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  1. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application

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    03 Dec 2019 | BioXFEL Publications | Contributor(s): Geoffrey W. Grime, Oliver B. Zeldin, Mary E. Snell, Edward D. Lowe, John F. Hunt, Gaetano T. Montelione, Liang Tong, Edward Snell, Elspeth F. Garman

    http://dx.doi.org/10.1021/jacs.9b09186 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Grime, G.W. et al., 2019. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. Journal of the American Chemical …

  2. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source

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    04 Apr 2019 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Lan Zhu, Derek Mendez, Ming-Yue Lee, Eugene Chun, Chufeng Li, Hao Hu, GANESH SUBRAMANIAN, David Kissick, Craig Ogata, Robert Henning, Andrii Ishchenko, Zachary Dobson, Shangji Zhang, Uwe Weierstall, John Spence, Petra Fromme, Nadia Zatsepin, Robert F. Fischetti, Vadim Cherezov, Wei Liu

    http://dx.doi.org/10.1107/s205225251900263x Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron …

  3. Hit Rate Calculator

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    01 Apr 2015 | Downloads | Contributor(s): Tom Grant

    Data Analysis Scripts 'hits' is a python script that can be used to quickly calculate hits and hit rates from a series of different experimental runs from an SFX experiment when using Cheetah for hit finding. It uses Cheetah's frames.txt file to calculate hits.  By default it will use your own …

  4. Hollow cone illumination for fast TEM, and outrunning damage with electrons

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    23 Sep 2015 | BioXFEL Publications | Contributor(s): J C H Spence, G Subramanian, P Musumeci

    http://dx.doi.org/10.1088/0953-4075/48/21/214003 J C H Spence and G Subramanian and P Musumeci Spence, J.C.H., Subramanian, G. & Musumeci, P., 2015. Hollow cone illumination for fast TEM, and outrunning damage with electrons. Journal of Physics B: Atomic, Molecular and Optical Physics, 48(21), …

  5. How 2'- O -Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation

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    06 Feb 2018 | BioXFEL Publications | Contributor(s): Junhong Choi, Gabriele Indrisiunaite, Hasan Demirci, Ka-Weng Ieong, Jinfan Wang, Alexey Petrov, Arjun Prabhakar, Gideon Rechavi, Dan Dominissini, Chuan He, Måns Ehrenberg, Joseph D. Puglisi

    http://dx.doi.org/10.1016/j.bpj.2017.11.3237 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Choi, J. et al., 2018. How 2’- O -Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation. Biophysical Journal, 114(3), p.592a. Available at: …

  6. How Cubic Can Ice Be?

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    28 Jun 2017 | BioXFEL Publications | Contributor(s): Andrew J. Amaya, Harshad Pathak, Viraj P. Modak, Hartawan Laksmono, N. Duane Loh, Jonas A. Sellberg, Raymond G. Sierra, Trevor A. McQueen, Matt J. Hayes, Garth J. Williams, Marc Messerschmidt, Sébastien Boutet, Michael J. Bogan, Anders Nilsson, Claudiu A. Stan, Barbara E. Wyslouzil

    http://dx.doi.org/10.1021/acs.jpclett.7b01142 journal-article Amaya, A.J. et al., 2017. How Cubic Can Ice Be? The Journal of Physical Chemistry Letters, pp.3216–3222. Available at: http://dx.doi.org/10.1021/acs.jpclett.7b01142. Andrew J. Amaya and Harshad Pathak and Viraj P. Modak and Hartawan …

  7. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

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    19 Nov 2020 | BioXFEL Publications | Contributor(s): Renee Otten, Ricardo A. P. Pádua, H. Adrian Bunzel, Vy Nguyen, Warintra Pitsawong, MacKenzie Patterson, Shuo Sui, Sarah Perry, Aina E. Cohen, Donald Hilvert, Dorothee Kern

    http://dx.doi.org/10.1126/science.abd3623 The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of NMR, crystallographic, and stopped-flow techniques to an …

  8. How good are my data?

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    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 …

  9. How the Conformations of an Internal Junction Contribute to Fold an RNA Domain

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    04 Oct 2018 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Julie L. Sutton, Lois Pollack

    http://dx.doi.org/10.1021/acs.jpcb.8b07262 journal-article Chen, Y.-L., Sutton, J.L. & Pollack, L., 2018. How the Conformations of an Internal Junction Contribute to Fold an RNA Domain. The Journal of Physical Chemistry B. Available at: http://dx.doi.org/10.1021/acs.jpcb.8b07262. Yen-Lin Chen …

