Support

Results (page 1 of 2)

1. time
2. real-time
3. time factors
4. Time resolved scattering
5. Time Resolved X-Ray Scattering
6. time-resolved nanocrystallography
7. time-resolved solution scattering
8. time-resolved serial femtosecond crystallography
9. chemical dynamics in the picoseconds and femtoseconds time regime are used to further understand the
10. chemical dynamics in the picoseconds and femtoseconds time regime are used to further understand the
11. chemical dynamics in the picoseconds and femtoseconds time regime are used to further understand the

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

   Publications 1 Jan 2010 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.… This has particular disadvantages that are circumvented when active substrate is directly provided…

   https://www.bioxfel.org/resources/Mix-and-Inject:-Reaction-Initiation

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

   BioXFEL Publications 4 Apr 2019 Contributor(s): Lan Zhu, Derek Mendez, Chufeng Li, GANESH SUBRAMANIAN, Zachary Dobson, Shangji Zhang, Uwe Weierstall, John Spence, Petra Fromme, Nadia Zatsepin, 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 laser sources. Synchrotron radiation flux may be…

   https://www.bioxfel.org/resources/1738

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

   BioXFEL Publications 12 May 2013 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.… This has particular disadvantages that are circumvented when active substrate is directly provided…

   https://www.bioxfel.org/resources/1301

4. De novo protein crystal structure determination from X-ray free-electron laser data

   Publications 9 Jan 2014 Contributor(s): Marc Messerschmidt

   The determination of protein crystal structures is hampered by the need for macroscopic crystals.… So far, all protein structure determinations carried out using FELs have been based on previous knowledge of related, known structures.… Using the emerging technique of serial femtosecond crystallography, we…

   https://www.bioxfel.org/resources/De-novo-protein-crystal-structure

5. Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

   BioXFEL Publications 22 Jul 2020 Contributor(s): suraj pandey, Ishwor Poudyal, Tek Narsingh Malla

   http://dx.doi.org/10.3390/cryst10070628 With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate.… Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at…

   https://www.bioxfel.org/resources/1932

6. Determining the Mechanism of DJ-1 Using Mix-and-Inject Synchrotron Serial Crystallography

   BioXFEL Publications 10 Apr 2025 Contributor(s): Kara Zielinski, Lois Pollack

   https://doi.org/10.1063/4.0000378 Determining the molecular basis of enzyme catalytic activity is a central challenge in biochemistry.… We used pink beam mix-and-inject serial crystallography (MISC) at the Advanced Photon Source (BioCARS 14-ID) to follow the conversion of methylglyoxal to L-lactate by human DJ-1 using serial Laue…

   https://www.bioxfel.org/resources/2247

7. In vivo protein crystallization opens new routes in structural biology

   Publications 1 Mar 2012 Contributor(s): Uwe Weierstall, Petra Fromme, Mark S. Hunter, Marc Messerschmidt, John Spence, Henry Chapman

   Protein crystallization in cells has been observed several times in nature.

   https://www.bioxfel.org/resources/In-vivo-protein-crystallization-opens

8. Approaches to time-resolved diffraction using an XFEL

   BioXFEL Publications 25 Mar 2014 Contributor(s): John Spence

   http://dx.doi.org/10.1039/c4fd00025k John C. H. Spence Spence, J.C.H., 2014. Approaches to time-resolved diffraction using an XFEL.… , 171, pp.429–438. Available at: http://dx.doi.org/10.1039/c4fd00025k. NSF-STC Biology with X-ray Lasers (NSF-1231306) We describe several schemes for time-resolved imaging of molecular motion…

   https://www.bioxfel.org/resources/899

9. Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis

   BioXFEL Publications 16 Aug 2022 Contributor(s): Ahmad Hosseinizadeh, Gebhard F.X. Schertler, Abbas Ourmazd

   http://dx.doi.org/10.1063/4.0000156 Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution.… To tackle these issues, one established procedure is that of splitting the data into time bins, and averaging the multiple measurements of…

   https://www.bioxfel.org/resources/2170

10. Filling data analysis gaps in time-resolved crystallography by machine learning

    BioXFEL Publications 21 Jan 2025 Contributor(s): Russell Fung, Peter Schwander, Ahmad Hosseinizadeh

    https://doi.org/10.1063/4.0000280 There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments.… Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data…

    https://www.bioxfel.org/resources/2226

11. Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

    BioXFEL Publications 22 Mar 2021 Contributor(s): Chufeng Li, suraj pandey, Mark S. Hunter, Uwe Weierstall, Nadia Zatsepin, John Spence, Marius Schmidt, haiguang liu

    http://dx.doi.org/10.1073/pnas.2020486118 Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells.… Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light…

    https://www.bioxfel.org/resources/1988

12. FD 171: Signal to noise considerations for single crystal femtosecond time resolved crystallography of Photoactive Yellow Protein

    Publications 1 Jan 2014 Contributor(s): Marius Schmidt, Brenda Hogue

    https://www.bioxfel.org/resources/FD-171:-Signal-to-noise

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

    BioXFEL Publications 29 Aug 2014

    journal-article http://dx.doi.org/10.1063/1.4893657 Bionta, M.R. et al., 2014. Spectral encoding method for measuring the relative arrival time between x-ray/optical pulses.

