Diffraction Techniques in Structural Biology

Martin Egli1

1 Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 7.13
DOI:  10.1002/cpnc.4
Online Posting Date:  June, 2016
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic‐resolution structural data. Diffraction‐based techniques such as single‐crystal X‐ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern‐day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high‐speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single‐crystal X‐ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping‐stone to more in‐depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc.

Keywords: crystallization; diffraction; electron microscopy; neutron scattering; structural biology; X‐ray crystallography

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Major Techniques in Structural Biology
  • Single Crystal X‐Ray Crystallography
  • Summary and Outlook
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
  Abola, E., Kuhn, P., Earnest, T., and Stevens, R.C. 2000. Automation of X‐ray crystallography. Nat. Struct. Biol. 7:973‐977. doi: 10.1038/80754.
  Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.‐W., Kapral, G.J., Grosse‐Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., and Zwart, P.H. 2010. PHENIX: A comprehensive Python‐based system for macromolecular structure solution. Acta Cryst. D 66:213‐221. doi: 10.1107/S0907444909052925.
  Afonine, P.V., Mustyakimov, M., Grosse‐Kunstleve, R.W., Moriarty, N.W., Langan, P., and Adams, P.D. 2010. Joint X‐ray and neutron refinement with phenix.refine. Acta Cryst. D 66:1153‐1163. doi: 10.1107/S0907444910026582.
  Anosova, I., Kowal, E.A., Dunn, M.R., Chaput, J.C, Van Horn, W.D., and Egli, M. 2016. The structural diversity of artificial genetic polymers. Nucleic Acids Res. 44:1007‐1021. doi: 10.1093/nar/gkv1472.
  Arai, S., Chatake, T., Ohhara, T., Kurihara, K., Tanaka, I., Suzuki, N., Fujimoto, Z., Mizuno, H., and Niimura, N. 2005. Complicated water orientations in the minor groove of the B‐DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements. Nucleic Acids Res. 33:3017‐3024. doi: 10.1093/nar/gki616.
  Baeyens, K.J., Jancarik, J., and Holbrook, S.R. 1994. Use of low‐molecular‐weight polyethylene glycol in the crystallization of RNA oligomers. Acta Cryst. D 50:764‐767. doi: 10.1107/S0907444994003458.
  Baumeister, W. and Steven, A.C. 2000. Macromolecular electron microscopy in the era of structural genomics. Trends Biochem. Sci. 25:624‐631. doi: 10.1016/S0968‐0004(00)01720‐5.
  Berger, I., Kang, C.H., Sinha, N., Wolters, M., and Rich, A. 1996. A highly efficient 24‐condition matrix for the crystallization of nucleic acid fragments. Acta Cryst. D 52:465‐468. doi: 10.1107/S0907444995013564.
  Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.‐H., Srinivasan, A.R., and Schneider, B. 1992. The nucleic acid database: A comprehensive relational database of three‐dimensional structures of nucleic acids. Biophys. J. 63:751‐759. doi: 10.1016/S0006‐3495(92)81649‐1.
  Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235‐242. doi: 10.1093/nar/28.1.235.
  Binshtein, E. and Ohi, M.D. 2015. Cryo‐electron microscopy and the amazing race to atomic resolution. Biochemistry 54:3133‐3141. doi: 10.1021/acs.biochem.5b00114.
  Blakeley, M.P., Langan, P., Niimura, N., and Podjarny, A. 2008. Neutron crystallography: Opportunities, challenges and limitations. Curr. Opin. Struct. Biol. 18:593‐600. doi: 10.1016/j.sbi.2008.06.009.
  Blundell, T.L. and Johnson, L.N. 1976. Protein Crystallography. Academic Press, London.
  Bragg, W.L. 1913. The diffraction of short electromagnetic waves by a crystal. Proc. Cambridge Philos. Soc. 17:43‐57.
  Brunger, A.T. 1992. The free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472‐474. doi: 10.1038/355472a0.
  Brunger, A.T. and Adams, P.D. 2002. Molecular dynamics applied to X‐ray structure refinement. Acc. Chem. Res. 35:404‐412. doi: 10.1021/ar010034r.
