Accurate determination of segmented X-ray detector geometry

Optics Express

Volumn 23, Issue 22, 2015, Pages 28459-28470

  Yefanov, Oleksandr ^a   Mariani, Valerio ^a   Gati, Cornelius ^a   White, Thomas A ^a   Chapman, Henry N ^a,b   Barty, Anton ^a  

^a DESY   (Germany)

^b UNIVERSITY OF HAMBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COHERENT SCATTERING; CRYSTALLOGRAPHY; FITS AND TOLERANCES; GEOMETRY; LOCATION; PIXELS; X RAY APPARATUS; X RAY SCATTERING;

COHERENT DIFFRACTIVE IMAGING; DETECTOR ELEMENTS; INTERACTION POINTS; INTERACTION REGION; MECHANICAL TOLERANCES; RELATIVE POSITIONS; SERIAL CRYSTALLOGRAPHY; X-RAY DETECTOR TECHNOLOGY;

X RAY CRYSTALLOGRAPHY;

ALGORITHM; CALIBRATION; COMPUTER ASSISTED DIAGNOSIS; DEVICE FAILURE ANALYSIS; DEVICES; EQUIPMENT DESIGN; EVALUATION STUDY; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CALIBRATION; CRYSTALLOGRAPHY, X-RAY; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; RADIOGRAPHIC IMAGE INTERPRETATION, COMPUTER-ASSISTED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84955711231     PISSN: None     EISSN: 10944087     Source Type: Journal    
DOI: 10.1364/OE.23.028459     Document Type: Article

References (30)