    https://www.bioxfel.org/resources/1321

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

    BioXFEL Publications 31 Mar 2015 Contributor(s): James Fraser

    http://dx.doi.org/10.1038/nmeth.3324 Henry van den Bedem and James S Fraser Van den Bedem, H.… S., 2015. Integrative, dynamic structural biology at atomic resolution—it’s about time.

    https://www.bioxfel.org/resources/889

15. Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography

    BioXFEL Publications 11 Sep 2023 Contributor(s): Nadia Zatsepin, Masahide Hikita, Chelsie E Conrad, Garrett Charles Nelson, Jesse David Coe, Shibom Basu, Mark S. Hunter, Petra Fromme

    http://dx.doi.org/10.1021/jacs.3c07803 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ishigami, I., Carbajo, S., Zatsepin, N., Hikita, M., Conrad, C. E., Nelson, G., Coe, J., Basu, S., Grant, T., Seaberg, M. H., Sierra, R. G., Hunter, M. S., Fromme, P., Fromme, R., Rousseau, D. L., & Yeh, S.-R. (2023). Detection of a Geminate…

    https://www.bioxfel.org/resources/2190

16. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

    BioXFEL Publications 8 Sep 2021 Contributor(s): suraj pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Ishwor Poudyal, Jay-How Yang, Kara Zielinski, Matthias Frank, Rebecca Jeanne Jernigan, Mitchell Miller, Garrett Charles Nelson, Abbas Ourmazd, John Spence, Peter Schwander, Henry Chapman, Petra Fromme, George Phillips, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1107/s2052252521008125 Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales.… The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the…

    https://www.bioxfel.org/resources/2070

17. Co-flow injection for serial crystallography at X-ray free-electron lasers

    BioXFEL Publications 16 Dec 2021 Contributor(s): Diandra Doppler, Sahir Ilyas Gandhi, Ana Egatz-Gomez, Mukul Sonker, Joe Chen, Faisal Hammad Mekky Koua, Victoria Mazalova, Megan Shelby, Max Oliver Wiedorn, Mark S. Hunter, Ahmad Hosseinizadeh, Reza Nazari, Konstantinos Karpos, Zachary Dobson, Erin Discianno, Shangji Zhang, James D Zook, Gihan Kaushylal Ketawala, Natasha Stander, Peter Schwander, Marius Schmidt, Marc Messerschmidt, Abbas Ourmazd, Nadia Zatsepin, Uwe Weierstall, Henry Chapman, Matthias Frank, John Spence, Sabine Botha, Petra Fromme, Richard Kirian, Alexandra Ros

    http://dx.doi.org/10.1107/s1600576721011079 Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature.… Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram…

    https://www.bioxfel.org/resources/2082

18. Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.11.2487 journal-article Kelley, A. M., Macdonald, C. B., & Fraser, J. (2022). Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD.

    https://www.bioxfel.org/resources/2119

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

    BioXFEL Publications 24 Nov 2014

    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.

    https://www.bioxfel.org/resources/1391

20. Synchronous RNA conformational changes trigger ordered phase transitions in crystals

    BioXFEL Publications 19 Mar 2021 Contributor(s): Chelsie E Conrad, Max Oliver Wiedorn, Chufeng Li, Mark S. Hunter, Nadia Zatsepin, suraj pandey, Marius Schmidt, John Spence, Henry Chapman

    http://dx.doi.org/10.1038/s41467-021-21838-5 AbstractTime-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice.… Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal…

    https://www.bioxfel.org/resources/1966

21. X-ray lasers for structural and dynamic biology

    Publications 1 Oct 2012 Contributor(s): Uwe Weierstall, John Spence, Henry Chapman

    Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from…

    https://www.bioxfel.org/resources/X-ray-lasers-for-structural-and

22. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

    BioXFEL Publications 4 Dec 2014 Contributor(s): Shibom Basu, Nadia Zatsepin, Kanupriya Pande, Matthias Frank, Mark S. Hunter, Christopher Kupitz, Chelsie E Conrad, Jesse David Coe, Shatabdi Roy-Chowdhury, Uwe Weierstall, Peter Schwander, Abbas Ourmazd, John Spence, Petra Fromme, Henry Chapman, Marius Schmidt

    http://dx.doi.org/10.1126/science.1259357Jason Tenboer and Shibom Basu and Nadia Zatsepin and Kanupriya Pande and Despina Milathianaki and Matthias Frank and Mark Hunter and Sébastien Boutet and Garth J.… Koglin and Dominik Oberthuer and Michael Heymann and Christopher Kupitz and Chelsie Conrad and Jesse Coe and Shatabdi…

