Diffraction before destruction

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 369, Issue 1647, 2014, Pages

  Chapman, Henry N ^a,b   Caleman, Carl ^a,c   Timneanu, Nicusor ^c  

^a DESY   (Germany)

^b UNIVERSITY OF HAMBURG   (Germany)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

Protein crystallography; Radiation damage; X ray lasers

Indexed keywords

CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DIFFRACTION; PROTEIN;

PROTEIN;

DEVICES; ELECTRON; LASER; PROCEDURES; PROTEIN CONFORMATION; ULTRASTRUCTURE; X RAY DIFFRACTION;

ELECTRONS; LASERS; PROTEIN CONFORMATION; PROTEINS; X-RAY DIFFRACTION;

EID: 84902670105     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2013.0313     Document Type: Article

References (64)

1. Henderson R. 1995 The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q. Rev. Biophys. 28, 171-193. (doi: 10. 1017/S003358350000305X).
2. Owen RL, Rudino-Pinera E, Garman EF. 2006 Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc. Natl Acad. Sci. USA 103, 4912-4917. (doi: 10. 1073/pnas. 0600973103).
3. Howells MR et al. 2009 An assessment of the resolution limitation due to radiation-damage in X-ray diffraction microscopy. J. Electr. Spectrosc. Relat. Phenom. 170, 4-12. (doi: 10. 1016/j. elspec. 2008. 10. 008).
4. Holton JM. 2009 A beginner's guide to radiation damage. J. Synchronton Radiat. 16, 133-142. (doi: 10. 1107/S0909049509004361).
5. Chapman HN et al. 2011 Femtosecond X-ray protein nanocrystallography. Nature 470, 73-77. (doi: 10. 1038/nature09750).
6. Boutet S et al. 2012 High-resolution protein structure determination by serial femtosecond crystallography. Science 337, 362-364. (doi: 10. 1126/science. 1217737).
7. Neutze R, Wouts R, van der Spoel D, Weckert E, Hajdu J. 2000 Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406, 753-757. (doi: 10. 1038/35021099).
8. Solem JC, Baldwin GC. 1982 Microholography of living organisms. Science 218, 229-235. (doi: 10. 1126/science. 218. 4569. 229).
9. Emma P et al. 2010 First lasing and operation of an Ångstrom-wavelength free-electron laser. Nat. Photon. 4, 641-647. (doi: 10. 1038/nphoton. 2010. 176).
10. Philipp HT, Hromalik M, Tate M, Koerner L, Gruner SM. 2011 Pixel array detector for X-ray free electron laser experiments. Nucl. Instrum. Methods A 649, 67-69. (doi: 10. 1016/j. nima. 2010. 11. 189).
11. Lomb L et al. 2011 Radiation damage in protein serial femtosecond crystallography using an X-ray free-electron laser. Phys. Rev. B 84, 214111. (doi: 10. 1103/PhysRevB. 84. 214111).
12. Barty A et al. 2012 Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat. Photon. 6, 35-40. (doi: 10. 1038/nphoton. 2011. 297).
13. Boutet S, Williams GJ. 2010 The coherent X-ray Imaging (CXI) instrument at the Linac coherent light source (LCLS). New J. Phys. 12, 035024. (doi: 10. 1088/1367-2630/12/3/035024).
14. Kirian RA et al. 2010 Femtosecond protein nanocrystallography: data analysis methods. Opt. Express. 18, 5713-5723. (doi: 10. 1364/OE. 18. 005713).
15. Frank J. 1996 Three-dimensional electron microscopy of macromolecular assemblies. San Diegeo, CA: Academic Press.
16. Huldt G, Szoke A, Hajdu J. 2003 Diffraction imaging of single particles and biomolecules. J. Struct. Biol. 144, 219-227. (doi: 10. 1016/j. jsb. 2003. 09. 025).
17. Barty A, Kirian RA, Maia F, Hantke M, Yoon C, White TA, Chapman H. 2014 CHEETAH: software for high throughput reduction and analysis of serial femtosecond X-ray diffraction data. J. Appl. Cryst. 47. (doi: 10. 1107/S1600576714007626).
18. 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. 45, 335-341. (doi: 10. 1107/S0021889812002312).
19. White TA, Barty A, Stellato F, Holton JM, Kirian RA, Zatsepin NA, Chapman HN. 2013 Crystallographic data processing for free-electron laser sources. Acta Crystallogr. D 69, 1231-1240. (doi: 10. 1107/S0907444913013620).
