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Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses

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Advanced Technologies for Protein Complex Production and Characterization

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1453))

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Abstract

The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.

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References

  1. Yoon CH, Yurkov MV, Schneidmiller EA, Samoylova L, Buzmakov A, Jurek Z, Ziaja B (2016) A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray free-electron laser. Sci Rep. https://doi.org/10.1038/srep24791

  2. Keable SM, Kölsch A, Simon PS, Dasgupta M, Chatterjee R, Subramanian SK, Hussein R (2021) Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I. Sci Rep 11:21787. https://doi.org/10.1038/s41598-021-00236-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Cox N, Pantazis DA, Lubitz W (2020) Current understanding of the mechanism of water oxidation in photosystem II and its relation to XFEL data. Annu Rev Biochem 89:795–820. https://doi.org/10.1146/annurev-biochem-011520-104801

    Article  CAS  PubMed  Google Scholar 

  4. Wiedorn MO, Oberthür D, Bean R, Schubert R, Werner N, Abbey B, Aepfelbacher M (2018) Megahertz serial crystallography. Nat Commun 9:4025. https://doi.org/10.1038/s41467-018-06156-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Schmidt M (2013) Mix and inject: reaction initiation by diffusion for time-resolved macromolecular crystallography. Adv Condens Matter Phys

    Google Scholar 

  6. Owen RL, Rudino-Pinera E, Garman EF (2006) Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc Natl Acad Sci 103:4912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Owen RL, Axford D, Nettleship JE, Owens RJ, Robinson JI, Morgan AW, Doré AS (2012) Outrunning free radicals in room-temperature macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. https://doi.org/10.1107/S0907444912012553

  8. de la Mora E, Mora E, Coquelle N, Bury CS, Rosenthal M, Holton JM, Carmichael I (2020) Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Proc Natl Acad Sci 117:4142

    Article  PubMed  PubMed Central  Google Scholar 

  9. Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glockner C (2013) Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science. https://doi.org/10.1126/science.1234273

  10. Boutet S, Lomb L, Williams GJ, Barends TRM, Aquila A, Doak RB, Weierstall U (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science. https://doi.org/10.1126/science.1217737

  11. Liu W, Wacker D, Gati C, Han GW, James D, Wang D, Nelson G (2013) Serial femtosecond crystallography of G protein-coupled receptors. Science. https://doi.org/10.1126/science.1244142

  12. Lomb L, Barends TRM, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L (2011) Radiation damage in protein serial femtosecond crystallography using an X-ray free-electron laser. Phys Rev B Condens Matter Mater Phys 84:214111. https://doi.org/10.1103/PhysRevB.84.214111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Nass K (2019) Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr Sect Struct Biol. https://doi.org/10.1107/s2059798319000317

  14. Abbey B, Dilanian RA, Darmanin C, Ryan RA, Putkunz CT, Martin AV, Wood D (2016) X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of buckminsterfullerene. Sci Adv 2:1601186. https://doi.org/10.1126/sciadv.1601186

    Article  CAS  Google Scholar 

  15. Amin M, Badawi A, Obayya SS (2016) Radiation damage in XFEL: case study from the oxygen-evolving complex of photosystem II. Sci Rep 6:36492. https://doi.org/10.1038/srep36492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Standfuss J (2019) Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 57:63–71. https://doi.org/10.1016/j.sbi.2019.02.001

    Article  CAS  PubMed  Google Scholar 

  17. Dickerson JL, McCubbin PTN, Garman EF (2020) RADDOSE-XFEL: femtosecond time-resolved dose estimates for macromolecular X-ray free-electron laser experiments. J Appl Crystallogr. https://doi.org/10.1107/s1600576720000643

  18. Suga M, Shimada A, Akita F, Shen J-R, Tosha T, Sugimoto H (2020) Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Biochim Biophys Acta Gen Subj 1864 2:129466. https://doi.org/10.1016/j.bbagen.2019.129466

    Article  CAS  Google Scholar 

  19. Borshchevskiy V, Round E, Erofeev I, Weik M, Ishchenko A, Gushchin I, Mishin A, Willbold D, Büldt G, Gordeliy V (2014) Low-dose X-ray radiation induces structural alterations in proteins. Acta Crystallogr D Biol Crystallogr 70:2675–2685. https://doi.org/10.1107/S1399004714017295