    https://www.bioxfel.org/resources/831

23. Time-resolved serial femtosecond crystallography at the European XFEL

    BioXFEL Publications 18 Nov 2019 Contributor(s): suraj pandey, Ishwor Poudyal, Christopher Kupitz, Mark S. Hunter, Austin Echelmeier, Diandra Doppler, Matthias Frank, Faisal Hammad Mekky Koua, Victoria Mazalova, Abbas Ourmazd, Peter Schwander, Henry Chapman, Alexandra Ros, Petra Fromme, Marius Schmidt

    http://dx.doi.org/10.1038/s41592-019-0628-z journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Pandey, S.… , 2019. Time-resolved serial femtosecond crystallography at the European XFEL.… Available at: http://dx.doi.org/10.1038/s41592-019-0628-z. Suraj Pandey and Richard Bean and Tokushi Sato and…

    https://www.bioxfel.org/resources/1843

24. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow

    BioXFEL Publications 16 Jan 2020 Contributor(s): Diana Monteiro, Martin Trebbin

    http://dx.doi.org/10.1107/s2052252519016865 Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses.… However, the study of many biologically relevant targets is still severely hindered by high sample consumption and…

    https://www.bioxfel.org/resources/2007

25. Biological function investigated by time-resolved structure determination

    BioXFEL Publications 21 Feb 2023 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1063/4.0000177 Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life.… …

    https://www.bioxfel.org/resources/2154

26. Mix-and-diffuse serial synchrotron crystallography

    BioXFEL Publications 9 Oct 2017 Contributor(s): Max Oliver Wiedorn, Kanupriya Pande, Henry Chapman

    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 and subsequently at synchrotron light sources allows…

    https://www.bioxfel.org/resources/1512

27. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

    BioXFEL Publications 31 Mar 2020 Contributor(s): suraj pandey, Melissa Carrillo, Robert William Bosman, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.7554/elife.53514 Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes.… The data reveal a twist of the D-ring, which leads to…

    https://www.bioxfel.org/resources/1871

28. Direct Observation of the Mechanism of Antibiotic Resistance by Mix-and-Inject at the European XFEL

    BioXFEL Publications 26 Nov 2020 Contributor(s): suraj pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Ishwor Poudyal, Jay-How Yang, Kara Zielinski, Matthias Frank, Rebecca Jeanne Jernigan, Mitchell Miller, Garrett Charles Nelson, Abbas Ourmazd, John Spence, Peter Schwander, Henry Chapman, Petra Fromme, George Phillips, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1101/2020.11.24.396689 AbstractIn this study, we follow the diffusion and buildup of occupancy of the substrate ceftriaxone in M. tuberculosis β-lactamase BlaC microcrystals by structural analysis of the enzyme substrate complex at single millisecond time resolution.… We use the ‘mix-and-inject’ technique…

    https://www.bioxfel.org/resources/2006

29. Protein structural ensembles are revealed by redefining X-ray electron density noise

    Publications 7 Jan 2014 Contributor(s): James Holton

    To increase the power of X-ray crystallography to determine not only the structures but also the motions of biomolecules, we developed methods to address two classic crystallographic problems: putting electron density maps on the absolute scale of e(-)/A(3) and calculating the noise at every point in the map.… Analyzing the…

    https://www.bioxfel.org/resources/Protein-structural-ensembles-are-revealed

30. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam

    BioXFEL Publications 7 Sep 2023 Contributor(s): Tek Narsingh Malla, Kara Zielinski, Mark S. Hunter, Christopher Kupitz, suraj pandey, Ishwor Poudyal, Abbas Ourmazd, Petra Fromme, Peter Schwander, Henry Chapman, Emina Stojkovic, George Phillips, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1038/s41467-023-41246-1 AbstractFor decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time.… In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in…

    https://www.bioxfel.org/resources/2185

31. Serial femtosecond crystallography of G protein-coupled receptors

    Publications 20 Dec 2013 Contributor(s): Vadim Cherezov, Uwe Weierstall, Petra Fromme, Marc Messerschmidt, John Spence, James Holton, Henry Chapman, Garrett Charles Nelson, Christopher Kupitz, Applications Manager

    X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to…

    https://www.bioxfel.org/resources/Serial-femtosecond-crystallography-of-G

32. Femtosecond X-ray protein nanocrystallography

    Publications 3 Feb 2011 Contributor(s): Uwe Weierstall, Stefan Hau-Riege, Petra Fromme, Matthias Frank, Mark S. Hunter, Marc Messerschmidt, Marius Schmidt, John Spence, James Holton, Henry Chapman

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size.… It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their…

    https://www.bioxfel.org/resources/Femtosecond-X-ray-protein-nanocrystallography

33. Single mimivirus particles intercepted and imaged with an X-ray laser

    Publications 3 Feb 2011 Contributor(s): Uwe Weierstall, Stefan Hau-Riege, Petra Fromme, Matthias Frank, Mark S. Hunter, Marc Messerschmidt, Marius Schmidt, John Spence, Henry Chapman

