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  1. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

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    11 Jan 2016 | BioXFEL Publications | Contributor(s): Arjen J. Jakobi, Daniel M. Passon, Kèvin Knoops, Francesco Stellato, Mengning Liang, Thomas A. White, Thomas Seine, Marc Messerschmidt, Henry Chapman, Matthias Wilmanns

    The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of …

  2. In Vitro and In Silico Study of Analogs of Plant Product Plastoquinone to Be Effective in Colorectal Cancer Treatment

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    23 Jan 2022 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Belgin Sever, Firdevs Ocak, Nilüfer Bayrak, Mahmut Yıldız, Hatice Yıldırım, Hasan Demirci, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Amaç Fatih TuYuN

    http://dx.doi.org/10.3390/molecules27030693 Plants have paved the way for the attainment of molecules with a wide-range of biological activities. However, plant products occasionally show low biological activities and/or poor pharmacokinetic properties. In that case, development of their …

  3. Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays

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    31 Jul 2017 | BioXFEL Publications | Contributor(s): Anton Classen, Kartik Ayyer, Henry Chapman, Ralf Röhlsberger, Joachim Von Zanthier

    http://dx.doi.org/10.1103/physrevlett.119.053401 journal-article Classen, A. et al., 2017. Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays. Physical Review Letters, 119(5). Available at: http://dx.doi.org/10.1103/physrevlett.119.053401. Anton Classen and Kartik Ayyer and …

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

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    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 …

  5. Indexing ambiguity in SFX resolved using expectation maximization algorithm

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    10 Nov 2015 | Teaching Materials

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

  6. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams

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    16 Feb 2015 | BioXFEL Publications | Contributor(s): Karol Nass, Lutz Foucar, Thomas R. M. Barends, Elisabeth Hartmann, Sabine Botha, Robert L. Shoeman, R. Bruce Doak, Roberto Alonso-Mori, Andrew Aquila, Saša Bajt, Anton Barty, Richard Bean, Kenneth R. Beyerlein, Maike Bublitz, Nikolaj Drachmann, Jonas Gregersen, H. Olof Jönsson, Wolfgang Kabsch, Stephan Kassemeyer, Jason E. Koglin, Michael Krumrey, Daniel Mattle, Marc Messerschmidt, Poul Nissen, Linda Reinhard, Oleg Sitsel, Dimosthenis Sokaras, Garth J. Williams, Stefan Hau-Riege, Nicusor Timneanu, Carl Caleman, Henry Chapman, Sébastien Boutet, Ilme Schlichting

    Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX),Clostridium …

  7. Innate Type 2 Immunity Controls Hair Follicle Commensalism by <i>Demodex</i> Mites

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    21 Jan 2022 | BioXFEL Publications | Contributor(s): Roberto Ricardo-Gonzalez, Maya E. Kotas, Claire E. O'Leary, Iliana Tenvooren, Diana M. Marquez, Katelyn Singh, William Damsky, Andrew W. Schroeder, Jarish N. Cohen, Marlys Fassett, Jinwoo Lee, Scott G. Daniel, Kyle Bittinger, Roberto Efraín Díaz, James Fraser, Mark Ansel, Matthew Spitzer, Hong-Erh Liang, Richard M. Locksley

    http://dx.doi.org/10.2139/ssrn.4013912 journal-article Ricardo-Gonzalez, R., Kotas, M. E., O'Leary, C. E., Tenvooren, I., Marquez, D. M., Singh, K., Damsky, W., Schroeder, A. W., Cohen, J. N., Fassett, M., Lee, J., Daniel, S. G., Bittinger, K., Díaz, R. E., Fraser, J. S., Ansel, M., …

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

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    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, …

  9. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

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    19 Nov 2013 | BioXFEL Publications | Contributor(s): Kristin A. Sutton, Paul J. Black, Kermit R. Mercer, Elspeth F. Garman, Robin L. Owen, Edward Snell, William A. Bernhard

    Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide …

  10. Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations

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    11 Jul 2022 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Weiwei He, Serdal Kirmizialtin, Lois Pollack

    http://dx.doi.org/10.1016/j.xcrp.2022.100971 journal-article Chen, Y.-L., He, W., Kirmizialtin, S., & Pollack, L. (2022). Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. Cell Reports Physical Science, 3(7), 100971. …

  11. Insulator-based dielectrophoresis of mitochondria

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    04 Mar 2014 | BioXFEL Publications | Contributor(s): Jinghui Luo, Bahige G. Abdallah, Gregory G. Wolken, Edgar A. Arriaga, Alexandra Ros

    journal-article http://dx.doi.org/10.1063/1.4866852 Luo, J. et al., 2014. Insulator-based dielectrophoresis of mitochondria. Biomicrofluidics, 8(2), p.021801. Available at: http://dx.doi.org/10.1063/1.4866852. Jinghui Luo and Bahige G. Abdallah and Gregory G. Wolken and Edgar A. Arriaga and …

  12. Insulator-based dielectrophoresis with β-galactosidase in nanostructured devices

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    12 Nov 2014 | BioXFEL Publications | Contributor(s): Asuka Nakano, Fernanda Camacho-Alanis, Alexandra Ros

    http://dx.doi.org/10.1039/c4an01503g Asuka Nakano and Fernanda Camacho-Alanis and Alexandra Ros Nakano, A., Camacho-Alanis, F. & Ros, A., 2015. Insulator-based dielectrophoresis with β-galactosidase in nanostructured devices. Analyst, 140(3), pp.860–868. Available at: …

  13. Integral equation models for solvent in macromolecular crystals

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    04 Jan 2022 | BioXFEL Publications | Contributor(s): Jonathon G. Gray, George M. Giambaşu, David Case, Tyler Luchko

    http://dx.doi.org/10.1063/5.0070869 journal-article Gray, J. G., Giambaşu, G. M., Case, D. A., & Luchko, T. (2022). Integral equation models for solvent in macromolecular crystals. The Journal of Chemical Physics, 156(1), 014801. https://doi.org/10.1063/5.0070869 Jonathon G. Gray and George M. …

  14. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

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    13 Jan 2014 | BioXFEL Publications | Contributor(s): R. B. Fenwick, H. Van Den Bedem, J. S. Fraser, P. E. Wright

    http://dx.doi.org/10.1073/pnas.1323440111 journal-article Fenwick, R.B. et al., 2014. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proceedings of the National Academy of Sciences, 111(4), pp.E445–E454. Available at: …