  Burke, J.E. and Butcher, S.E. 2012. Nucleic acid structure characterization by small angle X‐ray scattering (SAXS). Curr. Protoc. Nucleic Acid Chem. 7.18.1‐7.18.18. doi: 10.1002/0471142700.nc0718s51.
  Carlon, A., Ravera, E., Hennig, J., Parigi, G., and Sattler, M. 2016. Improved accuracy from joint X‐ray and NMR refinement of a protein‐RNA complex structure. J. Am. Chem. Soc. 138:1601‐1610. doi: 10.1021/jacs.5b11598.
  Carter, C.W. Jr. and Sweet, R.M. (eds.) 1997a. Methods in Enzymology, Macromolecular Crystallography, Part A. Vol. 276. Academic Press, San Diego.
  Carter, C.W. Jr. and Sweet, R.M. (eds.) 1997b. Methods in Enzymology, Macromolecular Crystallography, Part B. Vol. 277. Academic Press, San Diego.
  Carter, C.W. Jr. and Sweet, R.M. (eds.) 2003a. Methods in Enzymology, Macromolecular Crystallography, Part C. Vol. 368. Academic Press, San Diego.
  Carter, C.W. Jr. and Sweet, R.M. (eds.) 2003b. Methods in Enzymology, Macromolecular Crystallography, Part D. Vol. 374. Academic Press, San Diego.
  Casadei, C.M., Gumiero, A., Metcalfe, C.L., Murphy, E.J., Basran, J., Concilio, M.G., Teixeira, S.C., Schrader, T.E., Fielding, A.J., Ostermann, A., Blakeley, M.P., Raven, E.L., and Moody, P.C. 2014. Heme enzymes. Neutron cryo‐crystallography captures the protonation state of ferryl heme in peroxidase. Science 345:193‐197. doi: 10.1126/science.1254398.
  CCP4 (Collaborative Computational Project, Number 4). 1994. The CCP4 suite: Programs for protein crystallography. Acta Cryst. D 50:760‐763. doi: 10.1107/S0907444994003112.
  Chandonia, J.M. and Brenner, S.E. 2006. The impact of structural genomics: Expectations and outcomes. Science 311:347‐351. doi: 10.1126/science.1121018.
  Chandrasekaran, R. and Stubbs, G. 2012. Crystallography of biological macromolecules. In International Tables for Crystallography, Vol. F, 2nd edition (E. Arnold, D.M. Himmel, and M.G. Rossmann, eds.) Part 19, Chapter 5, pp. 583‐592. Wiley (commissioned by the International Union of Crystallography), Hoboken, N.J.
  Chapman, H.N., Fromme, P., Barty, A., White, T.A., Kirian, R.A., Aquila, A., Hunter, M.S., Schulz, J., DePonte, D.P., Weierstall, U., Doak, R.B., Maia, F.R.N.C., Martin, A.V., Schlichting, I., Lomb, L., Coppola, N., Shoeman, R.L., Epp, S.W., Hartmann, R., Rolles, D., Rudenko, A., Foucar, L., Kimmel, N., Weidenspointner, G., Holl, P., Liang, M., Barthelmess, M., Caleman, C., Boutet, S., Bogan, M.J., Krzywinski, J., Bostedt, C., Bajt, S., Gumprecht, L., Rudek, B., Erk, B., Schmidt, C., Hömke, A., Reich, C., Pietschner, D., Strüder, L., Hauser, G., Gorke, H., Ullrich, J., Herrmann, S., Schaller, G., Schopper, F., Soltau, H., Kühnel, K.U., Messerschmidt, M., Bozek, J.D., Hau‐Riege, S.P., Frank, M., Hampton, C.Y., Sierra, R.G., Starodub, D., Williams, G.J., Hajdu, J., Timneanu, N., Seibert, M.M., Andreasson, J., Rocker, A., Jönsson, O., Svenda, M., Stern, S., Nass, K., Andritschke, R., Schröter, C.D., Krasniqi, F., Bott, M., Schmidt, K.E., Wang, X., Grotjohann, I., Holton, J.M., Barends, T.R.M., Neutze, R., Marchesini, S., Fromme, R., Schorb, S., Rupp, D., Adolph, M., Gorkhover, T., Andersson, I., Hirsemann, H., Potdevin, G., Graafsma, H., Nilsson, B., and Spence, J.C.H. 2011. Femtosecond X‐ray protein nanocrystallography. Nature 470:73‐77. doi: 10.1038/nature09750.