    X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions.… The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a…

    https://www.bioxfel.org/resources/Single-mimivirus-particles-intercepted-and

34. Reply to 'Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein'

    Publications 1 Jan 2011 Contributor(s): Marius Schmidt, Daniel Tsung-tai Lee

    2014

    https://www.bioxfel.org/resources/Reply-to-'Contradictions-in-X-ray

35. Practical considerations for the analysis of time-resolved x-ray data

    BioXFEL Publications 16 Aug 2023 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1063/4.0000196 The field of time-resolved macromolecular crystallography has been expanding rapidly after free electron lasers for hard x rays (XFELs) became available.… Although time-scales and data collection modalities can differ substantially between these types of light sources, the analysis of the…

    https://www.bioxfel.org/resources/2187

36. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein

    BioXFEL Publications 9 Apr 2014 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1039/c4fd00011k Jasper J. van Thor and Mark M. Warren and Craig N. Lincoln and Matthieu Chollet and Henrik Till Lemke and David M. Fritz and Marius Schmidt and Jason Tenboer and Zhong Ren and Vukica Srajer and Keith Moffat and Tim Graber Van Thor, J.J. et al., 2014. Signal to noise considerations for single crystal femtosecond…

    https://www.bioxfel.org/resources/901

37. The Coherent X-ray Imaging Data Bank

    Publications 1 Jan 2011 Contributor(s): Nadia Zatsepin

    www.cxidb.orgThe Coherent X-ray Imaging Data Bank (CXIDB) is a database offering scientists access to data from Coherent X-ray Imaging (CXI) experiments, including serial femtosecond crystallography and single particle imaging.www.cxidb.orgThe Coherent X-ray Imaging Data BankFilipe R N C MaiaNature Methods 9, 854–855 (2012)…

    https://www.bioxfel.org/resources/The-Coherent-X-ray-Imaging-Data

38. Time-resolved Crystallography on Protein Photoreceptors and Enzymes

    BioXFEL Publications 8 Dec 2023 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1039/bk9781837670154-00203 Time-resolved macromolecular crystallography (TRX) unifies structure determination of biomolecules with chemical kinetics.… With TR-SFX, femtosecond time-resolution is possible and cyclic and non-cyclic macromolecular reactions can be equally well investigated.… …

    https://www.bioxfel.org/resources/2199

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

    Teaching Materials 13 Oct 2015

    Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation.… Authors: H.-C. Poon, M. Schmidt, and D. K. Saldin View article Video Summary

    https://www.bioxfel.org/resources/655

40. The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source

    BioXFEL Publications 22 Feb 2019 Contributor(s): Mark S. Hunter, Hasan Demirci, Brandon Hayes, Christopher Kupitz

    http://dx.doi.org/10.1107/s1600577519001577 The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from…

    https://www.bioxfel.org/resources/2037

41. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

    BioXFEL Publications 19 Nov 2020 Contributor(s): Reza Nazari, Brian Abbey, Henry Chapman, Alice Contreras, Hasan Demirci, Matthias Frank, Brenda Hogue, Ahmad Hosseinizadeh, Mark S. Hunter, Richard Kirian, Abbas Ourmazd, Peter Schwander

    http://dx.doi.org/10.1038/s41597-020-00745-2 AbstractSingle Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772…

    https://www.bioxfel.org/resources/1929

42. Scaling and merging time-resolved pink-beam diffraction with variational inference

    BioXFEL Publications 8 Nov 2024 Contributor(s): Kara Zielinski, Lois Pollack

    https://doi.org/10.1063/4.0000269 Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution.… Extracting small, time-dependent changes in signal is frequently a bottleneck for practitioners.… However, the…

    https://www.bioxfel.org/resources/2230

43. Time-resolved protein nanocrystallography using an X-ray free-electron laser

    Publications 30 Jan 2012 Contributor(s): Uwe Weierstall, Stefan Hau-Riege, Petra Fromme, Matthias Frank, Mark S. Hunter, Marc Messerschmidt, Marius Schmidt, John Spence, James Holton, Henry Chapman

    We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet.… The result correlates with the microsecond kinetics of electron transfer from…

    https://www.bioxfel.org/resources/Time-resolved-protein-nanocrystallography-using-an

44. Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography

    BioXFEL Publications 13 Oct 2017 Contributor(s): suraj pandey, George Douglas Calvey, Andrea Katz, Christopher Kupitz, Mark S. Hunter, Max Oliver Wiedorn, Kanupriya Pande, Mitchell Miller, Shatabdi Roy-Chowdhury, Jesse David Coe, Nirupa Nagaratnam, James D Zook, Jacob Christopher Verburgt, Tyler Norwood, Ishwor Poudyal, Yun Zhao, Garrett Charles Nelson, GANESH SUBRAMANIAN, Peter Schwander, Matthias Frank, Uwe Weierstall, Nadia Zatsepin, John Spence, Petra Fromme, Henry Chapman, Lois Pollack, Lee Tremblay, Abbas Ourmazd, George Phillips, Marius Schmidt

    http://dx.doi.org/10.1101/202432 Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth.… Here, we demonstrate a general method for capturing…

    https://www.bioxfel.org/resources/1713

45. First Experiments in Structural Biology at the European X-ray Free-Electron Laser

    BioXFEL Publications 25 May 2020

    http://dx.doi.org/10.3390/app10103642 Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination from sub-micron crystals as well as…