1. H. N. Chapman, P. Fromme, A. Barty, T. A. White, R. A. Kirian, A. Aquila, M. S. Hunter, J. Schulz, D. P. DePonte, U. Weierstall, R. B. Doak, F. R. N. C. Maia, A. V. Martin, I. Schlichting, L. Lomb, N. Coppola, R. L. Shoeman, S. W. Epp, R. Hartmann, D. Rolles, A. Rudenko, L. Foucar, N. Kimmel, G. Weidenspointner, P. Holl, M. Liang, M. Barthelmess, C. Caleman, S. Boutet, M. J. Bogan, J. Krzywinski, C. Bostedt, S. Bajt, L. Gumprecht, B. Rudek, B. Erk, C. Schmidt, A. Hömke, C. Reich, D. Pietschner, L. Strüder, G. Hauser, H. Gorke, J. Ullrich, S. Herrmann, G. Schaller, F. Schopper, H. Soltau, K.-U. Kühnel, M. Messerschmidt, J. D. Bozek, S. P. Hau-Riege, M. Frank, C. Y. Hampton, R. G. Sierra, D. Starodub, G. J. Williams, J. Hajdu, N. Timneanu, M. M. Seibert, J. Andreasson, A. Rocker, O. Jönsson, M. Svenda, S. Stern, K. Nass, R. Andritschke, C.-D. Schröter, F. Krasniqi, M. Bott, K. E. Schmidt, X. Wang, I. Grotjohann, J. M. Holton, T. R. M. Barends, R. Neutze, S. Marchesini, R. Fromme, S. Schorb, D. Rupp, M. Adolph, T. Gorkhover, I. Andersson, H. Hirsemann, G. Potdevin, H. Graafsma, B. Nilsson, and J. C. H. Spence, "Femtosecond X-ray protein nanocrystallography, " Nature 470(7332), 73-77 (2011).
2. S. Boutet, L. Lomb, G. J. Williams, T. R. M. Barends, A. Aquila, R. B. Doak, U. Weierstall, D. P. DePonte, J. Steinbrener, R. L. Shoeman, M. Messerschmidt, A. Barty, T. A. White, S. Kassemeyer, R. A. Kirian, M. M. Seibert, P. A. Montanez, C. Kenney, R. Herbst, P. Hart, J. Pines, G. Haller, S. M. Gruner, H. T. Philipp, M. W. Tate, M. Hromalik, L. J. Koerner, N. van Bakel, J. Morse, W. Ghonsalves, D. Arnlund, M. J. Bogan, C. Caleman, R. Fromme, C. Y. Hampton, M. S. Hunter, L. C. Johansson, G. Katona, C. Kupitz, M. Liang, A. V. Martin, K. Nass, L. Redecke, F. Stellato, N. Timneanu, D. Wang, N. A. Zatsepin, D. Schafer, J. Defever, R. Neutze, P. Fromme, J. C. H. Spence, H. N. Chapman, and I. Schlichting, "High-resolution protein structure determination by serial femtosecond crystallography, " Science 337(6092), 362-364 (2012).
3. M. Frank, D. B. Carlson, M. S. Hunter, G. J. Williams, M. Messerschmidt, N. A. Zatsepin, A. Barty, W. H. Benner, K. Chu, A. T. Graf, S. P. Hau-Riege, R. A. Kirian, C. Padeste, T. Pardini, B. Pedrini, B. Segelke, M. M. Seibert, J. C. H. Spence, C.-J. Tsai, S. M. Lane, X.-D. Li, G. Schertler, S. Boutet, M. Coleman, and J. E. Evans, "Femtosecond X-ray diffraction from two-dimensional protein crystals, " IUCrJ 1(Pt 2), 95-100 (2014).
4. P. Hart, S. Boutet, G. Carini, M. Dubrovin, B. Duda, D. Fritz, G. Haller, R. Herbst, S. Herrmann, C. Kenney, N. Kurita, H. Lemke, M. Messerschmidt, M. Nordby, J. Pines, D. Schafer, M. Swift, M. Weaver, G. Williams, D. Zhu, N. van Bakel, and J. Morse, "The CSPAD megapixel x-ray camera at LCLS, " Proc. SPIE 8506, 85040C (2012).
5. L. Strüder, S. Epp, D. Rolles, R. Hartmann, P. Holl, G. Lutz, H. Soltau, R. Eckart, C. Reich, K. Heinzinger, C. Thamm, A. Rudenko, F. Krasniqi, K.-U. Kühnel, C. Bauer, C.-D. Schröter, R. Moshammer, S. Techert, D. Miessner, M. Porro, O. Hälker, N. Meidinger, N. Kimmel, R. Andritschke, F. Schopper, G. Weidenspointner, A. Ziegler, D. Pietschner, S. Herrmann, U. Pietsch, A. Walenta, W. Leitenberger, C. Bostedt, T. Möller, D. Rupp, M. Adolph, H. Graafsma, H. Hirsemann, K. Gärtner, R. Richter, L. Foucar, R. L. Shoeman, I. Schlichting, and J. Ullrich, "Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources, " Nucl. Instrum. Methods Phys. Res., Sect. A 614, 483-496 (2010).