    Article  CAS  PubMed  Google Scholar 

  20. Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, Hunter MS (2011) Femtosecond X-ray protein nanocrystallography. Nature 470:73–77. https://doi.org/10.1038/nature09750

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Redecke L, Nass K, DePonte DP, White TA, Rehders D, Barty A, Stellato F (2013) Natively inhibited trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339:227–230. https://doi.org/10.1126/science.1229663

    Article  CAS  PubMed  Google Scholar 

  22. Barends TRM, Foucar L, Sabine Botha RBD, Shoeman RL, Nass K, Koglin JE (2014) De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505:244–247. https://doi.org/10.1038/nature12773

    Article  CAS  PubMed  Google Scholar 

  23. Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J (2012) Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express 20:2706–2716. https://doi.org/10.1364/OE.20.002706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Standfuss J, Spence J (2017) Serial crystallography at synchrotrons and X-ray lasers. IUCrJ. https://doi.org/10.1107/S2052252517001877

  25. Grünbein ML, Bielecki J, Gorel A, Stricker M, Bean R, Cammarata M, Dörner K, Fröhlich L, Hartmann E, Hauf S, Hilpert M, Kim Y, Kloos M, Letrun R, Messerschmidt M, Mills G, Nass Kovacs G, Ramilli M, Roome CM, Sato T, Scholz M, Sliwa M, Sztuk-Dambietz J, Weik M, Weinhausen B, Al-Qudami N, Boukhelef D, Brockhauser S, Ehsan W, Emons M, Esenov S, Fangohr H, Kaukher A, Kluyver T, Lederer M, Maia L, Manetti M, Michelat T, Münnich A, Pallas F, Palmer G, Previtali G, Raab N, Silenzi A, Szuba J, Venkatesan S, Wrona K, Zhu J, Doak RB, Shoeman RL, Foucar L, Colletier J-P, Mancuso AP, Barends TRM, Stan CA, Schlichting I (2018) Megahertz data collection from protein microcrystals at an X-ray free-electron laser. Nat Commun 9:3487. https://doi.org/10.1038/s41467-018-05953-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Suga M, Akita F, Hirata K, Ueno G, Murakami H, Nakajima Y, Shimizu T (2015) Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. Nature 517:99–103. https://doi.org/10.1038/nature13991

    Article  CAS  PubMed  Google Scholar 

  27. Pandey S, Bean R, Sato T, Poudyal I, Bielecki J, Villarreal JC, Yefanov O (2020) Time-resolved serial femtosecond crystallography at the European XFEL. Nat Methods 17:73–78. https://doi.org/10.1038/s41592-019-0628-z

    Article  CAS  PubMed  Google Scholar 

  28. Miao J, Ishikawa T, Robinson IK, Murnane MM (2015) Beyond crystallography: diffractive imaging using coherent X-ray light sources. Science 348:530–535. https://doi.org/10.1126/science.aaa1394

    Article  CAS  PubMed  Google Scholar 

  29. Neutze R, Wouts R, Spoel D, Weckert E, Hajdu J (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406:752–757. https://doi.org/10.1038/35021099

    Article  CAS  PubMed  Google Scholar 

  30. Altarelli M (2006) XFEL: the European X-ray free-electron laser. Technical design report

    Google Scholar 

  31. Sun Z, Fan J, Li H, Jiang H (2018) Current status of single particle imaging with X-ray lasers. Appl Sci. https://doi.org/10.3390/app8010132

  32. Giewekemeyer K, Aquila A, Loh N-TD, Chushkin Y, Shanks KS, Weiss JT, Tate MW (2019) Experimental 3D coherent diffractive imaging from photon-sparse random projections. IUCrJ 6:357–365. https://doi.org/10.1107/S2052252519002781