    https://www.bioxfel.org/resources/1935

46. Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography

    BioXFEL Publications 31 Jan 2024 Contributor(s): Marius Schmidt, Emina Stojkovic

    http://dx.doi.org/10.1063/4.0000233 Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales.… TR serial crystallography (TR-SX) is an extension of TRLX. As the foundations of TRLX were evolving from the late 1980s to the turn of the millennium,…

    https://www.bioxfel.org/resources/2194

47. Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography

    BioXFEL Publications 31 Jan 2024 Contributor(s): Marius Schmidt, Emina Stojkovic

    https://doi.org/10.1063/4.0000233 Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales.… TR serial crystallography (TR-SX) is an extension of TRLX. As the foundations of TRLX were evolving from the late 1980s to the turn of the millennium, TR-SX…

    https://www.bioxfel.org/resources/2229

48. Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

    BioXFEL Publications 24 May 2017 Contributor(s): Chelsie E Conrad, Garrett Charles Nelson, Natasha Stander, Nadia Zatsepin, James D Zook, Lan Zhu, Nirupa Nagaratnam, Shatabdi Roy-Chowdhury, Jesse David Coe, GANESH SUBRAMANIAN, Uwe Weierstall, John Spence, Vadim Cherezov, Petra Fromme, Wei Liu

    http://dx.doi.org/10.1107/s205225251700570x Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources.… Owing to the longer exposure times that are needed at synchrotrons, serial…

    https://www.bioxfel.org/resources/1466

49. Observations of phase changes in monoolein during high viscous injection

    BioXFEL Publications 21 Mar 2022 Contributor(s): Mark S. Hunter, Richard Kirian, Derek Mendez, Max Oliver Wiedorn, Brian Abbey

    http://dx.doi.org/10.1107/s1600577522001862 Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam.… However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not…

    https://www.bioxfel.org/resources/2097

50. Time-resolved crystallography and protein design

    Publications 1 Jan 2013

    https://www.bioxfel.org/resources/Time-resolved-crystallography-and-protein-design

51. FD 171: Approaches to time-resolved diffraction using an XFEL

    Publications 1 Jan 2011 Contributor(s): John Spence

    https://www.bioxfel.org/resources/FD-171:-Approaches-to-time-resolved

52. Extraction of Fast Changes in the Structure of a Disordered Ensemble of Photoexcited Biomolecules

    BioXFEL Publications 22 May 2013

    journal-articleH.-C. Poon and M. Schmidt and D. K. SaldinPoon, H.-C., Schmidt, M. & Saldin, D.K., 2013. Extraction of Fast Changes in the Structure of a Disordered Ensemble of Photoexcited Biomolecules.… 1–5. Available at: http://dx.doi.org/10.1155/2013/750371.Using pump-probe experiments of varying time intervals between pump…

    https://www.bioxfel.org/resources/1352

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

    BioXFEL Publications 2 May 2013 Contributor(s): Vadim Cherezov

    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 two-photon-excited ultraviolet fluorescence microscopy…

    https://www.bioxfel.org/resources/1838

54. Coherent Convergent-Beam Time-resolved X-ray Diffraction

    Publications 1 Jan 2011 Contributor(s): John Spence, Applications Manager

    https://www.bioxfel.org/resources/Coherent-Convergent-Beam-Time-resolved-X-ray-Diffraction

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

    BioXFEL Publications 2 Sep 2015 Contributor(s): Roger Kornberg

    journal-article http://dx.doi.org/10.1038/nature14882 Fazal, F.M. et al., 2015. Real-time observation of the initiation of RNA polymerase II transcription.

    https://www.bioxfel.org/resources/1270

56. Time-Resolved Spectra from Millivolt EELS Data

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

    http://dx.doi.org/10.1017/s1431927614000890 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Li, C., Subramanian, G. & Spence, J.C.H., 2014. Time-Resolved Spectra from Millivolt EELS Data.

    https://www.bioxfel.org/resources/1408

57. Structural biology in the time of COVID-19: perspectives on methods and milestones

    BioXFEL Publications 22 Apr 2021 Contributor(s): Miranda Lynch, Edward Snell, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s2052252521003948 The global COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has wreaked unprecedented havoc on global society, in terms of a huge loss of life and burden of morbidity, economic upheaval and social disruption.… Structural biology has been at the…

    https://www.bioxfel.org/resources/1996

58. Time-resolved cryogenic electron tomography for the study of transient cellular processes

    BioXFEL Publications 8 May 2024 Contributor(s): Kara Zielinski, Christopher Kupitz, Mark S. Hunter, Lois Pollack

    https://doi.org/10.1091/mbc.e24-01-0042 Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which…

    https://www.bioxfel.org/resources/2236

59. Singular Value Decomposition as a tool for background corrections in time-resolved X-FEL scattering data

    Publications 1 Jan 2013

    https://www.bioxfel.org/resources/Singular-Value-Decomposition-as-a

60. Time-resolved cryogenic electron tomography for the study of transient cellular processes

    BioXFEL Publications 8 May 2024 Contributor(s): Kara Zielinski, Christopher Kupitz, Mark S. Hunter, Lois Pollack