6. T. Kameshima, S. Ono, T. Kudo, K. Ozaki, Y. Kirihara, K. Kobayashi, Y. Inubushi, M. Yabashi, T. Horigome, A. Holland, K. Holland, D. Burt, H. Murao, and T. Hatsui, "Development of an X-ray pixel detector with multiport charge-coupled device for X-ray free-electron laser experiments, " Rev. Sci. Instrum. 85(3), 033110 (2014).
7. B. Henrich, J. Becker, R. Dinapoli, P. Goettlicher, H. Graafsma, H. Hirsemann, R. Klanner, H. Krueger, R. Mazzocco, A. Mozzanica, H. Perrey, G. Potdevin, B. Schmitt, X. Shi, A. K. Srivastava, U. Trunk, and C. Youngman, "The adaptive gain integrating pixel detector AGIPD a detector for the European XFEL, " Nucl. Instrum. Methods Phys. Res., Sect. A 633, S11-S14 (2011).
8. C. B. Wunderer, A. Marras, M. Bayer, J. Correa, S. Lange, I. Shevyakov, S. Smoljanin, M. Viti, Q. Xia, M. Zimmer, G. Cautero, A. Gianoncelli, D. Giuressi, R. H. Menk, L. Stebel, H. Yousef, N. Tartoni, J. Marchal, N. Rees, J. Thompson, R. Turchetta, I. Sedgwick, D. Das, B. Marsh, and H. Graafsma, "Percival: an international collaboration to develop a MAPS-based soft X-ray imager, " Synchrotron Radiat. News 27(4), 30-34 (2014).
9. P. Denes, "Two-dimensional imaging detectors for structural biology with X-ray lasers, " Philos. Trans. R. Soc. Lond. B Biol. Sci. 369(1647), 20130334 (2014).
10. A. Barty, R. A. Kirian, F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White, and H. Chapman, "Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data, " J. Appl. Cryst. 47(3), 1118-1131 (2014).
11. T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty, and H. N. Chapman, "CrystFEL: a software suite for snapshot serial crystallography, " J. Appl. Cryst. 45(2), 335-341 (2012).
12. J. Hattne, N. Echols, R. Tran, J. Kern, R. J. Gildea, A. S. Brewster, R. Alonso-Mori, C. Glöckner, J. Hellmich, H. Laksmono, R. G. Sierra, B. Lassalle-Kaiser, A. Lampe, G. Han, S. Gul, D. DiFiore, D. Milathianaki, A. R. Fry, A. Miahnahri, W. E. White, D. W. Schafer, M. M. Seibert, J. E. Koglin, D. Sokaras, T. C. Weng, J. Sellberg, M. J. Latimer, P. Glatzel, P. H. Zwart, R. W. Grosse-Kunstleve, M. J. Bogan, M. Messerschmidt, G. J. Williams, S. Boutet, J. Messinger, A. Zouni, J. Yano, U. Bergmann, V. K. Yachandra, P. D. Adams, and N. K. Sauter, "Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers, " Nat. Methods 11(5), 545-548 (2014).
13. D. P. DePonte, U. Weierstall, K. Schmidt, J. Warner, D. Starodub, J. Spence, and R. B. Doak, "Gas dynamic virtual nozzle for generation of microscopic droplet streams, " J. Phys. D Appl. Phys. 41(19), 195505 (2008).
