Cited by 144Enzyme Structure and FunctionAdvanced X-ray Imaging TechniquesX-ray Diffraction in Crystallography

Goniometer-based femtosecond crystallography with X-ray free electron lasers

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Cohen, Aina E., Soltis, S. Michael, González, Ana, Aguila, Laura, Alonso-Mori, Roberto, Barnes, Christopher O., Baxter, Elizabeth L., Brehmer, Winnie +37 more·2014·Proceedings of the National Academy of Sciences

Abstract

Significance: The extremely short and bright X-ray pulses produced by X-ray free-electron lasers unlock new opportunities in crystallography-based structural biology research. Efficient methods to deliver crystalline material are necessary due to damage or destruction of the crystal by the X-ray pulse. Crystals for the first experiments were 5 µm or smaller in size, delivered by a liquid injector. We describe a highly automated goniometer-based approach, compatible with crystals of larger and varied sizes, and accessible at cryogenic or ambient temperatures. These methods, coupled with improvements in data-processing algorithms, have resulted in high-resolution structures, unadulterated by the effects of radiation exposure, from only 100 to 1,000 diffraction images.

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  • Similar improvements in limiting resolution of XFEL versus synchrotron diffraction images have been observed for GPCRs.

    “We note that similar improvements in limiting resolution of XFEL versus synchrotron diffraction images have been observed for GPCRs60.”

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  1. Neutze R, Wouts R, van der Spoel D, Weckert E, Hajdu J (2000) Potential for bio- molecular imaging with femtosecond X-ray pulses. Nature 406(6797):752-757.
  2. Lomb L, et al. (2011) Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B 84(21):214111.
  3. Barty A, et al. (2012) Self-terminating diffraction gates femtosecond X-ray nano- crystallography measurements. Nat Photonics 6(1):35-40.
  4. Owen RL, Rudiño-Piñera E, Garman EF (2006) Experimental determination of the radia- tion dose limit for cryocooled protein crystals. Proc Natl Acad Sci USA 103(13):4912-4917.
  5. Alonso-Mori R, et al. (2012) Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proc Natl Acad Sci USA 109(47):19103-19107.
  6. Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC (1998) X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 282(5395):1853-1858.
  7. Yano J, et al. (2005) X-ray damage to the Mn4Ca complex in single crystals of pho- tosystem II: A case study for metalloprotein crystallography. Proc Natl Acad Sci USA 102(34):12047-12052.
  8. Meharenna YT, Doukov T, Li H, Soltis SM, Poulos TL (2010) Crystallographic and sin- gle-crystal spectral analysis of the peroxidase ferryl intermediate. Biochemistry 49(14): 2984-2986.
  9. Davis KM, Kosheleva I, Henning RW, Seidler GT, Pushkar Y (2013) Kinetic modeling of the X-ray-induced damage to a metalloprotein. J Phys Chem B 117(31):9161-9169.
  10. Kim Y-J, Hill JP, Kim J, Casa D (2012) Hard X-ray resonant inelastic X-ray scattering at the advanced photon source. Synchrotron Radiat News 25(4):3-8.
  11. Schmerge JF, et al. (2013) SSRL performance enhancements. 11th International Con- ference on Synchrotron Radiation Instrumentation (Sri 2012). J Phys Conf Ser 425(2013):042011.
  12. Chapman HN, et al. (2011) Femtosecond X-ray protein nanocrystallography. Nature 470(7332):73-77.
  13. DePonte DP, et al. (2008) Gas dynamic virtual nozzle for generation of microscopic droplet streams. J Phys D Appl Phys 41(19):195505.
  14. Boutet S, et al. (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science 337(6092):362-364.
  15. Redecke L, et al. (2013) Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339(6116):227-230.
  16. Stevenson HP, et al. (2014) Use of transmission electron microscopy to identify nano- crystals of challenging protein targets. Proc Natl Acad Sci USA 111(23):8470-8475.
  17. Johansson LC, et al. (2012) Lipidic phase membrane protein serial femtosecond crys- tallography. Nat Methods 9(3):263-265.
  18. Barends TR, et al. (2014) De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505(7482):244-247.
  19. Liu W, et al. (2013) Serial femtosecond crystallography of G protein-coupled re- ceptors. Science 342(6165):1521-1524.
  20. Fraser JS, et al. (2011) Accessing protein conformational ensembles using room- temperature X-ray crystallography. Proc Natl Acad Sci USA 108(39):16247-16252.
  21. Stevenson HP, et al. (2014) Transmission electron microscopy as a tool for nanocrystal characterization pre-and post-injector. Philos Trans R Soc Lond B Biol Sci 369(1647): 20130322.
  22. Dhouib K, et al. (2009) Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis. Lab Chip 9(10):1412-1421.
  23. Zhu D, et al. (2012) A single-shot transmissive spectrometer for hard x-ray free elec- tron lasers. Appl Phys Lett 101(3):034103.
  24. Snigirev A, Kohn V, Snigireva I, Lengeler B (1996) A compound refractive lens for focusing high-energy X-rays. Nature 384(6604):49-51.
  25. Cohen AE, Ellis PJ, Miller MD, Deacon AM, Phizackerley RP (2002) An automated system to mount cryo-cooled protein crystals on a synchrotron beam line, using compact sample cassettes and a small-scale robot. J Appl Cryst 35(6):720-726.
  26. Hattne J, et al. (2014) Accurate macromolecular structures using minimal measure- ments from X-ray free-electron lasers. Nat Methods 11(5):545-548.
  27. Ring AM, et al. (2013) Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody. Nature 502(7472):575-579.
  28. Leslie AGW, Powell HR, Read RJ, Sussman JL (2007) Processing diffraction data with MOSFLM. Evolving Methods for Macromolecular Crystallography, eds Read RJ, Sussman JL (Springer, New York), Vol 245, pp 41-51.
  29. Hirata K, et al. (2014) Determination of damage-free crystal structure of an X-ray- sensitive protein using an XFEL. Nat Methods 11(7):734-736.
  30. Anonymous (2013) IPAC2013: Proceedings of the 4th International Particle Accelerator Conference. Available at accelconf.web.cern.ch/AccelConf/IPAC2013/. Accessed August 1, 2014.