    http://dx.doi.org/10.1091/mbc.e24-01-0042 Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which…

    https://www.bioxfel.org/resources/2220

61. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer

    Publications 1 Jan 2010 Contributor(s): Marius Schmidt, Dilano Saldin

    https://www.bioxfel.org/resources/Enzyme-transient-state-kinetics-in

62. Towards a generalised approach for the time-resolved crystallographic study of enzymes

    BioXFEL Publications 5 Jan 2016 Contributor(s): Edward Snell

    http://dx.doi.org/10.1107/s205327331509957x Diana C. F. Monteiro and Vijay Patel and Christopher P. Bartlett and Shingo Nozaki and Thomas D. Grant and James A. Gowdy and Gary S. Thompson and Arnout P. Kalverda and Edward H. Snell and Hironori Niki and Arwen R. Pearson and Michael E. Webb Monteiro, D.C.F. et al., 2015. Towards a generalised approach…

    https://www.bioxfel.org/resources/960

63. Time-Resolved Contrast Variation SAXS for Studying RNA-Protein Interactions

    BioXFEL Publications 15 Feb 2019 Contributor(s): Andrea Katz, George Douglas Calvey, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1733 poster Pabit, S.A. et al., 2019. Time-Resolved Contrast Variation SAXS for Studying RNA-Protein Interactions.

    https://www.bioxfel.org/resources/1729

64. Time-resolved mixing-jet X-ray free-electron laser crystallography experiments

    BioXFEL Publications 19 Dec 2017 Contributor(s): Max Oliver Wiedorn, Henry Chapman

    http://dx.doi.org/10.1107/s2053273317087393 journal-article Oberthuer, D. et al., 2017. Time-resolved mixing-jet X-ray free-electron laser crystallography experiments.

    https://www.bioxfel.org/resources/1522

65. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free electron lasers

    Publications 1 Jan 2011

    https://www.bioxfel.org/resources/Opportunities-and-challenges-for-time-resolved

66. Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments

    BioXFEL Publications 11 May 2021 Contributor(s): Kara Zielinski, Lois Pollack

    http://dx.doi.org/10.1107/s0108767320099663 journal-article Zielinski, K. & Pollack, L., 2020. Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments.

    https://www.bioxfel.org/resources/2015

67. Time-Resolved Macromolecular Crystallography at Modern X-Ray Sources

    BioXFEL Publications 1 Jun 2017 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1007/978-1-4939-7000-1_11 book-chapter NSF-STC Biology with X-ray Lasers (NSF-1231306) Schmidt, M., 2017. Time-Resolved Macromolecular Crystallography at Modern X-Ray Sources.

    https://www.bioxfel.org/resources/1537

68. Coherent convergent-beam time-resolved X-ray diffraction

    BioXFEL Publications 10 Jun 2014

    http://dx.doi.org/10.1098/rstb.2013.0325 J. C. H. Spence and N. A. Zatsepin and C. Li Spence, J.C.H., Zatsepin, N.A. & Li, C., 2014. Coherent convergent-beam time-resolved X-ray diffraction.

    https://www.bioxfel.org/resources/789

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

    BioXFEL Publications 11 Apr 2015

    http://dx.doi.org/10.1063/1.4916980 K. Pande and M.… Schwander and D.… Saldin Pande, K.… , 2015. Simulations on time-resolved structure determination of uncrystallized biomolecules in the presence of shot noise.

    https://www.bioxfel.org/resources/883

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

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

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

    https://www.bioxfel.org/resources/906

71. Transient state measurements on proteins by time-resolved crystallography

    BioXFEL Publications 22 Apr 2022 Contributor(s): Tek Narsingh Malla, Marius Schmidt

    http://dx.doi.org/10.1016/j.sbi.2022.102376 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Malla, T. N., & Schmidt, M. (2022). Transient state measurements on proteins by time-resolved crystallography.

    https://www.bioxfel.org/resources/2100

72. Virus Dynamics Studied by Time-Resolved Small Angle X-Ray Scattering

    BioXFEL Publications 15 Feb 2019 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.2321 journal-article San Emeterio, J., & Pollack, L. (2019). Virus Dynamics Studied by Time-Resolved Small Angle X-Ray Scattering.

    https://www.bioxfel.org/resources/2175

73. Advances in microfluidic mixers for time-resolved structural biology with X-rays

    BioXFEL Publications 23 May 2025 Contributor(s): Kara Zielinski, Lois Pollack

    https://doi.org/10.1007/s12551-025-01321-x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zielinski, K. A., & Pollack, L. (2025). Advances in microfluidic mixers for time-resolved structural biology with X-rays.

    https://www.bioxfel.org/resources/2246

74. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer

    BioXFEL Publications 28 Mar 2014 Contributor(s): Marius Schmidt, Dilano Saldin

    http://dx.doi.org/10.1063/1.4869472 Marius Schmidt and Dilano K. Saldin Schmidt, M. & Saldin, D.K., 2014. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer.