20. Redecke L et al. 2013 Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339, 227-230. (doi: 10. 1126/science. 1229663).
21. Johansson LC et al. 2012 Lipidic phase membrane protein serial femtosecond crystallography. Nat. Methods 9, 263-265. (doi: 10. 1038/nmeth. 1867).
22. Johansson LC et al. 2013 Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat. Commun. 4, 2911. (doi: 10. 1038/ncomms3911).
23. Liu W et al. 2013 Serial femtosecond crystallography of G protein-coupled receptors. Science 342, 1521-1524. (doi: 10. 1126/science. 1244142).
24. Jurek Z, Faigel G. 2009 The effect of inhomogenities on single-molecule imaging by hard XFEL pulses. Europhys. Lett. 86, 68003. (doi: 10. 1209/0295-5075/86/68003).
25. Nass K. 2013 Investigation of protein structure determination using X-ray free-electron lasers, PhD thesis, University of Hamburg, Germany.
26. Son S-K, Young L, Santra R. 2011 Impact of hollowatom formation on coherent X-ray scattering at high intensity. Phys. Rev. A 83, 033402. (doi: 10. 1103/PhysRevA. 83. 033402).
27. Son S-K, Chapman HN, Santra R. 2013 Determination of multiwavelength anomalous diffraction coefficients at high X-ray intensity. J. Phys. B 46, 164015. (doi: 10. 1088/0953-4075/46/16/164015).
28. Young L et al. 2010 Femtosecond electronic response of atoms to ultra-intense X-rays. Nature 466, 56-61. (doi: 10. 1038/nature09177).
29. Hoener M et al. 2010 Ultraintense X-ray induced ionization, dissociation, and frustrated absorption in molecular nitrogen. Phys. Rev. Lett. 104, 253002. (doi: 10. 1103/PhysRevLett. 104. 253002).
30. Henke B, Gullikson E, Davis J. 1993 X-ray interactions: photoabsorption, scattering, transmission, and reflection at E = 50-30, 000 eV, Z = 1-92. Atom. Nucl. Data Tables 54, 181-342. (doi: 10. 1006/adnd. 1993. 1013).
31. Creagh DC, Hubbell JH. 2006 X-ray absorption (or attenuation) coefficients. Int. Tables Crystallogr, vol. C, chap. 4. 2, 220-229.
32. Son S-K, Chapman HN, Santra R. 2011b Multiwavelength anomalous diffraction at high Xray intensity. Phys. Rev. Lett. 107, 218102. (doi: 10. 1103/PhysRevLett. 107. 218102).
33. Paithankar KS, Owen RL, Garman EF. 2009 Absorbed dose calculations for macromolecular crystals: improvements to RADDOSEJ. Synchronton Radiat. 16, 152-162. (doi: 10. 1107/S0909049508040430).
34. Campbell JL, Papp T. 2001 Widths of the atomic K-N7 levels. Atom. Nucl. Data Tables 77, 1-56. (doi: 10. 1006/adnd. 2000. 0848).
35. Bruch R, Chung KT, Luken WL, Culberson JC. 1985 Recalibration of the KLL Auger spectrum of carbon. Phys. Rev. A 31, 310-315. (doi: 10. 1103/PhysRevA. 31. 310).
36. Ziaja B, van der Spoel D, Szo{double acute}ke A, Hajdu J. 2001 Radiation induced electron cascade in diamond and amorphous carbon. Phys. Rev. B 64, 214104. (doi: 10. 1103/PhysRevB. 64. 214104).
37. Ziaja B, London RA, Hajdu J. 2005 Unified model of secondary electron cascades in diamond. J. Appl. Phys. 97, 064905. (doi: 10. 1063/1. 1853494).
38. Timneanu N, Caleman C, Hajdu J, van der Spoel D. 2004 Auger electron cascades in water and ice. Chem. Phys. 299, 277-283. (doi: 10. 1016/j. chemphys. 2003. 10. 011).
39. Ziaja B, de Castro A, Weckert E, Möller T. 2006 Modelling dynamics of samples exposed to freeelectron-laser radiation with Boltzmann equations. Eur. Phys. J. D 40, 465-480. (doi: 10. 1140/epjd/e2006-00240-x).
40. Caleman C, Ortiz C, Marklund E, Bultmark F, Gabrysch M, Parak FG, Hajdu J, Klintenberg M, Tîmneanu N. 2009 Radiation damage in biological material: electronic properties and electron impact ionization in urea. Europhys. Lett. 85, 18005, and erratum 88, 29901. (doi: 10. 1209/0295-5075/88/29901).
41. Caleman C, Huldt G, Maia FRNC, Ortiz C, Parak FG, Hajdu J, van der Spoel D, Chapman HN, Timneanu N. 2011 On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. ACS Nano 5, 139-146. (doi: 10. 1021/nn1020693).
