A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

Acta Crystallographica Section D: Biological Crystallography

Volumn 71, Issue , 2015, Pages 1987-1997

  Murray, Thomas D ^a,b   Lyubimov, Artem Y ^c   Ogata, Craig M ^d   Vo, Huy ^e   Uervirojnangkoorn, Monarin ^c   Brunger, Axel T ^c   Berger, James M ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c STANFORD UNIVERSITY   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e Johns Hopkins University   (United States)

Author keywords

microcrystals; microfluidics; microfocus beamline; serial data collection; silicon nitride; X ray crystallography; XFEL

Indexed keywords

HEN EGG LYSOZYME; LYSOZYME; SILICON DERIVATIVE; SILICON NITRIDE;

ANIMAL; CHEMICAL PHENOMENA; CHEMISTRY; CHICKEN; CRYSTALLIZATION; DEVICES; EQUIPMENT DESIGN; LIGHT; X RAY CRYSTALLOGRAPHY;

ANIMALS; CHICKENS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; EQUIPMENT DESIGN; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGHT; MURAMIDASE; SILICON COMPOUNDS;

EID: 84944260506     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004715015011     Document Type: Article

References (81)

1. Adams, P. D., et al. (2010). Acta Cryst. D66, 213-221.
2. Barends, T. R. M., Foucar, L., Botha, S., Doak, R. B., Shoeman, R. L., Nass, K., Koglin, J. E., Williams, G. J., Boutet, S., Messerschmidt, M. & Schlichting, I. (2014). Nature (London), 505, 244-247.
3. Biasci, J. C., et al. (2014). Synchrotron Radiat. News. 27, 8-12.
4. Borland, M. (2013). J. Phys. Conf. Ser. 425, 042016.
5. Botha, S., Nass, K., Barends, T. R. M., Kabsch, W., Latz, B., Dworkowski, F., Foucar, L., Panepucci, E., Wang, M., Shoeman, R. L., Schlichting, I. & Doak, R. B. (2015). Acta Cryst. D71, 387-397.
6. Boutet, S., et al. (2012). Science. 337, 362-364.
7. Chapman, H. N., et al. (2006). Nature Phys. 2, 839-843.
8. Chapman, H. N., et al. (2011). Nature (London), 470, 73-77.
9. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
10. Cherezov, V., Rosenbaum, D. M., Hanson, M. A., Rasmussen, S. G. F., Thian, F. S., Kobilka, T. S., Choi, H.-J., Kuhn, P., Weis, W. I., Kobilka, B. K. & Stevens, R. C. (2007). Science. 318, 1258-1265.
11. Cipriani, F., Röwer, M., Landret, C., Zander, U., Felisaz, F. & Márquez, J. A. (2012). Acta Cryst. D68, 1393-1399.
12. Cohen, A. E., et al. (2014). Proc. Natl Acad. Sci. USA. 111, 17122-17127.
13. Coquelle, N., Brewster, A. S., Kapp, U., Shilova, A., Weinhausen, B., Burghammer, M. & Colletier, J.-P. (2015). Acta Cryst. D71, 1184-1196.
14. Coulibaly, F., Chiu, E., Ikeda, K., Gutmann, S., Haebel, P.W., Schulze-Briese, C., Mori, H. & Metcalf, P. (2007). Nature (London), 446, 97-101.
15. Cowan, J. A. & Nave, C. (2008). J. Synchrotron Rad. 15, 458-462.
16. Cusack, S., Belrhali, H., Bram, A., Burghammer, M., Perrakis, A. & Riekel, C. (1998). Nature Struct. Mol. Biol. 5, 634-637.
17. Decker, G. (2014). Synchrotron Radiat. News. 27, 13-17.
18. DePonte, D. P., Weierstall, U., Schmidt, K., Warner, J., Starodub, D., Spence, J. C. H. & Doak, R. B. (2008). J. Phys. D Appl. Phys. 41, 195505.
19. Dhouib, K., Khan Malek, C., Pfleging, W., Gauthier-Manuel, B., Duffait, R., Thuillier, G., Ferrigno, R., Jacquamet, L., Ohana, J., Ferrer, J.-L., Théobald-Dietrich, A., Giegé, R., Lorber, B. & Sauter, C. (2009). Lab Chip. 9, 1412-1421.
20. Einfeld, D. (2014). Synchrotron Radiat. News. 27, 4-7.
21. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