  15. Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline

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    02 May 2013 | BioXFEL Publications | Contributor(s): Jeremy T. Madden, Scott J. Toth, Christopher M. Dettmar, Justin A. Newman, Robert A. Oglesbee, Hartmut G. Hedderich, R. Michael Everly, Michael Becker, Judith A. Ronau, Susan K. Buchanan, Vadim Cherezov, Marie E. Morrow, Shenglan Xu, Dale Ferguson, Oleg Makarov, Chittaranjan Das, Robert Fischetti, Garth J. Simpson

    http://dx.doi.org/10.1107/s0909049513007942 Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and …

  16. Integration of software tools for integrative modeling of biomolecular systems

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    08 Feb 2022 | BioXFEL Publications | Contributor(s): Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, Billy Poon, James Fraser, Paul Adams, Andrej Sali

    http://dx.doi.org/10.1016/j.jsb.2022.107841 journal-article Hancock, M., Peulen, T.-O., Webb, B., Poon, B., Fraser, J. S., Adams, P., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Journal of Structural Biology, 214(1), 107841. …

  17. Integration of software tools for integrative modeling of biomolecular systems

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    11 Feb 2022 | BioXFEL Publications | Contributor(s): Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, James Fraser, Paul D. Adams, Andrej Sali

    http://dx.doi.org/10.1016/j.bpj.2021.11.2555 journal-article Hancock, M., Peulen, T.-O., Webb, B., Fraser, J. S., Adams, P. D., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Biophysical Journal, 121(3), 31a. …

  18. Integrative, dynamic structural biology at atomic resolution—it's about time

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    31 Mar 2015 | BioXFEL Publications | Contributor(s): Henry Van Den Bedem, James Fraser

    http://dx.doi.org/10.1038/nmeth.3324 Henry van den Bedem and James S Fraser Van den Bedem, H. & Fraser, J.S., 2015. Integrative, dynamic structural biology at atomic resolution—it’s about time. Nat Meth, 12(4), pp.307–318. Available at: http://dx.doi.org/10.1038/nmeth.3324. NSF-STC Biology …

  19. Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder

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    31 Mar 2023 | BioXFEL Publications | Contributor(s): J.P.J. Chen, K. Pande, J.J. Donatelli, A.V. Martin, K. Ayyer, H.N. Chapman, R. Bean, K.E. Schmidt, R.A. Kirian

    http://dx.doi.org/10.1016/j.ultramic.2023.113728 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chen, J. P. J., Pande, K., Donatelli, J. J., Martin, A. V., Ayyer, K., Chapman, H. N., Bean, R., Schmidt, K. E., & Kirian, R. A. (2023). Inter-Bragg crystallographic phase retrieval …

  20. Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases

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    25 Apr 2022 | BioXFEL Publications | Contributor(s): Hasan Demirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vögeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G. Sierra, Mark S. Hunter, E. Han Dao, Halil I. Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmüller, Tobias J. Erb, Esteban Vöhringer-Martinez, Soichi Wakatsuki

    http://dx.doi.org/10.1021/acscentsci.2c00057 journal-article DeMirci, H., Rao, Y., Stoffel, G. M., Vögeli, B., Schell, K., Gomez, A., Batyuk, A., Gati, C., Sierra, R. G., Hunter, M. S., Dao, E. H., Ciftci, H. I., Hayes, B., Poitevin, F., Li, P.-N., Kaur, M., Tono, K., Saez, D. A., Deutsch, S., …

  21. Interview with Dilano Saldin

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    05 Jan 2016 | Teaching Materials

    Combining data from new facilities with mathematical methods, Professor Dilano Saldin is in pursuit of a technique to determine the structure of molecules without the need for purification or crystallization.

  22. Intro to Structural Biology

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    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.

  23. Introduction to Biological Small Angle Scattering

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    08 May 2014 | Seminars | Contributor(s): Tom Grant

    (YouTube Video Below) An introductory course to small angle X-ray scattering intended for beginners in the field and those interesting in learning more about solution-based scattering. Topics covered include: - What is small angle scattering? - Reciprocal space to real space - Electron density and …

  24. Introduction to CrystFEL

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    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 …

  25. Introduction to serial femtosecond crystallography data analysis

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    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. 

  26. Introduction to XFELs in Structural Biology

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    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.

  27. Introduction to XRayView Crystallographic Software

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    04 Nov 2015 | Teaching Materials

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

  28. Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data

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    06 Aug 2020 | BioXFEL Publications | Contributor(s): Jeffrey J. Donatelli, John Spence

    http://dx.doi.org/10.1103/physrevlett.125.065502 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Donatelli, J.J. & Spence, J.C.H., 2020. Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data. …

  29. Investigation of femtosecond collisional ionization rates in a solid-density aluminium plasma

    0.0 out of 5 stars 

    03 Mar 2015 | BioXFEL Publications | Contributor(s): S. M. Vinko, O. Ciricosta, T. R. Preston, D. S. Rackstraw, C.R.D. Brown, T. Burian, J. Chalupský, B. I. Cho, H.-K. Chung, K. Engelhorn, R. W. Falcone, R. Fiokovinini, V. Hájková, P. A. Heimann, L. Juha, H. J. Lee, R. W. Lee, M. Messerschmidt, B. Nagler, W. Schlotter, J. J. Turner, L. Vysin, U. Zastrau, J. S. Wark

    http://dx.doi.org/10.1038/ncomms7397 S. M. Vinko and O. Ciricosta and T. R. Preston and D. S. Rackstraw and C.R.D. Brown and T. Burian and J. Chalupský and B. I. Cho and H.-K. Chung and K. Engelhorn and R. W. Falcone and R. Fiokovinini and V. Hájková and P. A. Heimann and L. Juha and H. J. Lee …

  30. Investigation of NO2 adsorption on reduced graphene oxide

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    15 Jan 2015 | BioXFEL Publications | Contributor(s): E.C. Mattson, K. Pande, S. Cui, M. Weinert, J.H. Chen, C.J. Hirschmugl

    journal-article http://dx.doi.org/10.1016/j.cplett.2015.01.018 Mattson, E.C. et al., 2015. Investigation of NO2 adsorption on reduced graphene oxide. Chemical Physics Letters, 622, pp.86–91. Available at: http://dx.doi.org/10.1016/j.cplett.2015.01.018. E.C. Mattson and K. Pande and S. Cui and …

