrew Aquila, Anton Barty, Sébastien Boutet, Henry Chapman, R. Bruce Doak, Mark S. Hunter, Daniel James, Richard Kirian, Christopher Kupitz, Robert M Lawrence, Haiguang Liu, Karol Nass, Ilme Schlichting, Kevin E. Schmidt, M. Marvin Seibert, Robert L. Shoeman, John Spence, Francesco Stellato, Uwe Weierstall, Garth J. Williams, Chunhong Yoon, Dingjie Wang, Nadia Zatsepin, Brenda Hogue, Nobuyuki Matoba, Petra Fromme, Tsafrir S. Mor

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein ofHuman immunodeficiency virus 1(HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral …

Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam

19 Aug 2014 | BioXFEL Publications | Contributor(s): M. R. Sawaya, D. Cascio, M. Gingery, J. Rodriguez, L. Goldschmidt, J.-P. Colletier, M. M. Messerschmidt, S. Boutet, J. E. Koglin, G. J. Williams, A. S. Brewster, K. Nass, J. Hattne, S. Botha, R. B. Doak, R. L. Shoeman, D. P. DePonte, H.-W. Park, B. A. Federici, N. K. Sauter, I. Schlichting, D. S. Eisenberg

http://dx.doi.org/10.1073/pnas.1413456111 journal-article Sawaya, M.R. et al., 2014. Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proceedings of the National Academy of Sciences, 111(35), pp.12769–12774. Available …

Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers

15 Aug 2014 | BioXFEL Publications | Contributor(s): S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, A. Barty, C. Bostedt, J. Bozek, R. Coffee, S. Epp, B. Erk, L. Foucar, R. Hartmann, N. Kimmel, K-U. Kühnel, J. Maurer, M. Messerschmidt, B. Rudek, D. Starodub, J. Thøgersen, G. Weidenspointner, T. A. White, H. Stapelfeldt, D. Rolles, H. N. Chapman, J. Küpper

http://dx.doi.org/10.1039/c4fd00028e S. Stern and L. Holmegaard and F. Filsinger and A. Rouzée and A. Rudenko and P. Johnsson and A. V. Martin and A. Barty and C. Bostedt and J. Bozek and R. Coffee and S. Epp and B. Erk and L. Foucar and R. Hartmann and N. Kimmel and K-U. Kühnel and J. Maurer and …

Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography

14 Aug 2014 | BioXFEL Publications | Contributor(s): Wei Liu, Andrii Ishchenko, Vadim Cherezov

http://dx.doi.org/10.1038/nprot.2014.141 journal-article Liu, W., Ishchenko, A. & Cherezov, V., 2014. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nature Protocols, 9(9), pp.2123–2134. Available at: http://dx.doi.org/10.1038/nprot.2014.141. Wei …

Fixed-target protein serial microcrystallography with an x-ray free electron laser

12 Aug 2014 | BioXFEL Publications | Contributor(s): Mark S. Hunter, Brent W. Segelke, Marc Messerschmidt, Garth J. Williams, Nadia Zatsepin, Anton Barty, W. Henry Benner, David B. Carlson, Matthew Coleman, Alexander Graf, Stefan Hau-Riege, Tommaso Pardini, M. Marvin Seibert, James Evans, Sébastien Boutet, Matthias Frank

http://dx.doi.org/10.1038/srep06026 Mark S. Hunter and Brent Segelke and Marc Messerschmidt and Garth J. Williams and Nadia A. Zatsepin and Anton Barty and W. Henry Benner and David B. Carlson and Matthew Coleman and Alexander Graf and Stefan P. Hau-Riege and Tommaso Pardini and M. Marvin Seibert …

E pluribus unum, no more: from one crystal, many conformations

09 Aug 2014 | BioXFEL Publications | Contributor(s): Rahel Woldeyes, David A Sivak, James Fraser

http://dx.doi.org/10.1016/j.sbi.2014.07.005 Rahel A Woldeyes and David A Sivak and James S Fraser Woldeyes, R.A., Sivak, D.A. & Fraser, J.S., 2014. E pluribus unum, no more: from one crystal, many conformations. Current Opinion in Structural Biology, 28, pp.56–62. Available at: …

Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases

06 Aug 2014 | BioXFEL Publications | Contributor(s): Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George Phillips, Brian G Fox

http://dx.doi.org/10.1186/1754-6834-7-109 journal-article Book, A.J. et al., 2014. Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases. Biotechnology for Biofuels, 7(1), p.109. Available at: http://dx.doi.org/10.1186/1754-6834-7-109. Adam J Book and …

Structure and Substrate Specificity of a Eukaryotic Fucosidase fromFusarium graminearum

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

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

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

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

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

Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules

31 Jul 2014 | BioXFEL Publications | Contributor(s): Rebecca Boll, Arnaud Rouzée, Marcus Adolph, Denis Anielski, Andrew Aquila, Sadia Bari, Cédric Bomme, Christoph Bostedt, John D. Bozek, Henry Chapman, Lauge Christensen, Ryan Coffee, Niccola Coppola, Sankar De, Piero Decleva, Sascha W. Epp, Benjamin Erk, Frank Filsinger, Lutz Foucar, Tais Gorkhover, Lars Gumprecht, André Hömke, Lotte Holmegaard, Per Johnsson, Jens S. Kienitz, Thomas Kierspel, Faton Krasniqi, Kai-Uwe Kühnel, Jochen Maurer, Marc Messerschmidt, Robert Moshammer, Nele L. M. Müller, Benedikt Rudek, Evgeny Savelyev, Ilme Schlichting, Carlo Schmidt, Frank Scholz, Sebastian Schorb, Joachim Schulz, Jörn Seltmann, Mauro Stener, Stephan Stern, Simone Techert, Jan Thøgersen, Sebastian Trippel, Jens Viefhaus, Marc Vrakking, Henrik Stapelfeldt, Jochen Küpper, Joachim Ullrich, Artem Rudenko, Daniel Rolles

This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump–probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular …

Endosomal GPCR signaling turned off by negative feedback actions of PKA and v-ATPase

27 Jul 2014 | BioXFEL Publications | Contributor(s): Alexandre Gidon, Mohammad M Al-Bataineh, Frederic G Jean-Alphonse, Hilary P Stevenson, Tomoyuki Watanabe, Claire Louet, Ashok Khatri, Guillermo Calero, Núria M Pastor-Soler, Thomas J Gardella, Jean-Pierre Vilardaga

http://dx.doi.org/10.1038/nchembio.1589 journal-article Gidon, A. et al., 2014. Endosomal GPCR signaling turned off by negative feedback actions of PKA and v-ATPase. Nature Chemical Biology, 10(9), pp.707–709. Available at: http://dx.doi.org/10.1038/nchembio.1589. Alexandre Gidon and Mohammad …

Identifying, studying and making good use of macromolecular crystals

25 Jul 2014 | BioXFEL Publications | Contributor(s): Guillermo Calero, Aina E. Cohen, Joseph Luft, Janet Newman, Edward Snell

Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name …

Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye–Semiconductor Interface

25 Jul 2014 | BioXFEL Publications | Contributor(s): Katrin R. Siefermann, Chaitanya D. Pemmaraju, Stefan Neppl, Andrey Shavorskiy, Amy A. Cordones, Josh Vura-Weis, Daniel S. Slaughter, Felix P. Sturm, Fabian Weise, Hendrik Bluhm, Matthew L. Strader, Hana Cho, Ming-Fu Lin, Camila Bacellar, Champak Khurmi, Jinghua Guo, Giacomo Coslovich, Joseph S. Robinson, Robert A. Kaindl, Robert W Schoenlein, Ali Belkacem, Daniel M. Neumark, Stephen R. Leone, Dennis Nordlund, Hirohito Ogasawara, Oleg Krupin, Joshua J. Turner, William F. Schlotter, Michael R. Holmes, Marc Messerschmidt, Michael P. Minitti, Sheraz Gul, Jin Z. Zhang, Nils Huse, David Prendergast, Oliver Gessner

http://dx.doi.org/10.1021/jz501264x journal-article Siefermann, K.R. et al., 2014. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye–Semiconductor Interface. The Journal of Physical Chemistry Letters, 5(15), pp.2753–2759. Available at: http://dx.doi.org/10.1021/jz501264x. Katrin …