  10. ID: 294 Tumor Cell Signaling Through Integrin alpha5beta1 Requires Urokinase Receptor Binding

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    06 Nov 2006 | BioXFEL Publications | Contributor(s): H. Chapman, C. Tang, L. Robillard, Y. Kim, Y. Wei

    http://dx.doi.org/10.1111/j.1538-7836.2006.00294.x journal-article Chapman, H. et al., 2006. ID: 294 Tumor Cell Signaling Through Integrin alpha5beta1 Requires Urokinase Receptor Binding. Journal of Thrombosis and Haemostasis, 4(s1), pp.78–78. Available at: …

  11. Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies

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    12 Oct 2022 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Belgin Sever, Esra Ayan, Mustafa Can, Hasan Demirci, Masami Otsuka, Amaç Fatih TuYuN, Hiroshi Tateishi, Mikako Fujita

    http://dx.doi.org/10.3390/ph15101255 The HIV-1 Gag protein binds to the host cell membrane and assembles into immature particles. Then, in the course of immature virion budding, activated protease cleaves Gag into its main components: MA, CA, NC, and p6 proteins. The highly basic residues of MA …

  12. Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors

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    27 Jul 2017 | BioXFEL Publications | Contributor(s): X. Edward Zhou, Yuanzheng He, Parker W. De Waal, Xiang Gao, Yanyong Kang, Ned Van Eps, Yanting Yin, Kuntal Pal, Devrishi Goswami, Thomas A. White, Anton Barty, Naomi R. Latorraca, Henry Chapman, Wayne L. Hubbell, Ron O. Dror, Raymond C. Stevens, Vadim Cherezov, Vsevolod V. Gurevich, Patrick R. Griffin, Oliver P. Ernst, Karsten Melcher, H. Eric Xu

    http://dx.doi.org/10.1016/j.cell.2017.07.002 journal-article Zhou, X.E. et al., 2017. Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors. Cell, 170(3), pp.457–469.e13. Available at: http://dx.doi.org/10.1016/j.cell.2017.07.002. X. Edward Zhou and …

  13. Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS

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    31 Oct 2023 | BioXFEL Publications | Contributor(s): Rafael Maldonado‐Hernández, Orestes Quesada, José A. González‐Feliciano, Abel Baerga‐Ortiz, José A. Lasalde‐Dominicci

    http://dx.doi.org/10.1002/pmic.202300151 AbstractThe Cys‐loop pentameric ligand‐gated ion channels comprise a dynamic group of proteins that have been extensively studied for decades, yielding a wealth of findings at both the structural and functional levels. The nicotinic acetylcholine …

  14. Identifying, studying and making good use of macromolecular crystals

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    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 …

  15. Image reconstruction in serial femtosecond nanocrystallography using x-ray free-electron lasers

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    21 Sep 2015 | BioXFEL Publications | Contributor(s): Joe Chen, Richard Kirian, Kenneth R. Beyerlein, Richard J. Bean, Andrew J. Morgan, Oleksandr M. Yefanov, Romain D. Arnal, David H. Wojtas, Phil J. Bones, Henry Chapman, John Spence, Rick P. Millane

    http://dx.doi.org/10.1117/12.2187610 Joe P. J. Chen and Richard A. Kirian and Kenneth R. Beyerlein and Richard J. Bean and Andrew J. Morgan and Oleksandr M. Yefanov and Romain D. Arnal and David H. Wojtas and Phil J. Bones and Henry N. Chapman and John C. H. Spence and Rick P. Millane Chen, J.P.J. …

  16. Imaging enzyme kinetics at atomic resolution

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    28 Jun 2016 | BioXFEL Publications | Contributor(s): John Spence, Eaton E Lattman

    http://dx.doi.org/10.1107/s2052252516010204 John Spence and Eaton Lattman Spence, J. & Lattman, E., 2016. Imaging enzyme kinetics at atomic resolution. IUCrJ, 3(4), pp.228–229. Available at: http://dx.doi.org/10.1107/s2052252516010204. journal-article

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

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    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 …

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

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

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

  19. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses

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    28 Jan 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

    http://dx.doi.org/10.1007/978-3-319-04507-8_27-2 Richard A. Kirian and Henry N. Chapman Kirian, R.A. & Chapman, H.N., 2015. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1–55. Available at: …