  31. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

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    04 Jan 2023 | BioXFEL Publications | Contributor(s): Stefan Gahbauer, Galen J. Correy, Marion Schuller, Matteo P. Ferla, Yagmur Umay Doruk, Moira Rachman, Taiasean Wu, Morgan Diolaiti, Siyi Wang, R. Jeffrey Neitz, Daren Fearon, Dmytro S. Radchenko, Yurii S. Moroz, John J. Irwin, Adam R. Renslo, Jenny C. Taylor, Jason E. Gestwicki, Frank Von Delft, Alan Ashworth, Ivan Ahel, Brian K. Shoichet, James Fraser

    http://dx.doi.org/10.1073/pnas.2212931120 The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great …

  32. Journal Club Seminars

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    01 Dec 2016 | Teaching Materials

    Videos of all past Journal Clubs 

  33. June 2016 Site Visit Agenda

    0.0 out of 5 stars 

    21 Apr 2016 | Downloads

    …

  34. Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes

    0.0 out of 5 stars 

    24 Dec 2014 | BioXFEL Publications | Contributor(s): Gira Bhabha, Justin T. Biel, James Fraser

    http://dx.doi.org/10.1021/ar5003158 Gira Bhabha and Justin T. Biel and James S. Fraser Bhabha, G., Biel, J.T. & Fraser, J.S., 2015. Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes. Acc. Chem. Res., 48(2), pp.423–430. Available at: …

  35. Large language models generate functional protein sequences across diverse families

    0.0 out of 5 stars 

    26 Jan 2023 | BioXFEL Publications | Contributor(s): Ali Madani, Ben Krause, Eric R. Greene, Subu Subramanian, Benjamin P. Mohr, James Holton, Jose Luis Olmos, Caiming Xiong, Zachary Z. Sun, Richard Socher, James Fraser, Nikhil Naik

    http://dx.doi.org/10.1038/s41587-022-01618-2 journal-article Madani, A., Krause, B., Greene, E. R., Subramanian, S., Mohr, B. P., Holton, J. M., Olmos, J. L., Xiong, C., Sun, Z. Z., Socher, R., Fraser, J. S., & Naik, N. (2023). Large language models generate functional protein sequences across …

  36. Laser control over the ultrafast Coulomb explosion of N22+ after Auger decay: A quantum-dynamics investigation

    0.0 out of 5 stars 

    24 Apr 2017 | BioXFEL Publications | Contributor(s): Athiya Mahmud Hanna, Oriol Vendrell, Abbas Ourmazd, Robin Santra

    http://dx.doi.org/10.1103/physreva.95.043419 journal-article Hanna, A.M. et al., 2017. Laser control over the ultrafast Coulomb explosion of N22+ after Auger decay: A quantum-dynamics investigation. Physical Review A, 95(4). Available at: http://dx.doi.org/10.1103/physreva.95.043419. Athiya …

  37. LCLS Beam-time Schedules

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    20 Dec 2016 | Downloads

    All Schedules on LCLS Website LCLS Run 15 Schedule (June 2017 - Nov 2017)LCLS Run 14 Schedule (Aug 2016 - Dec 2016)LCLS Run 13 Schedule (Mar 2016 - Aug 2016)LCLS Run 12 Schedule (Oct 2015 - Mar 2016)LCLS Run 11 Schedule (Mar 2015 - Aug 2015)LCLS Run 10 Schedule (Oct 2014 - Mar 2015)

  38. LCLS serial femtosecond crystallography data analysis instructions

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

    SFX data analysis at LCLS Overview.

  39. Learned motivation drives circadian physiology in the absence of the master circadian clock

    0.0 out of 5 stars 

    12 Oct 2016 | BioXFEL Publications | Contributor(s): Oliver Rawashdeh, Shannon J. Clough, Randall L. Hudson, Margarita L. Dubocovich

    http://dx.doi.org/10.1096/fj.201600926r journal-article Rawashdeh, O. et al., 2017. Learned motivation drives circadian physiology in the absence of the master circadian clock. The FASEB Journal, 31(1), pp.388–399. Available at: http://dx.doi.org/10.1096/fj.201600926r. Oliver Rawashdeh and …

  40. Lecture Series

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    01 Dec 2016 | Teaching Materials

    BioXFEL Lecture Series videos are kept here.

  41. Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes

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    25 May 2020 | BioXFEL Publications | Contributor(s): Mohammad T. Rabbani, Christoph F. Schmidt, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.0c00794 journal-article Rabbani, M.T., Schmidt, C.F. & Ros, A., 2020. Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.0c00794. Mohammad T. Rabbani …

  42. Ligand binding remodels protein side-chain conformational heterogeneity

    0.0 out of 5 stars 

    21 Mar 2022 | BioXFEL Publications | Contributor(s): Stephanie A Wankowicz, Saulo H De Oliveira, Daniel W Hogan, Henry Van Den Bedem, James Fraser

    http://dx.doi.org/10.7554/elife.74114 While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but …

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

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    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: …

  44. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography

    0.0 out of 5 stars 

    14 Feb 2014 | BioXFEL Publications | Contributor(s): Uwe Weierstall, Daniel James, Chong Wang, Thomas A. White, Dingjie Wang, Wei Liu, John Spence, R. Bruce Doak, Garrett Charles Nelson, Petra Fromme, Raimund Fromme, Ingo Grotjohann, Christopher Kupitz, Nadia Zatsepin, Haiguang Liu, Shibom Basu, Daniel Wacker, Gye Won Han, Vsevolod Katritch, Sébastien Boutet, Marc Messerschmidt, Garth J. Williams, Jason E. Koglin, M. Marvin Seibert, Markus Klinker, Cornelius Gati, Robert L. Shoeman, Anton Barty, Henry Chapman, Richard Kirian, Kenneth R. Beyerlein, Raymond C. Stevens, Dianfan Li, Syed T. A. Shah, Nicole Howe, Martin Caffrey, Vadim Cherezov

    journal-article Uwe Weierstall and Daniel James and Chong Wang and Thomas A. White and Dingjie Wang and Wei Liu and John C. H. Spence and R. Bruce Doak and Garrett Nelson and Petra Fromme and Raimund Fromme and Ingo Grotjohann and Christopher Kupitz and Nadia A. Zatsepin and Haiguang Liu and …

  45. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.