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Authors
Cohen, A. E., Soltis, S. M., González, A., Aguila, L., Alonso-Mori, R., Barnes, C. O., Baxter, E. L., Brehmer, W., Brewster, A. S., Brunger, A. T., Calero, G., Chang, J. F., Chollet, M., Ehrensberger, P., Eriksson, T. L., Feng, Y., Hattne, J., Hedman, B., Hollenbeck, M., Holton, J. M., Keable, S., Kobilka, B. K., Kovaleva, E. G., Kruse, A. C., Lemke, H. T., Lin, G., Lyubimov, A. Y., Manglik, A., Mathews, I. I., McPhillips, S. E., Nelson, S., Peters, J. W., Sauter, N. K., Smith, C. A., Song, J., Stevenson, H. P., Tsai, Y., Uervirojnangkoorn, M., Vinetsky, V., Wakatsuki, S., Weis, W. I., Zadvornyy, O. A., Zeldin, O. B., Zhu, D., & Hodgson, K. O.
Affiliations
  • Stanford Synchrotron Radiation Lightsource (US)
  • Stanford Synchrotron Radiation Lightsource,
  • Linac Coherent Light Source, and
  • University of Pittsburgh (US)
  • Lawrence Berkeley National Laboratory (US)
  • Molecular and Cellular Physiology, and
  • Linac Coherent Light Source (US)
  • Montana State University (US)
  • Howard Hughes Medical Institute (US)
  • Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025;
Venue
Proceedings of the National Academy of Sciences
Published
2014-10-31
Volume
111
Issue
48
Pages
17122-17127
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
OpenAlex
W2073679797
Cited by
144
References
0
Citations by year
2026: 3 · 2025: 6 · 2024: 3 · 2023: 5 · 2022: 6 · 2021: 8 · 2020: 12 · 2019: 18 · 2018: 15 · 2017: 19 · 2016: 20 · 2015: 28 · 2014: 1
FWCI
10.29
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • NIH (P41GM103393, GM102520, GM095887, GM073210, GM082250, GM094625)
  • HHMI (HHMI Collaborative Innovation Award (HCIA))
Topics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
  • Physical Sciences › Materials Science › Materials Chemistry › X-ray Diffraction in Crystallography
Keywords
X-ray free-electron laser, metalloenzymes, hydrogenase, myoglobin, beta2-adrenergic receptor, RNA polymerase II, Linac Coherent Light Source, electron density mapping
MeSH terms
Chemistry, Physical, Crystallization, Electrons, Lasers, Models, Molecular, Myoglobin, Protein Conformation, Proteins, RNA Polymerase II, X-Ray Diffraction, X-Rays, Reproducibility of Results, Synchrotrons, Receptors, Adrenergic, beta-2, Crystallography, X-Ray

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