An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Yamashita, Keitaro ^a   Pan, Dongqing ^b   Okuda, Tomohiko ^b   Sugahara, Michihiro ^a   Kodan, Atsushi ^c   Yamaguchi, Tomohiro ^b   Murai, Tomohiro ^b   Gomi, Keiko ^d   Kajiyama, Naoki ^d   Mizohata, Eiichi ^e   Suzuki, Mamoru ^a,e   Nango, Eriko ^a   Tono, Kensuke ^f   Joti, Yasumasa ^f   Kameshima, Takashi ^f   Park, Jaehyun ^a   Song, Changyong ^a   Hatsui, Takaki ^a   Yabashi, Makina ^a   Iwata, So ^a,b   Kato, Hiroaki ^a,b   Ago, Hideo ^a   Yamamoto, Masaki ^a   Nakatsu, Toru ^a,b   more..

^a RIKEN SPring 8 Center   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d KIKKOMAN CORPORATION   (Japan)

^e OSAKA UNIVERSITY   (Japan)

^f JAPAN SYNCHROTRON RADIATION RESEARCH INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

CHEMISTRY; MOLECULAR MODEL; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEINS;

EID: 84941333790     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14017     Document Type: Article

References (41)

1. Chapman, H. N. et al. Femtosecond X-ray protein nanocrystallography. Nature 470, 73-77 (2011).
2. Redecke, L. et al. Natively inhibited Trypanosoma brucei Cathepsin B structure determined by using an X-ray laser. Science 339, 227-230 (2013).
3. Kupitz, C. et al. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature 513, 261-265 (2014).
4. Tenboer, J. et al. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 346, 1242-1246 (2014).
5. Spence, J. C. H. et al. Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals. Opt. Exp. 19, 2866-2873 (2011).
6. Son, S.-K., Chapman, H. N. & Santra, R. Multiwavelength anomalous diffraction at high X-ray intensity. Phys. Rev. Lett. 107, 218102 (2011).
7. Barends, T. R. M. et al. De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505, 244-247 (2014).
8. Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
9. Ishikawa, T. et al. A compact X-ray free-electron laser emitting in the sub-angstrom region. Nat. Photo. 6, 540-544 (2012).
10. Sugahara, M. et al. Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions. Acta Crystallogr. D 61, 1302-1305 (2005).
11. Gomi, K. & Kajiyama, N. Oxyluciferin, a luminescence product of firefly luciferase, is enzymatically regenerated into luciferin. J. Biol. Chem. 276, 36508-36513 (2001).
12. White, T. A. et al. CrystFEL: a software suite for snapshot serial crystallography. J. Appl. Cryst. 45, 335-341 (2012).
13. Howell, P. L. & Smith, G. D. Identification of heavy-atom derivatives by normal probability methods. J. Appl. Cryst. 25, 81-86 (1992).
14. Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D 66, 479-485 (2010).
15. Langer, G. G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171-1179 (2008).
16. Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355-367 (2011).
17. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486-501 (2010).
18. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352-367 (2012).
19. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12-21 (2010).
20. Kirian, R. A. et al. Femtosecond protein nanocrystallography-data analysis methods. Opt. Exp. 18, 5713-5723 (2010).
21. Kirian, R. A. et al. Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallogr. A 67, 131-140 (2011).
22. Kabsch, W. Processing of X-ray snapshots from crystals in random orientations. Acta Crystallogr. D 70, 2204-2216 (2014).
23. Sauter, N. K. XFEL diffraction: developing processing methods to optimize data quality. J. Synchrotron Rad. 22, 239-248 (2015).
24. Uervirojnangkoorn, M. et al. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. eLife 4 (2015), doi: 10.7554/eLife.05421.
25. Sugahara, M. et al. Grease matrix as a versatile carrier of proteins for serial crystallography. Nat. Meth. 12, 61-63 (2015).
26. Kameshima, T. et al. Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments. Rev. Sci. Instrum. 85 (2014).
27. Duisenberg, A. J. M. Indexing in single-crystal diffractometry with an obstinate list of reflections. J. Appl. Cryst. 25, 92-96 (1992).
28. Leslie, A. G. W. & Powell, H. R. Processing diffraction data with mosflm vol. 245, 41-51 (Springer Netherlands, 2007).
29. Kabsch, W. XDS. Acta Crystallogr. D 66, 125-132 (2010).
30. Hattne, J. et al. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat. Meth. 11, 545-548 (2014).
31. Sasaki, S. Numerical Tables of Anomalous Scattering Factors Calculated by the Cromer and Liberman Method. KEK Report 88-14, 1-136 (1989).
32. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
33. Paithankar, K. S., Owen, R. L. & Garman, E. F. Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE. J. Synchrotron Rad. 16, 152-162 (2009).
34. Murray, J. W., Garman, E. F. & Ravelli, R. B. G. X-ray absorption by macromolecular crystals: the effects of wavelength and crystal composition on absorbed dose. J. Appl. Cryst. 37, 513-522 (2004).
35. Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 32, 922-923 (1976).
36. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria (2008).
37. Wickham, H. ggplot2: elegant graphics for data analysis (Springer New York, 2009).
38. Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. J. Appl. Cryst. 35, 126-136 (2002).
39. Schrödinger, L. L. C. The PyMOL Molecular Graphics System, Version 1.3r1 (2010).
40. Diederichs, K. & Karplus, P. A. Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat. Struct. Biol. 4, 269-275 (1997).
41. Karplus, P. A. & Diederichs, K. Linking Crystallographic Model and Data Quality. Science 336, 1030-1033 (2012).