42. Vinko SM et al. 2012 Creation and diagnosis of a solid-density plasma with an X-ray free-electron laser. Nature 482, 59-62. (doi: 10. 1038/nature10746).
43. Barends TRM et al. 2014 De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505, 244-247. (doi: 10. 1038/nature12773).
44. Kern J et al. 2013 Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science 340, 491-495. (doi: 10. 1126/science. 1234273).
45. Caleman C, Timneanu N, Martin AV, Aquila A, Barty A, Scott HA, White TA, Chapman HN. Self-gating Bragg diffraction of exploding nanocrystals. In preparation.
46. Caleman C, Bergh M, Scott HA, Spence JC, Chapman HN, Tîmneanu N. 2011 Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses. J. Mod. Opt. 58, 1486-1497. (doi: 10. 1080/09500340. 2011. 597519).
47. Hau-Riege SP et al. 2004 Speden: reconstructing single particles from their diffraction patterns. Acta Crystallogr. A 60, 294-305. (doi: 10. 1107/S0108767304010293).
48. Beye M, Schreck S, Sorgenfrei F, Trabant C, Pontius N, Schuszler-Langeheine C, Wurth W, Fohlisch A. 2013 Stimulated X-ray emission for materials science. Nature 501, 191-194. (doi: 10. 1038/nature12449).
49. Hau-Riege SP, London RA, Szoke A. 2002 Dynamics of biological molecules irradiated by short X-ray pulses. Phys. Rev. E 69, 051906. (doi: 10. 1103/PhysRevE. 69. 051906).
50. Erk B et al. 2013 Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. Phys. Rev. Lett. 110, 053003. (doi: 10. 1103/PhysRevLett. 110. 053003).
51. Cercek B, Cercek L. 1973 Pulse-radiolysis study of a biological matrix. Int. J. Radiat. Biol. 24, 137-142. (doi: 10. 1080/09553007314550931).
52. Allan EG, Kander MC, Carmichael I, Garman EF. 2013 To scavenge or not to scavenge, that is still the question. J. Synchronton Radiat. 20, 23-36. (doi: 10. 1107/S0909049512046237).
53. Davis KM, Kosheleva I, Henning RW, Seidler GT, Pushkar Y. 2013 Kinetic modeling of the X-rayinduced damage to a metalloprotein. J. Phys. Chem. B 117, 9161-9169. (doi: 10. 1021/jp403654n).
54. Garman E, Weik M. 2013 Radiation damage to biological macromolecules: some answers and more questions. J. Synchronton Radiat. 20, 1-6. (doi: 10. 1107/S0909049512050418).
55. Taylor G. 2003 The phase problem. Acta Crystallogr. D59, 1881-1890. (doi: 10. 1107/S0907444903017815).
56. Ravelli RB, Leiros H-KS, Pan B, Caffrey M, McSweeney S. 2003 Specific radiation damage can be used to solve macromolecular crystal structures. Structure 11, 217-224. (doi: 10. 1016/S0969-2126 (03)00006-6).
57. Cowley JM. 1981 Diffraction physics. Amsterdam, The Netherlands: North-Holland.
58. Geloni G, Kocharyan V, Saldin E. 2011 A novel selfseeding scheme for hard X-ray FELs. J. Mod. Opt. 58, 1391-1403. (doi: 10. 1080/09500340. 2011. 586473).
59. Hau-Riege SP, London RA, Chapman HN, Szoke A, Timneanu N. 2007 Encapsulation and diffractionpattern-correction methods to reduce the effect of damage in X-ray diffraction imaging of single biological molecules. Phys. Rev. Lett. 98, 198302. (doi: 10. 1103/PhysRevLett. 98. 198302).
60. Fourme R, Honkimäki V, Girard E, Medjoubi K, Dhaussy A-C, Kahn R. 2012 Reduction of radiation damage and other benefits of short wavelengths for macromolecular crystallography data collection. J. Appl. Crystallogr. 45, 652-661. (doi: 10. 1107/S0021889812019164).
61. Holton JM, Frankel KA. 2010 The minimum crystal size needed for a complete diffraction data set. Acta Crystallogr. D 66, 393-408. (doi: 10. 1107/S0907444910007262).
62. 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. 41, 195505. (doi: 10. 1088/0022-3727/41/19/195505).
63. Gati C et al. 2014 Serial crystallography on in vivo grown microcrystals using synchrotron radiation. IUCr J. 1, 87-94. (doi: 10. 1107/S205225251303 3939).
64. Stellato F et al. In press. Room temperature macromolecular serial crystallography using synchrotron radiation. IUCrJ.