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Poudyal I, Marius S, Peter S (2020) Single-particle imaging by x-ray free-electron lasers – how many snapshots are needed? Struct Dyn 7:024102. https://doi.org/10.1063/1.5144516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Aquila A, Barty A, Bostedt C, Boutet S, Carini G, dePonte D, Drell P (2015) The linac coherent light source single particle imaging road map. Struct Dyn 2:041701. https://doi.org/10.1063/1.4918726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Mariani V, Morgan A, Yoon CH, Lane TJ, White TA, O’Grady C, Kuhn M (2016) OnDa: online data analysis and feedback for serial X-ray imaging. J Appl Crystallogr 49:1073–1080. https://doi.org/10.1107/S1600576716007469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fortmann-Grote C, Buzmakov A, Jurek Z, Loh N-TD, Samoylova L, Santra R, Schneidmiller EA (2017) Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray free-electron laser. IUCrJ. https://doi.org/10.1107/s2052252517009496

  37. Daurer BJ, Okamoto K, Bielecki J, Maia FRNC, Kerstin Mühlig MMS, Hantke MF (2017) Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ 4:251–262. https://doi.org/10.1107/S2052252517003591

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bielecki J, Maia FRNC, Mancuso AP (2020) Perspectives on single particle imaging with X rays at the advent of high repetition rate X-ray free electron laser sources. Struct Dyn 7:040901. https://doi.org/10.1063/4.0000024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Sobolev E, Zolotarev S, Giewekemeyer K, Bielecki J, Okamoto K, Reddy HKN, Andreasson J (2020) Megahertz single-particle imaging at the European XFEL. Commun Phys 3:1–11. https://doi.org/10.1038/s42005-020-0362-y

    Article  Google Scholar 

  40. Pande K, Donatelli JJ, Malmerberg E, Foucar L, Poon BK, Sutter M, Botha S (2018) Free-electron laser data for multiple-particle fluctuation scattering analysis. Sci Data 5. https://doi.org/10.1038/sdata.2018.201

  41. Malmerberg E, Kerfeld CA, Zwart PH (2015) Operational properties of fluctuation X-ray scattering data. IUCrJ 2:309–316. https://doi.org/10.1107/S2052252515002535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Levantino M, Schirò G, Lemke HT, Cottone G, Glownia JM, Zhu D, Chollet M, Ihee H, Cupane A, Cammarata M (2015) Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser. Nat Commun 6. https://doi.org/10.1038/ncomms7772

  43. Arnlund D, Johansson LC, Wickstrand C, Barty A, Williams GJ, Malmerberg E, Davidsson J (2014) Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nat Methods. https://doi.org/10.1038/nmeth.3067

  44. Lee Y, Kim JG, Lee SJ, Muniyappan S, Kim TW, Ki H, Kim H (2021) Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering. Nat Commun 12:3677. https://doi.org/10.1038/s41467-021-23947-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Murillo GEP, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D (2023) Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS) abstract. Commun Biol 6:1057. https://doi.org/10.1038/s42003-023-05416-7

  46. Spence JCH, Weierstall U, Howells M (2004) Coherence and sampling requirements for diffractive imaging. Ultramicroscopy 101:149–152. https://doi.org/10.1016/j.ultramic.2004.05.005

    Article  CAS  PubMed  Google Scholar 

  47. Fuller FD, Gul S, Ruchira Chatterjee ESB, Young ID, Lebrette H, Srinivas V (2017) Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 14:443–449. https://doi.org/10.1038/nmeth.4195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Juncheng E, Stransky M, Jurek Z, Fortmann-Grote C, Juha L, Santra R, Ziaja B, Mancuso AP (2021) Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray free-electron laser. Sci Rep 11:1–11. https://doi.org/10.1038/s41598-021-97142-5

    Article  CAS  Google Scholar 

  49. Ekeberg T, Svenda M, Abergel C, Maia FRNC, Seltzer V, Claverie J-M, Hantke M (2015) Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser. Phys Rev Lett 114:098102. https://doi.org/10.1103/PhysRevLett.114.098102

    Article  CAS  PubMed  Google Scholar 

  50. Kurta RP, Donatelli JJ, Yoon CH, Berntsen P, Bielecki J, Daurer BJ, DeMirci H (2017) Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses. Phys Rev Lett 119:158102. https://doi.org/10.1103/PhysRevLett.119.158102

    Article  PubMed  PubMed Central  Google Scholar 

  51. Hantke MF, Hasse D, Ekeberg T, John K, Martin Svenda NDL (2014) High-throughput imaging of heterogeneous cell organelles with an X-ray laser. Nat Photonics 8. https://doi.org/10.1038/nphoton.2014.270