  Chatake, T., Tanaka, I., Umino, H., Arai, S., and Niimura, N. 2005. The hydration structure of a Z‐DNA hexameric duplex determined by a neutron diffraction technique. Acta Cryst. D 61:1088‐1098. doi: 10.1107/S0907444905015581.
  Chiu, W., Burnett, R.M., and Garcea, R.L. (eds.) 1997. Structural Biology of Viruses. Oxford University Press, Oxford.
  Coates, L., Stoica, A.D., Hoffmann, C., Richards, J., and Cooper, R. 2010. The macromolecular neutron diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge: Enhanced optics, high‐resolution neutron detectors and simulated diffraction. J. Appl. Cryst. 43:570‐577. doi: 10.1107/S0021889810008587.
  Collins, K.D. 2004. Ions from the Hofmeister series and osmolytes: Effects on proteins in solution and in the crystallization process. Methods 34:300‐311. doi: 10.1016/j.ymeth.2004.03.021.
  Conn, G.L., Gittis, A.G., Lattman, E.E., Misra, V.K., and Draper, D.E. 2002. A compact RNA tertiary structure contains a buried backbone‐K+ complex. J. Mol. Biol. 318:963‐973. doi: 10.1016/S0022‐2836(02)00147‐X.
  Czepas, J., Devedjiev, Y., Krowarsch, D., Derewenda, U., Otlewski, J., and Derewenda, Z.S. 2004. The impact of Lys→Arg surface mutations on the crystallization of the globular domain of RhoGDI. Acta Cryst. D 60:275‐280. doi: 10.1107/S0907444903026271.
  Dafforn, T.R. 2007. So how do you know you have a macromolecular complex? Acta Cryst. D 63:17‐25. doi: 10.1107/S0907444906047044.
  Dong, A., Xu, X., Edwards, A.M., Midwest Center for Structural Genomics, Chang, C., Chruszcz, M., Cuff, M., Cymborowski, M., Di Leo, R., Egorova, O., Evdokimova, E., Filippova, E., Gu, J., Guthrie, J., Ignatchenko, A., Joachimiak, A., Klostermann, N., Kim, Y., Korniyenko, Y., Minor, W., Que, Q., Savchenko, A., Skarina, T., Tan, K., Yakunin, A., Yee, A., Yim, V., Zhang, R., Zheng, H., Structural Genomics Consortium, Akutsu, M., Arrowsmith, C., Avvakumov, G.V., Bochkarev, A., Dahlgren, L.G., Dhe‐Paganon, S., Dimov, S., Dombrovski, L., Finerty, P. Jr., Flodin, S., Flores, A., Gräslund, S., Hammerström, M., Herman, M.D., Hong, B.S., Hui, R., Johansson, I., Liu, Y., Nilsson, M., Nedyalkova, L., Nordlund, P., Nyman, T., Min, J., Ouyang, H., Park, H.W., Qi, C., Rabeh, W., Shen, L., Shen, Y., Sukumard, D., Tempel, W., Tong, Y., Tresagues, L., Vedadi, M., Walker, J.R., Weigelt, J., Welin, M., Wu, H., Xiao, T., Zeng, H., and Zhu, H. 2007. In situ proteolysis for protein crystallization and structure determination. Nat. Methods 4:1019‐1021. doi: 10.1038/nmeth1118.
  Doublié, S. 1997. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276:523‐530. doi: 10.1016/S0076‐6879(97)76075‐0.
  Doublié, S. (ed.). 2007a. Methods in Molecular Biology Book 363, Macromolecular Crystallography Protocols: Preparation and Crystallization of Macromolecules, Vol. 1. Humana Press, Totowa, N.J.
  Doublié, S. (ed.). 2007b. Methods in Molecular Biology Book 364, Macromolecular Crystallography Protocols: Structure Determination, Vol. 2. Humana Press, Totowa, N.J.
