Serial femtosecond crystallography

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Serial femtosecond crystallography (SFX) is a form of X-ray crystallography developed for use at X-ray free-electron lasers (XFELs). [1] [2] [3] Single pulses at free-electron lasers are bright enough to generate resolvable Bragg diffraction from sub-micron crystals. However, these pulses also destroy the crystals, meaning that a full data set involves collecting diffraction from many crystals. This method of data collection is referred to as serial, referencing a row of crystals streaming across the X-ray beam, one at a time. It can be performed at room temperature, allowing for the study of biochemical dynamics. [4] It can be used to visualize samples prone to radiation damage, such as metalloproteins, and to observe transient structures, such as reaction intermediates, which would not be captured using conventional X-ray crystallography. [5]

Contents

Serial Femtosecond Crystallography (SFX) schematic Sfx schematic dffn.jpg
Serial Femtosecond Crystallography (SFX) schematic

History

While the idea of serial crystallography had been proposed earlier, [6] it was first demonstrated with XFELs by Chapman et al. [7] at the Linac Coherent Light Source (LCLS) in 2011. This method has since been extended to solve unknown structures, perform time-resolved experiments, and later even brought back to synchrotron X-ray sources.

Methods

In comparison to conventional crystallography, where a single (relatively large) crystal is rotated in order to collect a 3D data set, some additional methods have to be developed to measure in the serial mode. First, a method is required to efficiently stream crystals across the beam focus. The other major difference is in the data analysis pipeline. Here, each crystal is in a random, unknown orientation which must be computationally determined before the diffraction patterns from all the crystals can be merged into a set of 3D hkℓ intensities.

Sample Delivery

The first sample delivery system used for this technique was the Gas Dynamic Virtual Nozzle (GDVN) which generates a liquid jet in vacuum (accelerated by a concentric helium gas stream) containing crystals. Since then, many other methods have been successfully demonstrated at both XFELs and synchrotron sources. A summary of these methods along with their key relative features is given below:

Data Analysis

In order to recover a 3D structure from the individual diffraction patterns, they must be oriented, scaled and merged to generate a list of hkℓ intensities. These intensities can then be passed to standard crystallographic phasing and refinement programs. The first experiments only oriented the patterns [15] and obtained accurate intensity values by averaging over a large number of crystals (> 100,000). Later versions correct for variations in individual pattern properties such as overall intensity variations and B-factor variations as well as refining the orientations to fix the "partialities" of the individual Bragg reflections. [16]

References

  1. Liu, W.; et al. (2013). "Serial Femtosecond Crystallography of G Protein–Coupled Receptors - PubAg". Science. 342 (6165). US: United States National Agricultural Library: 1521–1524. doi:10.1126/science.1244142. PMC   3902108 . PMID   24357322 . Retrieved 2019-02-26.
  2. Mizohata E, Nakane T, Fukuda Y, Nango E, Iwata S (April 2018). "Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology". Biophysical Reviews. 10 (2): 209–218. doi:10.1007/s12551-017-0344-9. PMC   5899704 . PMID   29196935.
  3. Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P (July 2016). "Serial femtosecond crystallography: A revolution in structural biology". Archives of Biochemistry and Biophysics. 602: 32–47. doi:10.1016/j.abb.2016.03.036. PMC   4909539 . PMID   27143509.
  4. "Serial Femtosecond Crystallography | Biology Linac Coherent Light Source". biology-lcls.slac.stanford.edu. Retrieved 2025-05-29.
  5. Barends, Thomas R. M.; Stauch, Benjamin; Cherezov, Vadim; Schlichting, Ilme (2022-08-04). "Serial femtosecond crystallography". Nature Reviews Methods Primers. 2 (1): 1–24. doi:10.1038/s43586-022-00141-7. ISSN   2662-8449. PMC   9833121 .
  6. Neutze R, et al. (August 2000). "Potential for biomolecular imaging with femtosecond X-ray pulses". Nature. 406 (6797): 752–757. doi:10.1038/35021099. PMID   10963603. S2CID   4300920.
  7. Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, et al. (February 2011). "Femtosecond X-ray protein nanocrystallography". Nature. 470 (7332): 73–7. Bibcode:2011Natur.470...73C. doi:10.1038/nature09750. PMC   3429598 . PMID   21293373.
  8. DePonte DP, Weierstall U, Schmidt K, Warner J, Starodub D, Spence JC, Doak RB (September 2008). "Gas dynamic virtual nozzle for generation of microscopic droplet streams". Journal of Physics D: Applied Physics. 41 (19): 195505. arXiv: 0803.4181 . Bibcode:2008JPhD...41s5505D. doi:10.1088/0022-3727/41/19/195505. S2CID   119259244.
  9. Wiedorn MO, Awel S, Morgan AJ, Ayyer K, Gevorkov Y, Fleckenstein H, et al. (September 2018). "Rapid sample delivery for megahertz serial crystallography at X-ray FELs". IUCrJ. 5 (Pt 5): 574–584. doi:10.1107/S2052252518008369. PMC   6126653 . PMID   30224961.
  10. Weierstall U, James D, Wang C, White TA, Wang D, Liu W, et al. (2014). "Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography". Nature Communications. 5: 3309. Bibcode:2014NatCo...5.3309W. doi:10.1038/ncomms4309. PMC   4061911 . PMID   24525480.
  11. Sugahara M, Mizohata E, Nango E, Suzuki M, Tanaka T, Masuda T, et al. (January 2015). "Grease matrix as a versatile carrier of proteins for serial crystallography". Nature Methods. 12 (1): 61–3. doi:10.1038/nmeth.3172. hdl: 2433/203008 . PMID   25384243. S2CID   25950836.
  12. Conrad CE, Basu S, James D, Wang D, Schaffer A, Roy-Chowdhury S, et al. (July 2015). "A novel inert crystal delivery medium for serial femtosecond crystallography". IUCrJ. 2 (Pt 4): 421–30. doi:10.1107/S2052252515009811. PMC   4491314 . PMID   26177184.
  13. Gati C, Bourenkov G, Klinge M, Rehders D, Stellato F, Oberthür D, et al. (March 2014). "Serial crystallography on in vivo grown microcrystals using synchrotron radiation". IUCrJ. 1 (Pt 2): 87–94. doi:10.1107/S2052252513033939. PMC   4062088 . PMID   25075324.
  14. Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, et al. (August 2017). "High-speed fixed-target serial virus crystallography". Nature Methods. 14 (8): 805–810. doi:10.1038/nmeth.4335. PMC   5588887 . PMID   28628129.
  15. White TA, Kirian RA, Martin AV, Aquila A, Nass K, Barty A, Chapman HN (April 2012). "CrystFEL: a software suite for snapshot serial crystallography" (PDF). Journal of Applied Crystallography. 45 (2): 335–41. doi:10.1107/S0021889812002312.
  16. White TA, Mariani V, Brehm W, Yefanov O, Barty A, Beyerlein KR, Chervinskii F, Galli L, Gati C, Nakane T, Tolstikova A, Yamashita K, Yoon CH, Diederichs K, Chapman HN (April 2016). "Recent developments in CrystFEL". Journal of Applied Crystallography. 49 (Pt 2): 680–689. doi:10.1107/S1600576716004751. PMC   4815879 . PMID   27047311.