  52. Reddy HKN, Yoon CH, Aquila A, Awel S, Ayyer K, Barty A, Berntsen P (2017) Coherent soft X-ray diffraction imaging of coliphage PR772 at the linac coherent light source. Sci Data 4. https://doi.org/10.1038/sdata.2017.79

  53. Munke A, Andreasson J, Aquila A, Awel S, Ayyer K, Barty A, Bean RJ (2016) Coherent diffraction of single rice dwarf virus particles using hard X-rays at the linac coherent light source. Sci Data 3. https://doi.org/10.1038/sdata.2016.64

  54. Mancuso AP, Aquila A, Batchelor L, Bean RJ, Bielecki J, Borchers G, Doerner K (2019) The single particles, clusters and biomolecules and serial femtosecond crystallography instrument of the European XFEL: initial installation. J Synchrotron Radiat 26:660–676. https://doi.org/10.1107/S1600577519003308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Yamashita M, Fenn JB (1984) Electrospray ion source. Another variation on the free-jet theme. J Phys Chem. https://doi.org/10.1021/j150664a002

  56. DePonte DP, Weierstall U, Schmidt K, Warner J, Starodub D, Spence JCH, Doak RB (2008) Gas dynamic virtual nozzle for generation of microscopic droplet streams. J Phys D Appl Phys. https://doi.org/10.1088/0022-3727/41/19/195505

  57. Grünbein ML, Shoeman RL, Doak RB (2018) Velocimetry of fast microscopic liquid jets by nanosecond dual-pulse laser illumination for megahertz X-ray free-electron lasers. Opt Express 26:7190–7203. https://doi.org/10.1364/OE.26.007190

    Article  PubMed  Google Scholar 

  58. Weierstall U, James D, Wang C, White TA, Wang D, Liu W, Spence JCH (2014) Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat Commun 5:3309

    Article  PubMed  Google Scholar 

  59. Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L (2017) Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541:242–246. https://doi.org/10.1038/nature20599

    Article  CAS  PubMed  Google Scholar 

  60. Kupitz C, Olmos JL Jr, Holl M, Tremblay L, Pande K, Pandey S, Oberthür D (2017) Structural enzymology using X-ray free electron lasers. Struct Dyn 4:044003. https://doi.org/10.1063/1.4972069

    Article  CAS  PubMed  Google Scholar 

  61. Calvey GD, Katz AM, Schaffer CB, Pollack L (2016) Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers. Struct Dyn 3:054301. https://doi.org/10.1063/1.4961971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Wang D, Weierstall U, Pollack L, Spence J (2014) Double-focusing mixing jet for XFEL study of chemical kinetics. J Synchrotron Radiat 21:1364–1366. https://doi.org/10.1107/S160057751401858X

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Trebbin M, Krüger K, DePonte D, Roth SV, Chapman HN, Förster S (2014) Microfluidic liquid jet system with compatibility for atmospheric and high-vacuum conditions. Lab Chip 14:1733–1745. https://doi.org/10.1039/C3LC51363G

    Article  CAS  PubMed  Google Scholar 

  64. Nelson G, Kirian RA, Weierstall U, Zatsepin NA, Faragó T, Baumbach T, Wilde F (2016) Three-dimensional-printed gas dynamic virtual nozzles for X-ray laser sample delivery. Opt Express 24:11515–11530. https://doi.org/10.1364/OE.24.011515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Bielecki J, Hantke MF, Daurer BJ, Reddy HKN, Hasse D, Larsson DSD, Gunn LH (2019) Electrospray sample injection for single-particle imaging with X-ray lasers. Sci Adv 5:8801. https://doi.org/10.1126/sciadv.aav8801

    Article  CAS  Google Scholar 

  66. Hantke MF, Bielecki J, Kulyk O, Westphal D, Larsson DSD, Svenda M, Reddy HKN (2018) Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams. IUCrJ 5:673–680. https://doi.org/10.1107/S2052252518010837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Roth N, Awel S, Horke DA, Küpper J (2018) Optimizing aerodynamic lenses for single-particle imaging. J Aerosol Sci. https://doi.org/10.1016/j.jaerosci.2018.06.010