2nd International BioXFEL Conference Logo

11 Jul 2014 | Downloads | Contributor(s): Tom Grant

Transparent background logo for 2nd BioXFEL Conference

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

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

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

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser

08 Jul 2014 | BioXFEL Publications | Contributor(s): Christopher Kupitz, Shibom Basu, Ingo Grotjohann, Raimund Fromme, Nadia Zatsepin, Kimberly N. Rendek, Mark S. Hunter, Robert L. Shoeman, Thomas A. White, Dingjie Wang, Daniel James, Jay-How Yang, Danielle E. Cobb, Brenda Reeder, Raymond G. Sierra, Haiguang Liu, Anton Barty, Andrew L. Aquila, Daniel Deponte, Richard Kirian, Sadia Bari, Jesse J. Bergkamp, Kenneth R. Beyerlein, Michael J. Bogan, Carl Caleman, Tzu-Chiao Chao, Chelsie E Conrad, Katherine M. Davis, Holger Fleckenstein, Lorenzo Galli, Stefan Hau-Riege, Stephan Kassemeyer, Hartawan Laksmono, Mengning Liang, Lukas Lomb, Stefano Marchesini, Andrew V. Martin, Marc Messerschmidt, Despina Milathianaki, Karol Nass, Alexandra Ros, Shatabdi Roy-Chowdhury, Kevin Schmidt, Marvin Seibert, Jan Steinbrener, Francesco Stellato, Lifen Yan, Chunhong Yoon, Thomas A. Moore, Ana L. Moore, Yulia Pushkar, Garth J. Williams, Sébastien Boutet, R. Bruce Doak, Uwe Weierstall, Matthias Frank, Henry Chapman, John Spence, Petra Fromme

http://dx.doi.org/10.1038/nature13453 Christopher Kupitz and Shibom Basu and Ingo Grotjohann and Raimund Fromme and Nadia A. Zatsepin and Kimberly N. Rendek and Mark S. Hunter and Robert L. Shoeman and Thomas A. White and Dingjie Wang and Daniel James and Jay-How Yang and Danielle E. Cobb and …

Revealing transient structures of nucleosomes as DNA unwinds

03 Jul 2014 | BioXFEL Publications | Contributor(s): Yujie Chen, Joshua M. Tokuda, Traci Topping, Julie L. Sutton, Steve P. Meisburger, Suzette A. Pabit, Lisa M. Gloss, Lois Pollack

http://dx.doi.org/10.1093/nar/gku562 journal-article Chen, Y. et al., 2014. Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Research, 42(13), pp.8767–8776. Available at: http://dx.doi.org/10.1093/nar/gku562. Yujie Chen and Joshua M. Tokuda and Traci Topping and …

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

02 Jul 2014 | BioXFEL Publications | Contributor(s): Diana Fusco, Timothy J. Barnum, Andrew E. Bruno, Joseph Luft, Edward Snell, Sayan Mukherjee, Patrick Charbonneau

http://dx.doi.org/10.1371/journal.pone.0101123 journal-article Fusco, D. et al., 2014. Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms B. Kobe, ed. PLoS ONE, 9(7), p.e101123. Available at: …

Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography

27 Jun 2014 | BioXFEL Publications | Contributor(s): Andrew E. Bruno, Amanda M. Ruby, Joseph Luft, Thomas D. Grant, Jayaraman Seetharaman, Gaetano T. Montelione, John F. Hunt, Edward Snell

journal-article http://dx.doi.org/10.1371/journal.pone.0100782 NSF-STC Biology with X-ray Lasers (NSF-1231306) Bruno, A.E. et al., 2014. Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular …

Genomic basis for the convergent evolution of electric organs

26 Jun 2014 | BioXFEL Publications | Contributor(s): J. R. Gallant, L. L. Traeger, J. D. Volkening, H. Moffett, P.-H. Chen, C. D. Novina, G. N. Phillips, R. Anand, G. B. Wells, M. Pinch, R. Guth, G. A. Unguez, J. S. Albert, H. H. Zakon, M. P. Samanta, M. R. Sussman

http://dx.doi.org/10.1126/science.1254432 journal-article Gallant, J.R. et al., 2014. Genomic basis for the convergent evolution of electric organs. Science, 344(6191), pp.1522–1525. Available at: http://dx.doi.org/10.1126/science.1254432. J. R. Gallant and L. L. Traeger and J. D. Volkening …

Crystallization screening: the influence of history on current practice

26 Jun 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Janet Newman, Edward Snell

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. …

First Annual NSF Site Visit Photo

23 Jun 2014 | Downloads | Contributor(s): Edward J Sobczak

The BioXFEL Center meets at Hauptman-Woodward in Buffalo for its first annual NSF site visit.

Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature

17 Jun 2014 | BioXFEL Publications | Contributor(s): J. A. Sellberg, C. Huang, T. A. McQueen, N. D. Loh, H. Laksmono, D. Schlesinger, R. G. Sierra, D. Nordlund, C. Y. Hampton, D. Starodub, D. P. DePonte, M. Beye, C. Chen, A. V. Martin, A. Barty, K. T. Wikfeldt, T. M. Weiss, C. Caronna, J. Feldkamp, L. B. Skinner, M. M. Seibert, M. Messerschmidt, G. J. Williams, S. Boutet, L. G. M. Pettersson, M. J. Bogan, A. Nilsson

journal-article http://dx.doi.org/10.1038/nature13266 Sellberg, J.A. et al., 2014. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature. Nature, 510(7505), pp.381–384. Available at: http://dx.doi.org/10.1038/nature13266. J. A. Sellberg and C. Huang and T. …

Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles

16 Jun 2014 | BioXFEL Publications | Contributor(s): Jo E. Lomax, Christopher M. Bianchetti, Aram Chang, George Phillips, Brian G. Fox, Ronald T. Raines

http://dx.doi.org/10.1016/j.jmb.2014.06.007 journal-article Lomax, J.E. et al., 2014. Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles. Journal of Molecular Biology, 426(17), pp.3041–3056. Available at: http://dx.doi.org/10.1016/j.jmb.2014.06.007. Jo E. Lomax …

Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases

13 Jun 2014 | BioXFEL Publications | Contributor(s): Sojin Moon, Ryan M. Bannen, Thomas J. Rutkoski, George Phillips, Euiyoung Bae

http://dx.doi.org/10.1002/prot.24627 journal-article Moon, S. et al., 2014. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins: Structure, Function, and Bioinformatics, 82(10), …

Enabling membrane protein structure and dynamics with X-ray free electron lasers

11 Jun 2014 | BioXFEL Publications | Contributor(s): Geoffrey K Feld, Matthias Frank

http://dx.doi.org/10.1016/j.sbi.2014.05.002 journal-article Feld, G.K. & Frank, M., 2014. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Current Opinion in Structural Biology, 27, pp.69–78. Available at: http://dx.doi.org/10.1016/j.sbi.2014.05.002. Geoffrey K …

Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules

10 Jun 2014 | BioXFEL Publications | Contributor(s): D Rolles, R Boll, M Adolph, A Aquila, C Bostedt, J D Bozek, H N Chapman, R Coffee, N Coppola, P Decleva, T Delmas, S W Epp, B Erk, F Filsinger, L Foucar, L Gumprecht, A Hömke, T Gorkhover, L Holmegaard, P Johnsson, Ch Kaiser, F Krasniqi, K-U Kühnel, J Maurer, M Messerschmidt, R Moshammer, W Quevedo, I Rajkovic, A Rouzée, B Rudek, I Schlichting, C Schmidt, S Schorb, C D Schröter, J Schulz, H Stapelfeldt, M Stener, S Stern, S Techert, J Thøgersen, M J J Vrakking, A Rudenko, J Küpper, J Ullrich

http://dx.doi.org/10.1088/0953-4075/47/12/124035 journal-article Rolles, D. et al., 2014. Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules. Journal of Physics B: Atomic, Molecular and Optical Physics, 47(12), p.124035. Available at: …

Diffraction before destruction

09 Jun 2014 | BioXFEL Publications | Contributor(s): H. N. Chapman, C. Caleman, N. Timneanu

http://dx.doi.org/10.1098/rstb.2013.0313 H. N. Chapman and C. Caleman and N. Timneanu Chapman, H.N., Caleman, C. & Timneanu, N., 2014. Diffraction before destruction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130313–20130313. Available at: …

Femtosecond crystallography of membrane proteins in the lipidic cubic phase

09 Jun 2014 | BioXFEL Publications | Contributor(s): W. Liu, D. Wacker, C. Wang, E. Abola, V. Cherezov

http://dx.doi.org/10.1098/rstb.2013.0314 W. Liu and D. Wacker and C. Wang and E. Abola and V. Cherezov Liu, W. et al., 2014. Femtosecond crystallography of membrane proteins in the lipidic cubic phase. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), …

Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system

09 Jun 2014 | BioXFEL Publications | Contributor(s): C. Kupitz, I. Grotjohann, C. E. Conrad, S. Roy-Chowdhury, R. Fromme, P. Fromme

http://dx.doi.org/10.1098/rstb.2013.0316 C. Kupitz and I. Grotjohann and C. E. Conrad and S. Roy-Chowdhury and R. Fromme and P. Fromme Kupitz, C. et al., 2014. Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model …

Coherent convergent-beam time-resolved X-ray diffraction

09 Jun 2014 | BioXFEL Publications | Contributor(s): J. C. H. Spence, N. A. Zatsepin, C. Li

http://dx.doi.org/10.1098/rstb.2013.0325 J. C. H. Spence and N. A. Zatsepin and C. Li Spence, J.C.H., Zatsepin, N.A. & Li, C., 2014. Coherent convergent-beam time-resolved X-ray diffraction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130325–20130325. …

High-resolution structure of viruses from random diffraction snapshots

09 Jun 2014 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, P. Schwander, A. Dashti, R. Fung, R. M. D'Souza, A. Ourmazd

http://dx.doi.org/10.1098/rstb.2013.0326 A. Hosseinizadeh and P. Schwander and A. Dashti and R. Fung and R. M. D'Souza and A. Ourmazd Hosseinizadeh, A. et al., 2014. High-resolution structure of viruses from random diffraction snapshots. Philosophical Transactions of the Royal Society B: …

Phasing coherently illuminated nanocrystals bounded by partial unit cells

09 Jun 2014 | BioXFEL Publications | Contributor(s): R. A. Kirian, R. J. Bean, K. R. Beyerlein, O. M. Yefanov, T. A. White, A. Barty, H. N. Chapman

http://dx.doi.org/10.1098/rstb.2013.0331 R. A. Kirian and R. J. Bean and K. R. Beyerlein and O. M. Yefanov and T. A. White and A. Barty and H. N. Chapman Kirian, R.A. et al., 2014. Phasing coherently illuminated nanocrystals bounded by partial unit cells. Philosophical Transactions of the Royal …

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

09 Jun 2014 | BioXFEL Publications | Contributor(s): O. Yefanov, C. Gati, G. Bourenkov, R. A. Kirian, T. A. White, J. C. H. Spence, H. N. Chapman, A. Barty

http://dx.doi.org/10.1098/rstb.2013.0333 O. Yefanov and C. Gati and G. Bourenkov and R. A. Kirian and T. A. White and J. C. H. Spence and H. N. Chapman and A. Barty Yefanov, O. et al., 2014. Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography. …

Liquid sample delivery techniques for serial femtosecond crystallography

09 Jun 2014 | BioXFEL Publications | Contributor(s): U. Weierstall

http://dx.doi.org/10.1098/rstb.2013.0337 U. Weierstall Weierstall, U., 2014. Liquid sample delivery techniques for serial femtosecond crystallography. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130337–20130337. Available at: …

7 A resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

09 Jun 2014 | BioXFEL Publications | Contributor(s): B. Pedrini, C.-J. Tsai, G. Capitani, C. Padeste, M. S. Hunter, N. A. Zatsepin, A. Barty, W. H. Benner, S. Boutet, G. K. Feld, S. P. Hau-Riege, R. A. Kirian, C. Kupitz, M. Messerschmitt, J. I. Ogren, T. Pardini, B. Segelke, G. J. Williams, J. C. H. Spence, R. Abela, M. Coleman, J. E. Evans, G. F. X. Schertler, M. Frank, X.-D. Li

http://dx.doi.org/10.1098/rstb.2013.0500 B. Pedrini and C.-J. Tsai and G. Capitani and C. Padeste and M. S. Hunter and N. A. Zatsepin and A. Barty and W. H. Benner and S. Boutet and G. K. Feld and S. P. Hau-Riege and R. A. Kirian and C. Kupitz and M. Messerschmitt and J. I. Ogren and T. Pardini and …

Conformations of macromolecules and their complexes from heterogeneous datasets

09 Jun 2014 | BioXFEL Publications | Contributor(s): P. Schwander, R. Fung, A. Ourmazd

http://dx.doi.org/10.1098/rstb.2013.0567 P. Schwander and R. Fung and A. Ourmazd Schwander, P., Fung, R. & Ourmazd, A., 2014. Conformations of macromolecules and their complexes from heterogeneous datasets. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), …

Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment

09 Jun 2014 | BioXFEL Publications | Contributor(s): K. Pande, P. Schwander, M. Schmidt, D. K. Saldin

http://dx.doi.org/10.1098/rstb.2013.0332 K. Pande and P. Schwander and M. Schmidt and D. K. Saldin Pande, K. et al., 2014. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Philosophical Transactions of the Royal Society B: …

'Hit and run' serial femtosecond crystallography of a membrane kinase in the lipid cubic phase

09 Jun 2014 | BioXFEL Publications | Contributor(s): M. Caffrey, D. Li, N. Howe, S. T. A. Shah

journal-article http://dx.doi.org/10.1098/rstb.2013.0621 NSF-STC Biology with X-ray Lasers (NSF-1231306) Caffrey, M. et al., 2014. “Hit and run” serial femtosecond crystallography of a membrane kinase in the lipid cubic phase. Philosophical Transactions of the Royal Society B: Biological …

Performance of a beam-multiplexing diamond crystal monochromator at the Linac Coherent Light Source

06 Jun 2014 | BioXFEL Publications | Contributor(s): Diling Zhu, Yiping Feng, Stanislav Stoupin, Sergey A. Terentyev, Henrik T. Lemke, David M. Fritz, Matthieu Chollet, J. M. Glownia, Roberto Alonso-Mori, Marcin Sikorski, Sanghoon Song, Tim B. Van Driel, Garth J. Williams, Marc Messerschmidt, Sébastien Boutet, Vladimir D. Blank, Yuri V. Shvyd'ko, Aymeric Robert

http://dx.doi.org/10.1063/1.4880724 journal-article Zhu, D. et al., 2014. Performance of a beam-multiplexing diamond crystal monochromator at the Linac Coherent Light Source. Review of Scientific Instruments, 85(6), p.063106. Available at: http://dx.doi.org/10.1063/1.4880724. Diling Zhu and …

BioXFEL Annual Report 2014

04 Jun 2014 | Downloads | Contributor(s): Jill Szczesek

BioXFEL will create a diverse and inclusive community of scholars who will transform our ability to visualize the building blocks of life at a molecular scale, advancing from today's static pictures to recording detailed motions. These "movies" will lead to deeper understanding and to the …

Temporal and Spatial Temperature Measurement in Insulator-Based Dielectrophoretic Devices

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

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

Introduction to XFELs in Structural Biology

03 Jun 2014 | Seminars | Contributor(s): Edward Snell

Dr. Edward Snell gives a brief overview of how X-ray free electron lasers work and how they can be used to investigate structural aspects of biological systems never before accessible to experiment.

Intro to Structural Biology

02 Jun 2014 | Seminars | Contributor(s): Dan Gewirth

Dr. Dan Gewirth of the Hauptman-Woodward Medical Research Institute gives a brief overview of structural biology and its importance as a tool to understanding biological processes. Be sure to grab the MP3 audio file to follow along with the PowerPoint slides.

Time-Resolved Spectra from Millivolt EELS Data

30 May 2014 | BioXFEL Publications | Contributor(s): Chufeng Li, GANESH SUBRAMANIAN, John Spence

http://dx.doi.org/10.1017/s1431927614000890 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Li, C., Subramanian, G. & Spence, J.C.H., 2014. Time-Resolved Spectra from Millivolt EELS Data. Microscopy and Microanalysis, 20(03), pp.837–846. Available at: …

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

29 May 2014 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, Henry Van den Bedem, David A. Sivak, Gregory A. Petsko, Dagmar Ringe, Mark A. Wilson, James S. Fraser

http://dx.doi.org/10.1016/j.str.2014.04.016 Daniel A. Keedy and Henry van den Bedem and David A. Sivak and Gregory A. Petsko and Dagmar Ringe and Mark A. Wilson and James S. Fraser Keedy, D.A. et al., 2014. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis …

Use of transmission electron microscopy to identify nanocrystals of challenging protein targets