    https://www.bioxfel.org/resources/761

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

    BioXFEL Publications 29 Aug 2016 Contributor(s): George Douglas Calvey, Andrea Katz, 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.

    https://www.bioxfel.org/resources/1382

76. Difference structures from time-resolved small-angle and wide-angle x-ray scattering

    BioXFEL Publications 17 May 2018 Contributor(s): Prakash Nepal

    http://dx.doi.org/10.1103/physrevb.97.195426 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Nepal, P. & Saldin, D.K., 2018. Difference structures from time-resolved small-angle and wide-angle x-ray scattering.

    https://www.bioxfel.org/resources/1631

77. Watching proteins function with time-resolved x-ray crystallography

    BioXFEL Publications 3 Jul 2017 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1088/1361-6463/aa7d32 journal-article Šrajer, V. & Schmidt, M., 2017. Watching proteins function with time-resolved x-ray crystallography.

    https://www.bioxfel.org/resources/1536

78. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering

    BioXFEL Publications 12 Feb 2021 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2020.11.1003 journal-article Menon, C.S.K. et al., 2021. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering.

    https://www.bioxfel.org/resources/1957

79. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET

    BioXFEL Publications 15 Feb 2019 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1931 poster Plumridge, A. & Pollack, L., 2019. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET.

    https://www.bioxfel.org/resources/1727

80. Data collection strategies for time-resolved X-ray free-electron laser diffraction, and 2-color methods

    BioXFEL Publications 12 Jun 2015 Contributor(s): Chufeng Li, John Spence

    journal-articleChufeng Li and Kevin Schmidt and John C. SpenceLi, C., Schmidt, K. & Spence, J.C., 2015. Data collection strategies for time-resolved X-ray free-electron laser

    https://www.bioxfel.org/resources/880

81. Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy

    BioXFEL Publications 7 Mar 2018 Contributor(s): GANESH SUBRAMANIAN, Uwe Weierstall, John Spence

    http://dx.doi.org/10.1021/acs.jpclett.8b00083 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Subramanian, G. et al., 2018. Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy.… 1542–1546. Available at:…

    https://www.bioxfel.org/resources/1561

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

    BioXFEL Publications 29 Jun 2015 Contributor(s): Gebhard F.X. Schertler

    journal-article http://dx.doi.org/10.1063/1.4922774 NSF-STC Biology with X-ray Lasers (NSF-1231306) Panneels, V. et al., 2015. Time-resolved structural studies with serial crystallography: A new light on retinal proteins.… 041718. Available at: http://dx.doi.org/10.1063/1.4922774. Valérie Panneels and Wenting Wu and Ching-Ju Tsai…

    https://www.bioxfel.org/resources/1281

83. Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources

    BioXFEL Publications 9 Dec 2015 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1080/08940886.2015.1101324 Marius Schmidt Schmidt, M., 2015. Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources.

    https://www.bioxfel.org/resources/886

84. Randomness in time-resolved serial crystallography data: alternatives to the binning and averaging approach

    BioXFEL Publications 17 Mar 2023

    http://dx.doi.org/10.1107/s2053273322095742 journal-article Casadei, C.… , Schertler, G., Ourmazd, A., & Santra, R. (2022). Randomness in time-resolved serial crystallography data: alternatives to the binning and averaging approach.… https://doi.org/10.1107/s2053273322095742 C. Casadei and A.

    https://www.bioxfel.org/resources/2171

85. Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins

    BioXFEL Publications 14 Oct 2022 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1016/j.sbi.2022.102481 journal-article Westenhoff, S., Meszaros, P., & Schmidt, M. (2022). Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins.

    https://www.bioxfel.org/resources/2161

86. Towards time-resolved serial crystallography in a microfluidic device

    BioXFEL Publications 26 Jun 2015 Contributor(s): Marius Schmidt, Sarah Perry

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

    https://www.bioxfel.org/resources/884

87. Time-resolved cryogenic electron tomography using mix-and-inject microfluidic devices

    BioXFEL Publications 10 Apr 2025 Contributor(s): Kara Zielinski, Christopher Kupitz, Mark S. Hunter, Lois Pollack

    https://doi.org/10.1063/4.0000362 Cryogenic electron tomography (cryo-ET) is the highest resolution three-dimensional imaging technique applicable to the life sciences, enabling sub-nanometer visualization of rapidly frozen biological specimens preserved in their near native states. The rapid freezing process lends itself to time-resolved studies,…

    https://www.bioxfel.org/resources/2250

88. Publisher's Note: “Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer” [Struct. Dyn. 1, 024701 (2014)]

    BioXFEL Publications 28 Nov 2017 Contributor(s): Marius Schmidt, Dilano Saldin

    http://dx.doi.org/10.1063/1.5016802 journal-article Schmidt, M. & Saldin, D.K., 2017. Publisher’s Note: “Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer” [Struct.

    https://www.bioxfel.org/resources/1510

89. Spectroscopic Studies of Model Photo-Receptors: Validation of a Nanosecond Time-Resolved Micro-Spectrophotometer Design Using Photoactive Yellow Protein and α-Phycoerythrocyanin