    0.0 out of 5 stars 

    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 …

  46. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

    0.0 out of 5 stars 

    22 Aug 2016 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Valerie Panneels, Garrett Charles Nelson, Cornelius Gati, Tetsunari Kimura, Christopher Milne, Despina Milathianaki, Minoru Kubo, Wenting Wu, Chelsie E Conrad, Jesse David Coe, Richard Bean, Yun Zhao, Petra Båth, Robert Dods, Rajiv Harimoorthy, Kenneth R. Beyerlein, Jan Rheinberger, Daniel James, Daniel DePonte, Chufeng Li, Leonardo Sala, Garth J. Williams, Mark S. Hunter, Jason E. Koglin, Peter Berntsen, Eriko Nango, So Iwata, Henry Chapman, Petra Fromme, Matthias Frank, Rafael Abela, Sébastien Boutet, Anton Barty, Thomas A. White, Uwe Weierstall, John Spence, Richard Neutze, Gebhard F.X. Schertler, Jörg Standfuss

    http://dx.doi.org/10.1038/ncomms12314 Przemyslaw Nogly and Valerie Panneels and Garrett Nelson and Cornelius Gati and Tetsunari Kimura and Christopher Milne and Despina Milathianaki and Minoru Kubo and Wenting Wu and Chelsie Conrad and Jesse Coe and Richard Bean and Yun Zhao and Petra Båth and …

  47. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

    0.0 out of 5 stars 

    15 Nov 2016 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Valerie Panneels, Garrett Charles Nelson, Cornelius Gati, Tetsunari Kimura, Christopher Milne, Despina Milathianaki, Minoru Kubo, Wenting Wu, Chelsie E Conrad, Jesse David Coe, Richard Bean, Yun Zhao, Petra Bath, Robert Dods, Rajiv Harimoorthy, Kenneth Beyerlein, Jan Rheinberger, Daniel James, Daniel DePonte, Chufeng Li, Leonardo Sala, Garth Williams, Mark S. Hunter, Jason E. Koglin, Peter Berntsen, Eriko Nango, So Iwata, Henry Chapman, Petra Fromme, Matthias Frank, Rafael Abela, Sébastien Boutet, Anton Barty, Thomas A. White, Uwe Weierstall, John Spence, Richard Neutze, Gebhard F.X. Schertler, Jörg Standfuss

    http://dx.doi.org/10.1107/s2053273316099368 Przemyslaw Nogly and Valerie Panneels and Garrett Nelson and Cornelius Gati and Tetsunari Kimura and Christopher Milne and Despina Milathianaki and Minoru Kubo and Wenting Wu and Chelsie Conrad and Jesse Coe and Richard Bean and Yun Zhao and Petra Bath …

  48. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

    0.0 out of 5 stars 

    02 Jan 2015 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Daniel James, Dingjie Wang, Thomas A. White, Nadia Zatsepin, Anastasya Shilova, Garrett Charles Nelson, Haiguang Liu, Linda Johansson, Michael Heymann, Kathrin Jaeger, Markus Metz, Cecilia Wickstrand, Wenting Wu, Petra Båth, Peter Berntsen, Dominik Oberthuer, Valerie Panneels, Vadim Cherezov, Henry Chapman, Gebhard F.X. Schertler, Richard Neutze, John Spence, Isabel Moraes, Manfred Burghammer, Joerg Standfuss, Uwe Weierstall

    journal-article Przemyslaw Nogly and Daniel James and Dingjie Wang and Thomas A. White and Nadia Zatsepin and Anastasya Shilova and Garrett Nelson and Haiguang Liu and Linda Johansson and Michael Heymann and Kathrin Jaeger and Markus Metz and Cecilia Wickstrand and Wenting Wu and Petra Båth and …

  49. Liquid explosions induced by X-ray laser pulses

    0.0 out of 5 stars 

    24 May 2016 | BioXFEL Publications | Contributor(s): Claudiu A. Stan, Despina Milathianaki, Hartawan Laksmono, Raymond G. Sierra, Trevor A. McQueen, Marc Messerschmidt, Garth J. Williams, Jason E. Koglin, Thomas J. Lane, Matt J. Hayes, Serge A. H. Guillet, Mengning Liang, Andrew L. Aquila, Philip R. Willmott, Joseph S. Robinson, Karl L. Gumerlock, Sabine Botha, Karol Nass, Ilme Schlichting, Robert L. Shoeman, Howard A. Stone, Sébastien Boutet

    http://dx.doi.org/10.1038/nphys3779 Claudiu A. Stan and Despina Milathianaki and Hartawan Laksmono and Raymond G. Sierra and Trevor A. McQueen and Marc Messerschmidt and Garth J. Williams and Jason E. Koglin and Thomas J. Lane and Matt J. Hayes and Serge A. H. Guillet and Mengning Liang and …

  50. Liquid sample delivery techniques for serial femtosecond crystallography

    0.0 out of 5 stars 

    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: …

  51. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

    0.0 out of 5 stars 

    18 Dec 2019 | BioXFEL Publications | Contributor(s): David C. Wych, James Fraser, David L. Mobley, Michael E. Wall

    http://dx.doi.org/10.1063/1.5132692 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Wych, D.C. et al., 2019. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Structural Dynamics, 6(6), p.064704. Available at: …

  52. Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles

    0.0 out of 5 stars 

    30 Jul 2018 | BioXFEL Publications | Contributor(s): Alexander W. Mauney, Joshua M. Tokuda, Lisa M. Gloss, Oscar Gonzalez, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.07.009 journal-article Mauney, A.W. et al., 2018. Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles. Biophysical Journal. Available at: http://dx.doi.org/10.1016/j.bpj.2018.07.009. Alexander W. Mauney and Joshua M. Tokuda …

  53. Loop dynamics of thymidine diphosphate-rhamnose 3′-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis

    0.0 out of 5 stars 

    18 Feb 2016 | BioXFEL Publications | Contributor(s): Lu Han, Shanteri Singh, Jon S. Thorson, George Phillips

    http://dx.doi.org/10.1063/1.4941368 Lu Han and Shanteri Singh and Jon S. Thorson and George N. Phillips Han, L. et al., 2016. Loop dynamics of thymidine diphosphate-rhamnose 3′-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis. Structural Dynamics, 3(1), p.012004. Available …