  68. Andreasson J, Martin AV, Liang M, Timneanu N, Aquila A, Wang F, Iwan B (2014) Automated identification and classification of single particle serial femtosecond X-ray diffraction data. Opt Express 22:2497–2510. https://doi.org/10.1364/OE.22.002497

    Article  PubMed  Google Scholar 

  69. Soares AS, Engel MA, Stearns R, Datwani S, Olechno J, Ellson R, Skinner JM, Allaire M, Orville AM (2011) Acoustically mounted microcrystals yield high-resolution X-ray structures. Biochemistry 50:4399–4401. https://doi.org/10.1021/bi200549x

    Article  CAS  PubMed  Google Scholar 

  70. Roessler CG, Agarwal R, Allaire M, Alonso-Mori R, Andi B, Bachega JFR, Bommer M (2016) Acoustic injectors for drop-on-demand serial femtosecond crystallography. Structure 24:631–640. https://doi.org/10.1016/j.str.2016.02.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Graceffa R, Burghammer M, Davies RJ, Riekel C (2012) Probing ballistic microdrop coalescence by stroboscopic small-angle X-ray scattering. Appl Phys Lett. https://doi.org/10.1063/1.4772631

  72. Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J (2017) High-speed fixed-target serial virus crystallography. Nat Methods 14:805–810. https://doi.org/10.1038/nmeth.4335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Tolstikova A, Levantino M, Yefanov O, Hennicke V, Fischer P, Meyer J, Mozzanica A (2019) 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector. IUCrJ. https://doi.org/10.1107/S205225251900914X

  74. Rupp B (2009) Biomolecular crystallography. Garland Science

    Google Scholar 

  75. Yefanov O, Oberthür D, Bean R, Wiedorn MO, Knoska J, Pena G, Awel S (2019) Evaluation of serial crystallographic structure determination within megahertz pulse trains. Struct Dyn. https://doi.org/10.1063/1.5124387

  76. Patel J, Round A, Bielecki J, Doerner K, Kirkwood H, Letrun R, Schulz J, Sikorski M, Vakili M, De Wijn R, Peele A, Mancuso AP, Abbey B (2022) Towards real-time analysis of liquid jet alignment in serial femtosecond crystallography. J Appl Crystallogr 55:944–952. https://doi.org/10.1107/S1600576722005891

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Henrich B, Becker J, Dinapoli R, Goettlicher P, Graafsma H, Hirsemann H, Klanner R, Krueger H, Mazzocco R, Mozzanica A, Perrey H, Potdevin G, Schmitt B, Shi X, Srivastava AK, Trunk U, Youngman C (2011) The adaptive gain integrating pixel detector AGIPD a detector for the European XFEL. Nucl Instrum Methods Phys Res Sect Accel Spectrometers Detect Assoc Equip 633:S11–S14. https://doi.org/10.1016/j.nima.2010.06.107

    Article  CAS  Google Scholar 

  78. Kuster M, Boukhelef D, Donato M, Dambietz J-S, Hauf S, Maia L, Raab N (2014) Detectors and calibration concept for the European XFEL. Synchrotron Radiat News. https://doi.org/10.1080/08940886.2014.930809

  79. Barty A, Kirian RA, Maia FRNC, Hantke M, Yoon CH, White TA, Chapman H (2014) Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J Appl Crystallogr 47:1118–1131. https://doi.org/10.1107/S1600576714007626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Hadian-Jazi M, Sadri A, Barty A, Yefanov O, Galchenkova M, Oberthuer D, Komadina D (2021) Data reduction for serial crystallography using a robust peak finder. J Appl Crystallogr 54:1360–1378. https://doi.org/10.1107/S1600576721007317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. McRee DE (1999) Practical Protein Crystallography. 2nd edition. Elsevier. https://doi.org/10.1016/B978-0-12-486052-0.X5000-3

  82. Kabsch W (2012) XDS. In: International Tables for Crystallography Vol. F, ch. 11.6, pp. 304–310. https://doi.org/10.1107/97809553602060000835

  83. Leslie AGW, Powell HR (2007) Processing diffraction data with Mosflm. Evol Methods Macromol Crystallogr. https://doi.org/10.1007/978-1-4020-6316-9_4