22. Falkner, J. C., Al-Somali, A. M., Jamison, J. A., Zhang, J., Adrianse, S. L., Simpson, R. L., Calabretta, M. K., Radding, W., Phillips, G. N. Jr & Colvin, V. L. (2005). Chem. Mater. 17, 2679-2686.
23. Feld, G. K. & Frank, M. (2014). Curr. Opin. Struct. Biol. 27, 69-78.
24. Finfrock, Y. Z., Stern, E. A., Yacoby, Y., Alkire, R. W., Evans-Lutterodt, K., Stein, A., Isakovic, A. F., Kas, J. J. & Joachimiak, A. (2010). Acta Cryst. D66, 1287-1294.
25. Fischetti, R. F., Xu, S., Yoder, D. W., Becker, M., Nagarajan, V., Sanishvili, R., Hilgart, M. C., Stepanov, S., Makarov, O. & Smith, J. L. (2009). J. Synchrotron Rad. 16, 217-225.
26. Fischetti, R. F., Yoder, D., Xu, S., Makarov, O., Ogata, C. & Smith, J. L. (2013). J. Phys. Conf. Ser. 425, 012006.
27. Frank, M., et al. (2014). IUCrJ. 1, 95-100.
28. Fraser, J. S., Clarkson, M. W., Degnan, S. C., Erion, R., Kern, D. & Alber, T. (2009). Nature (London), 462, 669-673.
29. Fraser, J. S., van den Bedem, H., Samelson, A. J., Lang, P. T., Holton, J. M., Echols, N. & Alber, T. (2011). Proc. Natl Acad. Sci. USA. 108, 16247-16252.
30. Greaves, E. D. & Manz, A. (2005). Lab Chip. 5, 382-391.
31. Guha, S., Perry, S. L., Pawate, A. S. & Kenis, P. J. (2012). Sens. Actuators B Chem. 174, 1-9.
32. Halle, B. (2004). Proc. Natl Acad. Sci. USA. 101, 4793-4798.
33. Hansen, C. L., Classen, S., Berger, J. M. & Quake, S. R. (2006). J. Am. Chem. Soc. 128, 3142-3143.
34. Hansen, C. L., Skordalakes, E., Berger, J. M. & Quake, S. R. (2002). Proc. Natl Acad. Sci. USA. 99, 16531-16536.
35. Hattne, J., et al. (2014). Nature Methods. 11, 545-548.
36. Heymann, M., Opthalage, A., Wierman, J. L., Akella, S., Szebenyi, D. M. E., Gruner, S. M. & Fraden, S. (2014). IUCrJ. 1, 349-360.
37. Hilgart, M. C., Sanishvili, R., Ogata, C. M., Becker, M., Venugopalan, N., Stepanov, S., Makarov, O., Smith, J. L. & Fischetti, R. F. (2011). J. Synchrotron Rad. 18, 717-722.
38. Hirata, K., et al. (2014). Nature Methods. 11, 734-736.
39. Hunter, M. S., et al. (2014). Sci. Rep. 4, 6026.
40. Jaeger, R. C. (2002). Introduction to Microelectronic Fabrication, 2nd ed., edited by G. W. Neudeck & R. F. Pierret, pp. 17-25. Upper Saddle River: Prentice Hall
41. Johansson, L. C., et al. (2013). Nature Commun. 4, 2911.
42. Johansson, L. C., et al. (2012). Nature Methods. 9, 263-265.
43. Keedy, D. A., van den Bedem, H., Sivak, D. A., Petsko, G. A., Ringe, D., Wilson, M. A. & Fraser, J. S. (2014). Structure. 22, 899-910.
44. Kern, J., et al. (2012). Proc. Natl Acad. Sci. USA. 109, 9721-9726.
45. Kern, J., et al. (2013). Science. 340, 491-495.
46. Kern, J., et al. (2014). Nature Commun. 5, 4371.
47. Khvostichenko, D. S., Schieferstein, J. M., Pawate, A. S., Laible, P. D. & Kenis, P. J. (2014). Cryst. Growth Des. 14, 4886-4890.
48. Kimura, T., Joti, Y., Shibuya, A., Song, C., Kim, S., Tono, K., Yabashi, M., Tamakoshi, M., Moriya, T., Oshima, T., Ishikawa, T., Bessho, Y. & Nishino, Y. (2014). Nature Commun. 5, 3052.
49. Kraus, J., Reichelt, R., Gunther, S., Gregoratti, L., Amati, M., Kiskinova, M., Yulaev, A., Vlassiouk, I. & Kolmakov, A. (2014). Nanoscale. 6, 14394-14403.
50. Kupitz, C., et al. (2014). Nature (London), 513, 261-265.
51. Liu, Q., Liu, Q. & Hendrickson, W. A. (2013). Acta Cryst. D69, 1314-1332.
52. Liu, W., Wacker, D., et al. (2013). Science. 342, 1521-1524.
53. Lyubimov, A. Y., Murray, T. D., Koehl, A., Araci, I. E., Uervirojnangkoorn, M., Zeldin, O. B., Cohen, A. E., Soltis, S. M., Baxter, E. L., Brewster, A. S., Sauter, N. K., Brunger, A. T. & Berger, J. M. (2015). Acta Cryst. D71, 928-940.