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

    0.0 out of 5 stars 

    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. …

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

    0.0 out of 5 stars 

    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 …

  56. Low-background pink-beam serial crystallography

    0.0 out of 5 stars 

    19 Dec 2017 | BioXFEL Publications | Contributor(s): A. Meents, M. O. Wiedorn, V. Srajer, R. Henning, I. Sarrou, J. Bergtholdt, M. Barthelmess, P. Reinke, D. Dierksmeyer, A. Tolstikova, S. Schaible, M. Messerschmidt, C. M. Ogata, D. J. Kissick, M. Taft, D. Manstein, J. Lieske, D. Oberthuer, R. F. Fischetti, H. N. Chapman

    http://dx.doi.org/10.1107/s0108767317096052 journal-article Meents, A. et al., 2017. Low-background pink-beam serial crystallography. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a405–a405. Available at: http://dx.doi.org/10.1107/s0108767317096052. A. Meents and M. O. …

  57. Low-signal limit of X-ray single particle diffractive imaging

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    12 Dec 2019 | BioXFEL Publications | Contributor(s): Kartik Ayyer, Andrew J. Morgan, Andrew Aquila, Hasan Demirci, Brenda Hogue, Richard Kirian, P. Lourdu Xavier, Chun Hong Yoon, Henry Chapman, Anton Barty

    http://dx.doi.org/10.1364/oe.27.037816 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ayyer, K. et al., 2019. Low-signal limit of X-ray single particle diffractive imaging. Optics Express, 27(26), p.37816. Available at: http://dx.doi.org/10.1364/oe.27.037816. Kartik Ayyer and …

  58. Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility

    0.0 out of 5 stars 

    07 Mar 2020 | BioXFEL Publications | Contributor(s): Darya Marchany-Rivera, Clyde A. Smith, Josiris D. Rodriguez-Perez, Juan J Lopez-Garriga

    http://dx.doi.org/10.1016/j.jinorgbio.2020.111055 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Marchany-Rivera, D. et al., 2020. Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility. Journal of Inorganic Biochemistry, 207, p.111055. Available at: …

  59. LucY: A Versatile New Fluorescent Reporter Protein

    0.0 out of 5 stars 

    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 …

  60. Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering

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    11 Aug 2020 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1107/s2052252520008830 Macromolecular structures can be determined from solution X-ray scattering. Small-angle X-ray scattering (SAXS) provides global structural information on length scales of 10s to 100s of Ångstroms, and many algorithms are available to convert SAXS data …

  61. Macromolecular diffractive imaging using imperfect crystals

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    10 Feb 2016 | BioXFEL Publications | Contributor(s): Kartik Ayyer, Oleksandr M. Yefanov, Dominik Oberthür, Shatabdi Roy-Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse David Coe, Chelsie E Conrad, Raimund Fromme, Alexander Schaffer, Katerina Dörner, Daniel James, Christopher Kupitz, Markus Metz, Garrett Charles Nelson, Paulraj Lourdu Xavier, Kenneth R. Beyerlein, Marius Schmidt, Iosifina Sarrou, John Spence, Uwe Weierstall, Thomas A. White, Jay-How Yang, Yun Zhao, Mengning Liang, Andrew Aquila, Mark S. Hunter, Joseph S. Robinson, Jason E. Koglin, Sébastien Boutet, Petra Fromme, Anton Barty, Henry Chapman

    http://dx.doi.org/10.1038/nature16949 Kartik Ayyer and Oleksandr M. Yefanov and Dominik Oberthür and Shatabdi Roy-Chowdhury and Lorenzo Galli and Valerio Mariani and Shibom Basu and Jesse Coe and Chelsie E. Conrad and Raimund Fromme and Alexander Schaffer and Katerina Dörner and Daniel James and …

  62. Macromolecular movies, storybooks written by nature

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    03 Nov 2021 | BioXFEL Publications | Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1007/s12551-021-00846-1 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Schmidt, M., 2021. Macromolecular movies, storybooks written by nature. Biophysical Reviews. Available at: http://dx.doi.org/10.1007/s12551-021-00846-1. Marius Schmidt

  63. Macromolecular phasing using diffraction from multiple crystal forms

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    08 Dec 2020 | BioXFEL Publications | Contributor(s): Markus Metz, Romain D. Arnal, Wolfgang Brehm, Henry Chapman, Andrew J. Morgan, Rick P. Millane

    http://dx.doi.org/10.1107/s2053273320013650 A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). …

  64. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy

    0.0 out of 5 stars 

    08 Apr 2015 | BioXFEL Publications | Contributor(s): Dario Mizrachi, Yujie Chen, Jiayan Liu, Hwei-Ming Peng, Ailong Ke, Lois Pollack, Raymond J. Turner, Richard J. Auchus, Matthew P. DeLisa

    journal-article http://dx.doi.org/10.1038/ncomms7826 Mizrachi, D. et al., 2015. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy. Nature Communications, 6, p.6826. Available at: http://dx.doi.org/10.1038/ncomms7826. Dario Mizrachi and Yujie Chen …

  65. Manifold Embedding

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

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

  66. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

    0.0 out of 5 stars 

    18 Sep 2023 | BioXFEL Publications | Contributor(s): Alexander M. Wolff, Eriko Nango, Iris Diane Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James Fraser, Michael Thompson

    http://dx.doi.org/10.1038/s41557-023-01329-4 AbstractUnderstanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric …

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

    0.0 out of 5 stars 

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

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

  68. Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography

    0.0 out of 5 stars 

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

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

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

    0.0 out of 5 stars 

    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. …

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

    0.0 out of 5 stars 

    13 Oct 2015 | Teaching Materials

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

  71. Mapping the decay of double core hole states of atoms and molecules

    0.0 out of 5 stars 

    10 Apr 2014 | BioXFEL Publications | Contributor(s): M Mucke, V Zhaunerchyk, R J Squibb, M Kamińska, J H D Eland, P V D Meulen, P Salén, P Linusson, R D Thomas, M Larsson, L J Frasinski, M Siano, T Osipov, L Fang, B Murphy, N Berrah, L Foucar, J Ullrich, K Motomura, S Mondal, K Ueda, R Richter, K C Prince, M N Piancastelli, M Glownia, J Cryan, R Coffee, C Bostedt, J Bozek, S Schorb, M Messerschmidt, O Takahashi, S Wada, R Feifel

    journal-article http://dx.doi.org/10.1088/1742-6596/488/3/032021 Mucke, M. et al., 2014. Mapping the decay of double core hole states of atoms and molecules. Journal of Physics: Conference Series, 488(3), p.032021. Available at: http://dx.doi.org/10.1088/1742-6596/488/3/032021. M Mucke and V …