28 May 2014 | BioXFEL Publications | Contributor(s): H. P. Stevenson, A. M. Makhov, M. Calero, A. L. Edwards, O. B. Zeldin, I. I. Mathews, G. Lin, C. O. Barnes, H. Santamaria, T. M. Ross, S. M. Soltis, C. Khosla, V. Nagarajan, J. F. Conway, A. E. Cohen, G. Calero

http://dx.doi.org/10.1073/pnas.1400240111 journal-article Stevenson, H.P. et al., 2014. Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proceedings of the National Academy of Sciences, 111(23), pp.8470–8475. Available at: …

Silicon Mirrors for High-Intensity X-Ray Pump and Probe Experiments

28 May 2014 | BioXFEL Publications | Contributor(s): Tom Pardini, Sébastien Boutet, Joseph Bradley, Tilo Döppner, Luke B. Fletcher, Dennis F. Gardner, Randy M. Hill, Mark S. Hunter, Jacek Krzywinski, Marc Messerschmidt, Arthur E. Pak, Florian Quirin, Klaus Sokolowski-Tinten, Garth J. Williams, Stefan Hau-Riege

journal-article http://dx.doi.org/10.1103/physrevapplied.1.044007 Pardini, T. et al., 2014. Silicon Mirrors for High-Intensity X-Ray Pump and Probe Experiments. Physical Review Applied, 1(4). Available at: http://dx.doi.org/10.1103/physrevapplied.1.044007. Tom Pardini and Sébastien Boutet and …

A new view on crystal harvesting

28 May 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Thomas D. Grant, Jennifer R. Wolfley, Edward Snell

X-ray crystallography typically requires the mounting of crystals, which can make the sample difficult to manipulate when it is small and the microscope objective is close to the crystallization plate. By simply moving the objective to the bottom of a clear crystallization plate (inverting the …

Using a commodity high-definition television for collaborative structural biology

28 May 2014 | BioXFEL Publications | Contributor(s): Ragothaman Yennamalli, Raj Arangarasan, Aaron Bryden, Michael Gleicher, George Phillips

Visualization of protein structures using stereoscopic systems is frequently needed by structural biologists working to understand a protein's structure–function relationships. Often several scientists are working as a team and need simultaneous interaction with each other and the graphics …

BioXFEL Strategic Plan 2013-2018

28 May 2014 | Downloads | Contributor(s): Jill Szczesek

We present a strategic plan for the operation of BioXFEL, a National Science Foundation Science and Technology Center, Biology with X-ray Lasers. The plan is the organic product of a meeting facilitated by Giant Leap at Arizona State University in February 2014, and covers the period 2013 – 2018.

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

25 May 2014 | BioXFEL Publications | Contributor(s): Marcus Fischer, Ryan G. Coleman, James Fraser, Brian K. Shoichet

http://dx.doi.org/10.1038/nchem.1954 journal-article Fischer, M. et al., 2014. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry, 6(7), pp.575–583. Available at: http://dx.doi.org/10.1038/nchem.1954. Marcus …

Small Angle X-Ray Scattering as a Complementary Tool for High-Throughput Structural Studies

21 May 2014 | Publications | Contributor(s): Tom Grant, Edward Snell

Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. …

Low Temperature Assembly of Functional 3D DNA-PNA-Protein Complexes

14 May 2014 | BioXFEL Publications | Contributor(s): Justin D. Flory, Chad R. Simmons, Su Lin, Trey Johnson, Alessio Andreoni, James D Zook, Giovanna Ghirlanda, Yan Liu, Hao Yan, Petra Fromme

http://dx.doi.org/10.1021/ja501228c journal-article Flory, J.D. et al., 2014. Low Temperature Assembly of Functional 3D DNA-PNA-Protein Complexes. Journal of the American Chemical Society, 136(23), pp.8283–8295. Available at: http://dx.doi.org/10.1021/ja501228c. Justin D. Flory and Chad R. …

Fast k-NNG Construction with GPU-Based Quick Multi-Select

08 May 2014 | BioXFEL Publications | Contributor(s): Ivan Komarov, Ali Dashti, Roshan M. D'Souza

http://dx.doi.org/10.1371/journal.pone.0092409 journal-article Komarov, I., Dashti, A. & D’Souza, R.M., 2014. Fast k-NNG Construction with GPU-Based Quick Multi-Select M. Gomez-Gesteira, ed. PLoS ONE, 9(5), p.e92409. Available at: http://dx.doi.org/10.1371/journal.pone.0092409. Ivan Komarov …