14. R. G. Sierra, H. Laksmono, J. Kern, R. Tran, J. Hattne, R. Alonso-Mori, B. Lassalle-Kaiser, C. Glöckner, J. Hellmich, D. W. Schafer, N. Echols, R. J. Gildea, R. W. Grosse-Kunstleve, J. Sellberg, T. A. McQueen, A. R. Fry, M. M. Messerschmidt, A. Miahnahri, M. M. Seibert, C. Y. Hampton, D. Starodub, N. D. Loh, D. Sokaras, T. C. Weng, P. H. Zwart, P. Glatzel, D. Milathianaki, W. E. White, P. D. Adams, G. J. Williams, S. Boutet, A. Zouni, J. Messinger, N. K. Sauter, U. Bergmann, J. Yano, V. K. Yachandra, and M. J. Bogan, "Nanoflow electrospinning serial femtosecond crystallography, " Acta Crystallogr., Sect. D: Biol. Crystallogr. 68(11), 1584- 1587 (2012).
15. U. Weierstall, D. James, C. Wang, T. A. White, D. Wang, W. Liu, J. C. H. Spence, R. Bruce Doak, G. Nelson, P. Fromme, R. Fromme, I. Grotjohann, C. Kupitz, N. A. Zatsepin, H. Liu, S. Basu, D. Wacker, G. W. Han, V. Katritch, S. Boutet, M. Messerschmidt, G. J. Williams, J. E. Koglin, M. Marvin Seibert, M. Klinker, C. Gati, R. L. Shoeman, A. Barty, H. N. Chapman, R. A. Kirian, K. R. Beyerlein, R. C. Stevens, D. Li, S. T. A. Shah, N. Howe, M. Caffrey, and V. Cherezov, "Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography, " Nat. Commun. 5, 3309 (2014).
16. W. Liu, D. Wacker, C. Wang, E. Abola, and V. Cherezov, "Femtosecond crystallography of membrane proteins in the lipidic cubic phase, " Philos. Trans. R. Soc. Lond. B Biol. Sci. 369(1647), 20130314 (2014).
17. A. E. Cohen, S. M. Soltis, A. González, L. Aguila, R. Alonso-Mori, C. O. Barnes, E. L. Baxter, W. Brehmer, A. S. Brewster, A. T. Brunger, G. Calero, J. F. Chang, M. Chollet, P. Ehrensberger, T. L. Eriksson, Y. Feng, J. Hattne, B. Hedman, M. Hollenbeck, J. M. Holton, S. Keable, B. K. Kobilka, E. G. Kovaleva, A. C. Kruse, H. T. Lemke, G. Lin, A. Y. Lyubimov, A. Manglik, I. I. Mathews, S. E. McPhillips, S. Nelson, J. W. Peters, N. K. Sauter, C. A. Smith, J. Song, H. P. Stevenson, Y. Tsai, M. Uervirojnangkoorn, V. Vinetsky, S. Wakatsuki, W. I. Weis, O. A. Zadvornyy, O. B. Zeldin, D. Zhu, and K. O. Hodgson, "Goniometer-based femtosecond crystallography with X-ray free electron lasers, " Proc. Natl. Acad. Sci. U.S.A. 111(48), 17122-17127 (2014).
18. W. Liu, D. Wacker, C. Gati, G. W. Han, D. James, D. Wang, G. Nelson, U. Weierstall, V. Katritch, A. Barty, N. A. Zatsepin, D. Li, M. Messerschmidt, S. Boutet, G. J. Williams, J. E. Koglin, M. M. Seibert, C. Wang, S. T. A. Shah, S. Basu, R. Fromme, C. Kupitz, K. N. Rendek, I. Grotjohann, P. Fromme, R. A. Kirian, K. R. Beyerlein, T. White, H. N. Chapman, M. Caffrey, J. C. H. Spence, R. C. Stevens, and V. Cherezov, "Serial femtosecondcrystallography of G protein-coupled receptors, " Science 342(6165), 1521-1524 (2013).
19. C. Gati, G. Bourenkov, M. Klinge, D. Rehders, F. Stellato, D. Oberthür, O. Yefanov, B. P. Sommer, S. Mogk, M. Duszenko, C. Betzel, T. R. Schneider, H. N. Chapman, and L. Redecke, "Serial crystallography on in vivo grown microcrystals using synchrotron radiation, " IUCrJ 1(2), 87-94 (2014).
20. F. Stellato, D. Oberthür, M. Liang, R. Bean, C. Gati, O. Yefanov, A. Barty, A. Burkhardt, P. Fischer, L. Galli, R. A. Kirian, J. Meyer, S. Panneerselvam, C. H. Yoon, F. Chervinskii, E. Speller, T. A. White, C. Betzel, A. Meents, and H. N. Chapman, "Room-temperature macromolecular serial crystallography using synchrotron radiation, " IUCrJ 1(4), 204-212 (2014).