  20. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses

    0.0 out of 5 stars 

    12 May 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

    http://dx.doi.org/10.1007/978-3-319-14394-1_27 Richard A. Kirian and Henry N. Chapman Kirian, R.A. & Chapman, H.N., 2016. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1135–1195. Available at: …

  21. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses

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    04 May 2020 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

    http://dx.doi.org/10.1007/978-3-030-23201-6_27 book-chapter Kirian, R.A. & Chapman, H.N., 2020. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1337–1397. Available at: …

  22. Imaging single cells in a beam of live cyanobacteria with an X-ray laser

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    11 Feb 2015 | BioXFEL Publications | Contributor(s): Gijs Van Der Schot, Martin Svenda, Filipe R. N. C. Maia, Max Hantke, Daniel P. DePonte, M. Marvin Seibert, Andrew Aquila, Joachim Schulz, Richard Kirian, Mengning Liang, Francesco Stellato, Bianca Iwan, Jakob Andreasson, Nicusor Timneanu, Daniel Westphal, F. Nunes Almeida, Dusko Odic, Dirk Hasse, Gunilla H. Carlsson, Daniel S. D. Larsson, Anton Barty, Andrew V. Martin, Sebastian Schorb, Christoph Bostedt, John D. Bozek, Daniel Rolles, Artem Rudenko, Sascha Epp, Lutz Foucar, Benedikt Rudek, Robert Hartmann, Nils Kimmel, Peter Holl, Lars Englert, Ne-Te Duane Loh, Henry Chapman, Inger Andersson, Janos Hajdu, Tomas Ekeberg

    http://dx.doi.org/10.1038/ncomms6704 Gijs van der Schot and Martin Svenda and Filipe R. N. C. Maia and Max Hantke and Daniel P. DePonte and M. Marvin Seibert and Andrew Aquila and Joachim Schulz and Richard Kirian and Mengning Liang and Francesco Stellato and Bianca Iwan and Jakob Andreasson and …

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

    0.0 out of 5 stars 

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

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

  24. Immunological Characterization of Plant-Based HIV-1 Gag/Dgp41 Virus-Like Particles

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    17 Mar 2016 | BioXFEL Publications | Contributor(s): Sarah A. Kessans, Mark D. Linhart, Lydia R. Meador, Jacquelyn Kilbourne, Brenda Hogue, Petra Fromme, Nobuyuki Matoba, Tsafrir S. Mor

    http://dx.doi.org/10.1371/journal.pone.0151842 Sarah A. Kessans and Mark D. Linhart and Lydia R. Meador and Jacquelyn Kilbourne and Brenda G. Hogue and Petra Fromme and Nobuyuki Matoba and Tsafrir S. Mor Kessans, S.A. et al., 2016. Immunological Characterization of Plant-Based HIV-1 Gag/Dgp41 …

  25. Implementation of simultaneous ultraviolet/visible and x-ray absorption spectroscopy with microfluidics

    0.0 out of 5 stars 

    10 Jan 2025 | BioXFEL Publications | Contributor(s): Olivia McCubbin Stepanic, Christopher J. Pollock, Kara Zielinski, William Foschi, Derek B. Rice, Lois Pollack, Serena DeBeer

    https://doi.org/10.1063/5.0218572 X-ray spectroscopies are uniquely poised to describe the geometric and electronic structure of metalloenzyme active sites under a wide variety of sample conditions. UV/Vis (ultraviolet/visible) spectroscopy is a similarly well-established technique that can …

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

    0.0 out of 5 stars 

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

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

  27. Improving Cryo-EM Experimental Data Fit with Automated Multiconformer Modeling for Proteins and Non-proteins

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    10 Apr 2025 | BioXFEL Publications | Contributor(s): Stephanie Wankowicz, Jessica Flowers, Daniel Hogan, Ashraya Ravikumar, James Fraser

    https://doi.org/10.1063/4.0000388 Biomolecules exchange between multiple conformational states in their folded state, crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble …

  28. Improving resolution in serial crystallography

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    05 Jan 2016 | BioXFEL Publications | Contributor(s): Kartik Ayyer, Oleksandr M. Yefanov, Dominik Oberthuer, Shatabdi Roy Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse David Coe, Chelsie E Conrad, Raimund Fromme, Katerina Doerner, Matthias Frank, Daniel James, Christopher Kupitz, Markus Metz, Garrett Charles Nelson, Xavier L. Paulraj, Kenneth Beyerlein, Marius Schmidt, Iosifina Sarrou, John Spence, Uwe Weierstall, Thomas A. White, Jayhow Yang, Nadia Zatsepin, Yun Zhao, Mengning Liang, Andrew Aquila, Mark S. Hunter, Joseph S. Robinson, Jason E. Koglin, Sébastien Boutet, Petra Fromme, Anton Barty, Henry Chapman

    http://dx.doi.org/10.1107/s2053273315099738 Kartik Ayyer and Oleksandr M. Yefanov and Dominik Oberthuer and Shatabdi Chowdhury and Lorenzo Galli and Valerio Mariani and Shibom Basu and Jesse Coe and Chelsie E. Conrad and Raimund Fromme and Katerina Doerner and Matthias Frank and Daniel James and …

  29. Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

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    15 Jul 2016 | BioXFEL Publications | Contributor(s): Hongxing He, Hengrui Fang, Mitchell Miller, George Phillips, Wu-Pei Su

    An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between …

  30. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

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    30 Jan 2020 | BioXFEL Publications | Contributor(s): Karol Nass, Lars Redecke, M. Perbandt, O. Yefanov, M. Klinge, R. Koopmann, F. Stellato, A. Gabdulkhakov, R. Schönherr, D. Rehders, J. M. Lahey-Rudolph, A. Aquila, A. Barty, S. Basu, R. B. Doak, R. Duden, M. Frank, R. Fromme, S. Kassemeyer, G. Katona, R. Kirian, H. Liu, I. Majoul, J. M. Martin-Garcia, M. Messerschmidt, R. L. Shoeman, U. Weierstall, S. Westenhoff, T. A. White, G. J. Williams, C. H. Yoon, N. Zatsepin, P. Fromme, M. Duszenko, H. N. Chapman, C. Betzel

    http://dx.doi.org/10.1038/s41467-020-14484-w journal-article Nass, K. et al., 2020. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nature Communications, 11(1). Available at: http://dx.doi.org/10.1038/s41467-020-14484-w. Karol …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

  33. 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 …

  34. 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 …

  35. Indexing ambiguity in SFX resolved using expectation maximization algorithm

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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., …

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

    0.0 out of 5 stars 

    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, …

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

    0.0 out of 5 stars 

    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 …

  40. 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. …

  41. 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 …

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

    0.0 out of 5 stars 

    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: …

  43. 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. …

  44. 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: …

  45. 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 …

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

    0.0 out of 5 stars 

    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. …

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

    0.0 out of 5 stars 

    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. …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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., …

  51. 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.

  52. 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.

  53. Introduction to Biological Small Angle Scattering

    0.0 out of 5 stars 

    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 …

  54. Introduction to CrystFEL

    0.0 out of 5 stars 

    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 …

  55. 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. 

  56. Introduction to XFELs in Structural Biology

    0.0 out of 5 stars 

    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.

  57. Introduction to XRayView Crystallographic Software

    0.0 out of 5 stars 

    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.

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

    0.0 out of 5 stars 

    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. …

  59. 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 …

  60. Investigation of NO2 adsorption on reduced graphene oxide

    0.0 out of 5 stars 

    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 …

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

    0.0 out of 5 stars 

    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 …

  62. Journal Club Seminars

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    01 Dec 2016 | Teaching Materials

    Videos of all past Journal Clubs 

  63. June 2016 Site Visit Agenda

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    21 Apr 2016 | Downloads

    …

  64. 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: …

  65. 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 …

  66. 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 …

  67. LCLS Beam-time Schedules

    0.0 out of 5 stars 

    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)

  68. LCLS serial femtosecond crystallography data analysis instructions

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

    SFX data analysis at LCLS Overview.

  69. 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 …

  70. Lecture Series

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    01 Dec 2016 | Teaching Materials

    BioXFEL Lecture Series videos are kept here.

  71. 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 …

  72. 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 …

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

    0.0 out of 5 stars 

    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: …

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

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    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 …

  75. 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 …

  76. 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 …

  77. 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 …

  78. 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 …

  79. 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 …

  80. 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: …

  81. 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: …

  82. 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 …

  83. 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 …

  84. 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. …

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

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    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 …

  86. Low-background pink-beam serial crystallography

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    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. …

  87. 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 …

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

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    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: …

  89. LucY: A Versatile New Fluorescent Reporter Protein

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    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 …

  90. 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 …

  91. 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 …

  92. 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

  93. 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). …

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

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    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 …

  95. 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.

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

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    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 …

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

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    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 …

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

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    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 …

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

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    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. …

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

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    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 …