    BioXFEL Publications 16 Sep 2013 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.3390/ijms140918881 journal-article Purwar, N. et al., 2013. Spectroscopic Studies of Model Photo-Receptors: Validation of a Nanosecond Time-Resolved Micro-Spectrophotometer Design Using Photoactive Yellow Protein and α-Phycoerythrocyanin.

    https://www.bioxfel.org/resources/1339

90. Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering

    BioXFEL Publications 15 Sep 2022 Contributor(s): Kara Zielinski, Andrea Katz, George Douglas Calvey, Lois Pollack

    http://dx.doi.org/10.1107/s2053273322099715 journal-article Zielinski, K., Katz, A., Calvey, G., Pabit, S., San Emeterio, J., & Pollack, L. (2022). Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering.

    https://www.bioxfel.org/resources/2177

91. X-ray scattering exhibits time-resolved view of rhodopsin activation

    BioXFEL Publications 10 Feb 2023 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2022.11.1170 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Perera, S. M. D. C., Kosheleva, I. V., Salas-Estrada, L., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2023). X-ray scattering exhibits time-resolved view of rhodopsin activation.

    https://www.bioxfel.org/resources/2179

92. Protein energy landscapes determined by five-dimensional crystallography

    BioXFEL Publications 19 Nov 2013 Contributor(s): Marius Schmidt

    Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012),Fundamentals of Enzyme Kinetics, 4th ed.… Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001),Chem.… 101, 1569–1581; Schmidtet…

    https://www.bioxfel.org/resources/817

93. Time-resolved functional expansion of visual rhodopsin detected by x-ray scattering

    BioXFEL Publications 11 Feb 2022 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2021.11.1313 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Alvarez, R. C., Perera, S. M. D. C., Kosheleva, I. V., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2022). Time-resolved functional expansion of visual rhodopsin detected by x-ray scattering.

    https://www.bioxfel.org/resources/2117

94. The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature

    BioXFEL Publications 29 Jul 2021 Contributor(s): suraj pandey, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1107/s2059798321005830 (6–4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6–4) photolyase [Dm(6–4)photolyase] at room and cryogenic temperatures are reported. The…

    https://www.bioxfel.org/resources/2069

95. Biological Networks across Scales—The Theoretical and Empirical Foundations for Time-Varying Complex Networks that Connect Structure and Function across Levels of Biological Organization

    BioXFEL Publications 21 May 2021 Contributor(s): Edward Snell

    http://dx.doi.org/10.1093/icb/icab069 Abstract Many biological systems across scales of size and complexity exhibit a time-varying complex network structure that emerges and self-organizes as a result of interactions with the environment.… A wide range of networks exist in biology, from gene regulatory networks…

    https://www.bioxfel.org/resources/2133

96. Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering

    BioXFEL Publications 2 May 2023 Contributor(s): Kara Zielinski, Andrea Katz, George Douglas Calvey, Lois Pollack

    http://dx.doi.org/10.1107/s2052252523003482 Advances in time-resolved structural techniques, mainly in macromolecular crystallography and small-angle X-ray scattering (SAXS), allow for a detailed view of the dynamics of biological macromolecules and reactions between binding partners.… Most mix-and-inject approaches rely on…

    https://www.bioxfel.org/resources/2172

97. The accurate assessment of small-angle X-ray scattering data

    BioXFEL Publications 24 Dec 2014 Contributor(s): Joseph Luft, Edward Snell

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models.… Here, a series of metrics to quantitatively describe SAXS data in an objective manner using…

    https://www.bioxfel.org/resources/947

98. Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization

    BioXFEL Publications 22 Nov 2024 Contributor(s): Tek Narsingh Malla, SRINIVASAN MUNIYAPPAN, Emina Stojkovic, Shibom Basu, Marius Schmidt

    https://doi.org/10.1107/s2052252524010868 The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected to enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution.… Here, we report experiments emerging…

    https://www.bioxfel.org/resources/2233

99. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein.

    Publications 5 Dec 2014 Contributor(s): Tom Grant

    Authors: Tenboer, J., Basu, S., Zatsepin, N., Pande, K.… , Frank, M., Hunter, M., Boutet, S., Williams, G. J., Koglin, J. E., Oberthuer, D., Heymann, M., Kupitz, C., Conrad, C., Coe, J., Roy-Chowdhury, S., Weierstall, U., James, D., Wang, D., Grant, T., Barty, A., Yefanov, O., Scales, J., Gati, C., Seuring, C., Srajer, V., Henning,…

    https://www.bioxfel.org/resources/411

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

     BioXFEL Publications 15 Nov 2016 Contributor(s): Garrett Charles Nelson, Chelsie E Conrad, Jesse David Coe, Yun Zhao, Robert Dods, Chufeng Li, Mark S. Hunter, Henry Chapman, Petra Fromme, Matthias Frank, Uwe Weierstall, John Spence, Gebhard F.X. Schertler

     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 and Robert Dods and Rajiv Harimoorthy and Kenneth…

     https://www.bioxfel.org/resources/1205