  72. Measuring and modeling diffuse scattering in protein X-ray crystallography

    0.0 out of 5 stars 

    07 Dec 2015 | BioXFEL Publications | Contributor(s): Andrew H Van Benschoten, Lin Liu, Ana Gonzalez, Aaron S Brewster, Nicholas K Sauter, James Fraser, Michael Wall

    X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density …

  73. Measuring and modeling diffuse scattering in protein X-ray crystallography

    0.0 out of 5 stars 

    28 Mar 2016 | BioXFEL Publications | Contributor(s): Andrew H. Van Benschoten, Lin Liu, Ana Gonzalez, Aaron S. Brewster, Nicholas K. Sauter, James Fraser, Michael E. Wall

    http://dx.doi.org/10.1073/pnas.1524048113 Andrew H. Van Benschoten and Lin Liu and Ana Gonzalez and Aaron S. Brewster and Nicholas K. Sauter and James S. Fraser and Michael E. Wall Van Benschoten, A.H. et al., 2016. Measuring and modeling diffuse scattering in protein X-ray crystallography. …

  74. Measuring the temporal structure of few-femtosecond free-electron laser X-ray pulses directly in the time domain

    0.0 out of 5 stars 

    24 Nov 2014 | 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/10.1038/nphoton.2014.278 journal-article Helml, W. et al., 2014. Measuring the temporal structure of few-femtosecond free-electron laser X-ray pulses directly in the time domain. Nature Photonics, 8(12), pp.950–957. Available at: http://dx.doi.org/10.1038/nphoton.2014.278. W. …

  75. Mechanism and X-ray damage: beware of artefacts in xylose isomerase

    0.0 out of 5 stars 

    19 Dec 2017 | BioXFEL Publications | Contributor(s): Helena Taberman, Charles S. Bury, Kristin A. Sutton, Edward Snell, Elspeth F. Garman

    http://dx.doi.org/10.1107/s205327331709341x journal-article Taberman, H. et al., 2017. Mechanism and X-ray damage: beware of artefacts in xylose isomerase. Acta Crystallographica Section A Foundations and Advances, 73(a2), pp.C232–C232. Available at: …

  76. Mechanism of Human Apohemoglobin Unfolding

    0.0 out of 5 stars 

    21 Feb 2017 | BioXFEL Publications | Contributor(s): Premila P. Samuel, William C. Ou, George Phillips, John S. Olson

    http://dx.doi.org/10.1021/acs.biochem.6b01235 journal-article Samuel, P.P. et al., 2017. Mechanism of Human Apohemoglobin Unfolding. Biochemistry, 56(10), pp.1444–1459. Available at: http://dx.doi.org/10.1021/acs.biochem.6b01235. Premila P. Samuel and William C. Ou and George N. Phillips and …

  77. Mediator structure and conformation change

    0.0 out of 5 stars 

    10 Feb 2021 | BioXFEL Publications | Contributor(s): Heqiao Zhang, Dong-Hua Chen, Rayees Mattoo, David Bushnell, Yannan Wang, Chao Yuan, Lin Wang, Chunnian Wang, Ralph E. Davis, Yan Nie, Roger Kornberg

    http://dx.doi.org/10.1016/j.molcel.2021.01.022 journal-article Heqiao Zhang and Dong-Hua Chen and Rayees U.H. Mattoo and David A. Bushnell and Yannan Wang and Chao Yuan and Lin Wang and Chunnian Wang and Ralph E. Davis and Yan Nie and Roger D. Kornberg

  78. Megahertz data collection from protein microcrystals at an X-ray free-electron laser

    0.0 out of 5 stars 

    22 Aug 2018 | BioXFEL Publications | Contributor(s): Marie Luise Grünbein, Johan Bielecki, Alexander Gorel, Miriam Stricker, Richard Bean, Marco Cammarata, Katerina Dörner, Lars Fröhlich, Elisabeth Hartmann, Steffen Hauf, Mario Hilpert, Yoonhee Kim, Marco Kloos, Romain Letrun, Marc Messerschmidt, Grant Mills, Gabriela Nass Kovacs, Marco Ramilli, Christopher M. Roome, Tokushi Sato, Matthias Scholz, Michel Sliwa, Jolanta Sztuk-Dambietz, Martin Weik, Britta Weinhausen, Nasser Al-Qudami, Djelloul Boukhelef, Sandor Brockhauser, Wajid Ehsan, Moritz Emons, Sergey Esenov, Hans Fangohr, Alexander Kaukher, Thomas Kluyver, Max Lederer, Luis Maia, Maurizio Manetti, Thomas Michelat, Astrid Münnich, Florent Pallas, Guido Palmer, Gianpietro Previtali, Natascha Raab, Alessandro Silenzi, Janusz Szuba, Sandhya Venkatesan, Krzysztof Wrona, Jun Zhu, R. Bruce Doak, Robert L. Shoeman, Lutz Foucar, Jacques-Philippe Colletier, Adrian P. Mancuso, Thomas R. M. Barends, Claudiu A. Stan, Ilme Schlichting

    http://dx.doi.org/10.1038/s41467-018-05953-4 journal-article Grünbein, M.L. et al., 2018. Megahertz data collection from protein microcrystals at an X-ray free-electron laser. Nature Communications, 9(1). Available at: http://dx.doi.org/10.1038/s41467-018-05953-4. Marie Luise Grünbein and …