21. T. A. White, A. Barty, F. Stellato, J. M. Holton, R. A. Kirian, N. A. Zatsepin, and H. N. Chapman, "Crystallographic data processing for free-electron laser sources, " Acta Crystallogr., Sect. D: Biol. Crystallogr. 69(7), 1231-1240 (2013).
22. T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, "De novo protein crystal structure determination from X-ray freeelectron laser data, " Nature 505(7482), 244-247 (2013).
23. M. Schmidt, K. Pande, S. Basu, and J. Tenboer, "Room temperature structures beyond 1.5 Å by serial femtosecond crystallography, " Struct. Dyn. 2(4), 041708 (2015).
24. L. Redecke, K. Nass, D. P. DePonte, T. A. White, D. Rehders, A. Barty, F. Stellato, M. Liang, T. R. M. Barends, S. Boutet, G. J. Williams, M. Messerschmidt, M. M. Seibert, A. Aquila, D. Arnlund, S. Bajt, T. Barth, M. J. Bogan, C. Caleman, T.-C. Chao, R. B. Doak, H. Fleckenstein, M. Frank, R. Fromme, L. Galli, I. Grotjohann, M. S. Hunter, L. C. Johansson, S. Kassemeyer, G. Katona, R. A. Kirian, R. Koopmann, C. Kupitz, L. Lomb, A. V. Martin, S. Mogk, R. Neutze, R. L. Shoeman, J. Steinbrener, N. Timneanu, D. Wang, U. Weierstall, N. A. Zatsepin, J. C. H. Spence, P. Fromme, I. Schlichting, M. Duszenko, C. Betzel, and H. N. Chapman, "Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser, " Science 339(6116), 227-230 (2013).
25. D. Li, L. Vogeley, A. Keogh, N. Howe, P. Stansfeld, M. Sansom, P. Fromme, R. Fromme, B. Basu, I. Grotjohann, C. Kupitz, K. Rendek, U. Weierstall, N. Zatsepin, V. Cherezov, W. Liu, S. Bandaru, N. English, C. Gati, A. Barty, O. Yefanov, H. Chapman, K. Diederichs, M. Messerschmidt, S. Boutet, G. Williams, M. Seibert, and M. Caffrey, "Ternary structure reveals mechanism of a membrane diacylglycerol kinas, " Nat. Commun. (posted 24 October 2014, in press).
26. Y. Kang, X. E. Zhou, X. Gao, Y. He, W. Liu, A. Ishchenko, A. Barty, T. A. White, O. Yefanov, G. W. Han, Q. Xu, P. W. de Waa, J. Ke, M. H. Tan, C. Zhang, A. Moeller, G. M. West, B. D. Pascal, N. Van Eps, L. N. Caro, S. A. Vishnivetskiy, R. J. Lee, K. M. Suino-Powell, X. Gu, K. Pal, J. Ma, X. Zhi, S. Boutet, G. J. Williams, M. Messerschmidt, C. Gati, N. A. Zatsepin, D. Wang, D. James, S. Basu, S. Roy-Chowdhury, C. E. Conrad, J. Coe, H. Liu, S. Lisova, C. Kupitz, I. Grotjohann, R. Fromme, Y. Jiang, M. Tan, H. Yang, J. Li, M. Wang, Z. Zheng, D. Li, N. Howe, Y. Zhao, J. Standfuss, K. Diederichs, Y. Dong, C. S. Potter, B. Carragher, M. Caffrey, H. Jiang, H. N. Chapman, J. C. Spence, P. Fromme, U. Weierstall, O. P. Ernst, V. Katritch, V. V. Gurevich, P. R. Griffin, W. L. Hubbell, R. C. Stevens, V. Cherezov, K. Melcher, and H. E. Xu, "Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser, " Nature 523(7562), 561-567 (2015).
27. T. Barends, "De novo protein crystal structure determination from X-ray free-electron laser data, " experimental data, http://www.cxidb.org/id-22.html.
28. P. A. Karplus and K. Diederichs, "Linking crystallographic model and data quality, " Science 336(6084), 1030- 1033 (2012).
29. S. Boutet, "High-resolution protein structure determination by serial femtosecond crystallography, " experimental data, http://www.cxidb.org/id-17.html.
30. W. Lui, "Serial femtosecond crystallography of G protein-coupled receptors, " experimental data, http://www.cxidb.org/id-21.html.