54. Marinaro, G., Accardo, A., De Angelis, F., Dane, T., Weinhausen, B., Burghammer, M. & Riekel, C. (2014). Lab Chip. 14, 3705-3709.
55. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
56. Meyer, J. C., Geim, A. K., Katsnelson, M. I., Novoselov, K. S., Booth, T. J. & Roth, S. (2007). Nature (London), 446, 60-63.
57. Moukhametzianov, R., Burghammer, M., Edwards, P. C., Petitdemange, S., Popov, D., Fransen, M., McMullan, G., Schertler, G. F. X. & Riekel, C. (2008). Acta Cryst. D64, 158-166.
58. Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. O., Riekel, C., Grothe, R. & Eisenberg, D. (2005). Nature (London), 435, 773-778.
59. Northen, M. T. & Turner, K. L. (2005). Nanotechnology. 16, 1159-1166.
60. Perrakis, A., Cipriani, F., Castagna, J.-C., Claustre, L., Burghammer, M., Riekel, C. & Cusack, S. (1999). Acta Cryst. D55, 1765-1770.
61. Rasmussen, S. G. F., Choi, H.-J., Rosenbaum, D. M., Kobilka, T. S., Thian, F. S., Edwards, P. C., Burghammer, M., Ratnala, V. R., Sanishvili, R., Fischetti, R. F., Schertler, G. F. X., Weis, W. I. & Kobilka, B. K. (2007). Nature (London), 450, 383-387.
62. Rasmussen, S. G. F., et al. (2011). Nature (London), 477, 549-555.
63. Redecke, L., et al. (2013). Science. 339, 227-230.
64. Sanchez-Weatherby, J., Bowler, M.W., Huet, J., Gobbo, A., Felisaz, F., Lavault, B., Moya, R., Kadlec, J., Ravelli, R. B. G. & Cipriani, F. (2009). Acta Cryst. D65, 1237-1246.
65. Sanishvili, R., Nagarajan, V., Yoder, D., Becker, M., Xu, S., Corcoran, S., Akey, D. L., Smith, J. L. & Fischetti, R. F. (2008). Acta Cryst. D64, 425-435.
66. Sanishvili, R., Yoder, D. W., Pothineni, S. B., Rosenbaum, G., Xu, S., Vogt, S., Stepanov, S., Makarov, O. A., Corcoran, S., Benn, R., Nagarajan, V., Smith, J. L. & Fischetti, R. F. (2011). Proc. Natl Acad. Sci. USA. 108, 6127-6132.
67. Sawaya, M. R., et al. (2014). Proc. Natl Acad. Sci. USA. 111, 12769-12774.
68. Sierra, R. G., et al. (2012). Acta Cryst. D68, 1584-1587.
69. Smith, J. L., Fischetti, R. F. & Yamamoto, M. (2012). Curr. Opin. Struct. Biol. 22, 602-612.
70. Stellato, F., et al. (2014). IUCrJ. 1, 204-212.
71. Stepanov, S., Makarov, O., Hilgart, M., Pothineni, S. B., Urakhchin, A., Devarapalli, S., Yoder, D., Becker, M., Ogata, C., Sanishvili, R., Venugopalan, N., Smith, J. L. & Fischetti, R. F. (2011). Acta Cryst. D67, 176-188.
72. Tanaka, H. (2014). Synchrotron Radiat. News. 27, 23-26.
73. Tilton, R. F. Jr, Dewan, J. C. & Petsko, G. A. (1992). Biochemistry. 31, 2469-2481.
74. Uervirojnangkoorn, M., Zeldin, O. B., Lyubimov, A. Y., Hattne, J., Brewster, A. S., Sauter, N. K., Brunger, A. T. & Weis, W. I. (2015). Elife. 4, e05421.
75. Walther, F., Davydovskaya, P., Zürcher, S., Kaiser, M., Herberg, H., Gigler, A. M. & Stark, R. W. (2007). J. Micromech. Microeng., 17, 524-531.
76. Warne, T., Serrano-Vega, M. J., Baker, J. G., Moukhametzianov, R., Edwards, P. C., Henderson, R., Leslie, A. G. W., Tate, C. G. & Schertler, G. F. X. (2008). Nature (London), 454, 486-491.
77. Weierstall, U., et al. (2014). Nature Commun. 5, 3309.
78. Weierstall, U., Spence, J. C. H. & Doak, R. B. (2012). Rev. Sci. Instrum. 83, 035108.
79. Wells, G. M. (1992). J. Vac. Sci. Technol. B. 10, 3252-3255.
80. Zarrine-Afsar, A., Barends, T. R. M., Müller, C., Fuchs, M. R., Lomb, L., Schlichting, I. & Miller, R. J. D. (2012). Acta Cryst. D68, 321-323.
81. Zheng, B., Tice, J. D., Roach, L. S. & Ismagilov, R. F. (2004). Angew. Chem. Int. Ed. 43, 2508-2511.