  79. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

    0.0 out of 5 stars 

    11 Aug 2022 | BioXFEL Publications | Contributor(s): Susannah Holmes, Henry J. Kirkwood, Richard Bean, Klaus Giewekemeyer, Andrew V. Martin, Marjan Hadian-Jazi, Max Oliver Wiedorn, Dominik Oberthür, Hugh Marman, Luigi Adriano, Nasser Al-Qudami, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sandor Brockhauser, Mathew A. Coleman, Francisco Cruz-Mazo, Cyril Danilevski, Katerina Dörner, Alfonso M. Gañán-Calvo, Rita Graceffa, Hans Fanghor, Michael Heymann, Matthias Frank, Alexander Kaukher, Yoonhee Kim, Bostjan Kobe, Juraj Knoška, Torsten Laurus, Romain Letrun, Luis Maia, Marc Messerschmidt, Markus Metz, Thomas Michelat, Grant Mills, Serguei Molodtsov, Diana Monteiro, Andrew J. Morgan, Astrid Münnich, Gisel E. Peña Murillo, Gianpietro Previtali, Adam Round, Tokushi Sato, Robin Schubert, Joachim Schulz, Megan Shelby, Carolin Seuring, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Stephan Stern, Jola Sztuk-Dambietz, Janusz Szuba, Martin Trebbin, Patrick Vagovic, Thomas Ve, Britta Weinhausen, Krzysztof Wrona, Paul Lourdu Xavier, Chen Xu, Oleksandr Yefanov, Keith A. Nugent, Henry Chapman, Adrian P. Mancuso, Anton Barty, Brian Abbey, Connie Darmanin

    http://dx.doi.org/10.1038/s41467-022-32434-6 AbstractThe European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work …

  80. Megahertz single-particle imaging at the European XFEL

    0.0 out of 5 stars 

    29 May 2020 | BioXFEL Publications | Contributor(s): Egor Sobolev, Sergei Zolotarev, Klaus Giewekemeyer, Johan Bielecki, Kenta Okamoto, Hemanth K. N. Reddy, Jakob Andreasson, Kartik Ayyer, Imrich Barak, Sadia Bari, Anton Barty, Richard Bean, Sergey Bobkov, Henry Chapman, Grzegorz Chojnowski, Benedikt J. Daurer, Katerina Dörner, Tomas Ekeberg, Leonie Flückiger, Oxana Galzitskaya, Luca Gelisio, Steffen Hauf, Brenda Hogue, Daniel A. Horke, Ahmad Hosseinizadeh, Vyacheslav Ilyin, Chulho Jung, Chan Kim, Yoonhee Kim, Richard Kirian, Henry Kirkwood, Olena Kulyk, Jochen Küpper, Romain Letrun, N. Duane Loh, Kristina Lorenzen, Marc Messerschmidt, Kerstin Mühlig, Abbas Ourmazd, Natascha Raab, Andrei V. Rode, Max Rose, Adam Round, Takushi Sato, Robin Schubert, Peter Schwander, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Changyong Song, John Spence, Stephan Stern, Jolanta Sztuk-Dambietz, Anthon Teslyuk, Nicusor Timneanu, Martin Trebbin, Charlotte Uetrecht, Britta Weinhausen, Garth J. Williams, P. Lourdu Xavier, Chen Xu, Ivan A. Vartanyants, Victor S. Lamzin, Adrian Mancuso, Filipe R. N. C. Maia

    http://dx.doi.org/10.1038/s42005-020-0362-y AbstractThe emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is …

  81. Melatonin receptor activation increases glutamatergic synaptic transmission in the rat medial lateral habenula

    0.0 out of 5 stars 

    22 Jan 2016 | BioXFEL Publications | Contributor(s): Katherine M. Evely, Randall L. Hudson, Margarita L. Dubocovich, Samir Haj-dahmane

    http://dx.doi.org/10.1002/syn.21892 journal-article Evely, K.M. et al., 2016. Melatonin receptor activation increases glutamatergic synaptic transmission in the rat medial lateral habenula. Synapse, 70(5), pp.181–186. Available at: http://dx.doi.org/10.1002/syn.21892. Katherine M. Evely and …

  82. Melatonin Receptors as Modulators of Methamphetamine-Mediated Behaviors

    0.0 out of 5 stars 

    01 Apr 2016 | BioXFEL Publications | Contributor(s): Shannon J. Clough, Anthony J. Hutchinson, Margarita L. Dubocovich

    http://dx.doi.org/10.1016/b978-0-12-800212-4.00016-9 book-chapter Clough, S.J., Hutchinson, A.J. & Dubocovich, M.L., 2016. Melatonin Receptors as Modulators of Methamphetamine-Mediated Behaviors. Neuropathology of Drug Addictions and Substance Misuse, pp.169–180. Available at: …

  83. Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

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    07 Feb 2020 | BioXFEL Publications | Contributor(s): Thomas D. Grant, Suchithranga M. Perera, Leslie A. Salas-Estrada, Andrey V. Struts, Udeep Chawla, Xiaolin Xu, Steven D. Fried, Nipuna Weerasinghe, D. Mendez, R. Alvarez, K. Karpos, S. Lisova, S. Zaare, R. Nazari, N.A. Zatsepsin, Abhishek Singharoy, S. Boutet, S. Carbajo, M.S. Hunter, M. Liang, M.D. Seaberg, Raimund Fromme, Petra Fromme, Alan Grossfield, Richard Kirian, Michael F. Brown

    http://dx.doi.org/10.1016/j.bpj.2019.11.2097 journal-article Grant, T.D. et al., 2020. Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser. Biophysical Journal, 118(3), p.365a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.2097. Thomas D. Grant …

  84. Membrane protein megahertz crystallography at the European XFEL

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    04 Nov 2019 | BioXFEL Publications | Contributor(s): Chris Gisriel, Jesse David Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha Stander, Stella Lisova, Valerio Mariani, Manuela Kuhn, Steve Aplin, Thomas D. Grant, Katerina Dörner, Tokushi Sato, Austin Echelmeier, Jorvani Cruz Villarreal, Mark S. Hunter, Max Oliver Wiedorn, Juraj Knoska, Victoria Mazalova, Shatabdi Roy-Chowdhury, Jay-How Yang, Alex Jones, Richard Bean, Johan Bielecki, Yoonhee Kim, Grant Mills, Britta Weinhausen, Jose D. Meza, Nasser Al-Qudami, Saša Bajt, Gerrit Brehm, Sabine Botha, Djelloul Boukhelef, Sandor Brockhauser, Barry D. Bruce, Matthew Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan Kaushylal Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D Zook, John Spence, Henry Chapman, Anton Barty, Richard Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, Nadia Zatsepin

    http://dx.doi.org/10.1038/s41467-019-12955-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Gisriel, C. et al., 2019. Membrane protein megahertz crystallography at the European XFEL. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-12955-3. Chris …