  84. White TA, Kirian RA, Martin AV, Aquila A, Nass K, Barty A, Chapman HN (2012) CrystFEL: a software suite for snapshot serial crystallography. J Appl Crystallogr. https://doi.org/10.1107/S0021889812002312

  85. Brehm W, Diederichs K (2014) Breaking the indexing ambiguity in serial crystallography. Acta Crystallogr D Biol Crystallogr. https://doi.org/10.1107/s1399004713025431

  86. Liu H, Spence JCH (2014) The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm. IUCrJ. https://doi.org/10.1107/s2052252514020314

  87. Li C, Li X, Kirian R, Spence JCH, Liu H, Zatsepin NA (2019) SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCrJ 6:72–84. https://doi.org/10.1107/S2052252518014951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JCH, Hunter M, Fromme P, White T, Chapman HN, Holton J (2010) Femtosecond protein nanocrystallography—data analysis methods. Opt Express 18:5713–5723. https://doi.org/10.1364/OE.18.005713

    Article  PubMed  Google Scholar 

  89. Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62:72–82. https://doi.org/10.1107/S0907444905036693

    Article  CAS  PubMed  Google Scholar 

  90. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221. https://doi.org/10.1107/S0907444909052925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Loh N-TD, Elser V (2009) Reconstruction algorithm for single-particle diffraction imaging experiments. Phys Rev. https://doi.org/10.1103/PhysRevE.80.026705

  92. Yoon CH, Schwander P, Abergel C, Andersson I, Andreasson J, Aquila A, Bajt S (2011) Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. Opt Express 19:16542–16549. https://doi.org/10.1364/OE.19.016542

    Article  PubMed  Google Scholar 

  93. Bobkov SA, Teslyuk AB, Kurta RP, Gorobtsov OY, Yefanov OM, Ilyin VA, Senin RA, Vartanyants IA (2015) Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers. J Synchrotron Radiat 22:1345–1352. https://doi.org/10.1107/S1600577515017348

    Article  CAS  PubMed  Google Scholar 

  94. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc. https://doi.org/10.1111/j.2517-6161.1977.tb01600.x

  95. Fienup JR (1978) Reconstruction of an object from the modulus of its fourier transform. Opt Lett. https://doi.org/10.1364/ol.3.000027

  96. Fienup JR (1982) Phase retrieval algorithms: a comparison. Appl Opt. https://doi.org/10.1364/ao.21.002758

  97. Chen C-C, Jianwei Miao CWW, Lee TK (2007) Application of optimization technique to noncrystalline X-ray diffraction microscopy: guided hybrid input-output method. Phys Rev B. https://doi.org/10.1103/physrevb.76.064113

  98. Marchesini S, He H, Chapman HN, Hau-Riege SP, Noy A, Howells MR, Weierstall U, Spence JCH (2003) X-ray image reconstruction from a diffraction pattern alone. Phys Rev B. https://doi.org/10.1103/physrevb.68.140101

  99. Thibault P, Dierolf M, Bunk O, Menzel A, Pfeiffer F (2009) Probe retrieval in ptychographic coherent diffractive imaging. Ultramicroscopy 109:338–343. https://doi.org/10.1016/j.ultramic.2008.12.011

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. European XFEL, Schenefeld, Germany

    Adam Round, E. Jungcheng, Carsten Fortmann-Grote, Klaus Giewekemeyer, Rita Graceffa, Chan Kim, Henry Kirkwood, Grant Mills, Ekaterina Round, Tokushi Sato, Sakura Pascarelli & Adrian Mancuso

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Correspondence to Adam Round .

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  1. Centro de Investigaciones Biologicas Margarita Salas (CIB-CSIC), Madrid, Spain

    M. Cristina Vega

  2. Abvance Biotech SL, Madrid, Spain

    Francisco J. Fernández

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Round, A. et al. (2024). Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses. In: Vega, M.C., Fernández, F.J. (eds) Advanced Technologies for Protein Complex Production and Characterization. Advances in Experimental Medicine and Biology, vol 1453. Springer, Cham. https://doi.org/10.1007/978-3-031-52193-5_10

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