  85. Mentoring Manual

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    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 …

  86. Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination

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    22 Sep 2017 | BioXFEL Publications | Contributor(s): Xuanxuan Li, John Spence, Brenda Hogue, Haiguang Liu

    http://dx.doi.org/10.1107/s2052252517012398 X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the …

  87. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes

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    24 Feb 2020 | BioXFEL Publications | Contributor(s): Tyler D. Huber, Jonathan Clinger, Yang Liu, Weijun Xu, Mitchell Miller, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1021/acschembio.9b00943 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Huber, T.D. et al., 2020. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chemical Biology, 15(3), pp.695–705. Available at: …

  88. Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus

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    27 Oct 2020 | BioXFEL Publications | Contributor(s): Christopher James Gisriel, Petra Fromme, Jose M. Martin-Garcia

    http://dx.doi.org/10.1007/978-1-0716-1012-1_8 book-chapter Gisriel, C., Fromme, P. & Martin-Garcia, J.M., 2020. Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus. Viruses as Therapeutics, pp.125–162. Available at: …

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

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    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 …

  90. Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

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    24 Apr 2018 | BioXFEL Publications | Contributor(s): Yannig Gicquel, Robin Schubert, Svetlana Kapis, Gleb Bourenkov, Thomas Schneider, Markus Perbandt, Christian Betzel, Henry Chapman, Michael Heymann

    http://dx.doi.org/10.3791/57133 journal-article Gicquel, Y. et al., 2018. Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography. Journal of Visualized Experiments, (134). Available at: http://dx.doi.org/10.3791/57133. Yannig …

  91. Microfluidic Mixing Injector Holder Enables Routine Structural Enzymology Measurements with Mix-and-Inject Serial Crystallography Using X-ray Free Electron Lasers

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    07 May 2019 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Lois Pollack

    http://dx.doi.org/10.1021/acs.analchem.9b00311 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Calvey, G.D., Katz, A.M. & Pollack, L., 2019. Microfluidic Mixing Injector Holder Enables Routine Structural Enzymology Measurements with Mix-and-Inject Serial Crystallography Using X-ray …

  92. Microfluidic Platforms for Bimolecular and Nanocrystal Separation

    5.0 out of 5 stars 

    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 …

  93. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography

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    07 Aug 2020 | BioXFEL Publications | Contributor(s): Mohammad Vakili, Ramakrishna Vasireddi, Paul V. Gwozdz, Diana Monteiro, Michael Heymann, Robert H. Blick, Martin Trebbin

    http://dx.doi.org/10.1063/5.0012806 journal-article Vakili, M. et al., 2020. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. Review of Scientific Instruments, 91(8), p.085108. Available at: http://dx.doi.org/10.1063/5.0012806. Mohammad Vakili and Ramakrishna …

  94. Microfluidic sample delivery for serial crystallography using XFELs

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    27 Jun 2019 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Mukul Sonker, Alexandra Ros

    http://dx.doi.org/10.1007/s00216-019-01977-x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Echelmeier, A., Sonker, M. & Ros, A., 2019. Microfluidic sample delivery for serial crystallography using XFELs. Analytical and Bioanalytical Chemistry, 411(25), pp.6535–6547. Available …

  95. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight

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    08 Apr 2021 | BioXFEL Publications | Contributor(s): E. H. Snell, J. R. Helliwell

    http://dx.doi.org/10.1080/0889311x.2021.1900833 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Snell, E.H. & Helliwell, J.R., 2021. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight. …

  96. Mighty small: Observing and modeling individual microbes becomes big science

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    05 Nov 2013 | BioXFEL Publications | Contributor(s): J.-U. Kreft, C. M. Plugge, V. Grimm, C. Prats, J. H. J. Leveau, T. Banitz, S. Baines, J. Clark, A. Ros, I. Klapper, C. J. Topping, A. J. Field, A. Schuler, E. Litchman, F. L. Hellweger

    journal-article http://dx.doi.org/10.1073/pnas.1317472110 Kreft, J.-U. et al., 2013. Mighty small: Observing and modeling individual microbes becomes big science. Proceedings of the National Academy of Sciences, 110(45), pp.18027–18028. Available at: http://dx.doi.org/10.1073/pnas.1317472110. …

  97. MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles

    0.0 out of 5 stars 

    06 Apr 2022 | BioXFEL Publications | Contributor(s): Jorvani Cruz Villarreal, Rory Kruithoff, Ana Egatz-Gomez, Paul D. Coleman, Robert Ros, Todd R. Sandrin, Alexandra Ros

    http://dx.doi.org/10.1007/s00216-022-04038-y journal-article Cruz Villarreal, J., Kruithoff, R., Egatz-Gomez, A., Coleman, P. D., Ros, R., Sandrin, T. R., & Ros, A. (2022). MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. …

  98. Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

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    12 May 2013 | BioXFEL Publications | Contributor(s): Marius Schmidt

    Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive …

  99. Mix-and-diffuse serial synchrotron crystallography

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    09 Oct 2017 | BioXFEL Publications | Contributor(s): Kenneth R. Beyerlein, Dennis Dierksmeyer, Valerio Mariani, Manuela Kuhn, Iosifina Sarrou, Angelica Ottaviano, Salah Awel, Juraj Knoska, Silje Fuglerud, Olof Jönsson, Stephan Stern, Max Oliver Wiedorn, Oleksandr Yefanov, Luigi Adriano, Richard Bean, Anja Burkhardt, Pontus Fischer, Michael Heymann, Daniel A. Horke, Katharina E. J. Jungnickel, Elena Kovaleva, Olga Lorbeer, Markus Metz, Jan Meyer, Andrew Morgan, Kanupriya Pande, Saravanan Panneerselvam, Carolin Seuring, Aleksandra Tolstikova, Julia Lieske, Steve Aplin, Manfred Roessle, Thomas A. White, Henry Chapman, Alke Meents, Dominik Oberthuer

    http://dx.doi.org/10.1107/s2052252517013124 Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers …

  100. Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers

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    29 Aug 2016 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Chris B. Schaffer, Lois Pollack

    http://dx.doi.org/10.1063/1.4961971 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Calvey, G.D. et al., 2016. Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers. Structural Dynamics, 3(5), p.054301. Available at: …