  Doudna, J.A., Grosshans, C., Gooding, A., and Kundrot, C.E. 1993. Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. Proc. Natl. Acad. Sci. U.S.A. 90:7829‐7833. doi: 10.1073/pnas.90.16.7829.
  Drenth, J. 2007. Principles of Protein X‐Ray Crystallography, 3rd edition. Springer‐Verlag, New York.
  Ducruix, A. and Giegé, R. (eds.) 1999. Crystallization of Nucleic Acids and Proteins: A Practical Approach, 2nd edition. Oxford University Press, Oxford.
  Egli, M. 2015. Structural and Biophysical Methods to Analyze Clock Function and Mechanism. In Methods in Enzymology, Circadian Rhythms and Biological Clocks, Part A. Vol. 551. (A. Seghal, ed.) pp. 223‐266, Elsevier, New York.
  Egli, M. and Johnson, C.H. 2015. Biochemistry that times the day. Biochemistry 54:104‐109. doi: 10.1021/bi5014968.
  Emsley, P. and Cowtan, K. 2004. Coot: Model‐building tools for molecular graphics. Acta Cryst. D 60:2126‐2132. doi: 10.1107/S0907444904019158.
  Ennifar, E. (ed.). 2015. Methods in Molecular Biology Book 1320, Methods and Protocols: Nucleic Acid Crystallography. Humana Press, New York.
  Fenn, T.D., Schnieders, M.J., Mustyakimov, M., Wu, C., Langan, P., Pande, V.S., and Brunger, A.T. 2011. Reintroducing electrostatics into macromolecular crystallographic refinement: Application to neutron crystallography and DNA hydration. Structure 19:523‐533. doi: 10.1016/j.str.2011.01.015.
  Ferré‐D'Amaré, A.R. and Doudna, J.A. 2000. Methods to crystallize RNA. Curr. Protoc. Nucleic Acid Chem. 7:6.1‐7.6.13. doi: 10.1002/0471142700.nc0706s00.
  Ferré‐D'Amaré, A.R., Zhou, K., and Doudna, J.M. 1998a. A general module for RNA crystallization. J. Mol. Biol. 279:621‐631. doi: 10.1006/jmbi.1998.1789.
  Ferré‐D'Amaré, A.R., Zhou, K., and Doudna, J.M. 1998b. Crystal structure of a hepatitis delta virus ribozyme. Nature 395:567‐574. doi:10.1038/26912.
  Friedrich, W., Knipping, P., and von Laue, M. 1912. Interferenz‐erscheinungen bei röntgenstrahlen [Interference phenomena at X‐rays]. Sitzungsber. Kgl. Bayer. Akad. Wiss. 303‐322.
  Fromme, P. 2014. Leading‐edge lasers. Nature 505:620‐621. doi: 10.1038/505620a.
  Gabanyi, M.J., Adams, P.D., Arnold, K., Bordoli, L., Carter, L.G., Flippen‐Andersen, J., Gifford, L., Haas, J., Kouranov, A., McLaughlin, W.A., Micallef, D.I., Minor, W., Shah, R., Schwede, T., Tao, Y.P., Westbrook, J.D., Zimmerman, M., and Berman, H.M. 2011. The structural biology knowledgebase: A portal to protein structures, sequences, functions, and methods. J. Struct. Funct. Genomics 12:45‐54. doi: 10.1007/s10969‐011‐9106‐2.
  Gait, M.J. (ed.) 1984. Oligonucleotide Synthesis: A Practical Approach. IRL Press, Oxford.
  Gallat, F.‐X., Matsugaki, N., Coussens, N.P., Yagi, K.J., Boudes, M., Higashi, T., Tsuji, D., Tatano, Y., Suzuki, M., Mizohata, E., Tono, K., Joti, Y., Kameshima, T., Park, J., Song, C., Hatsui, T., Yabashi, M., Nango, E., Itoh, K., Coulibaly, F., Tobe, S., Ramaswamy, S., Stay, B., Iwata, S., and Chavas, L.M.G. 2014. In vivo crystallography at X‐ray free‐electron lasers: The next generation of structural biology. Phil. Trans. R. Soc. B 369:20130497. doi: 10.1098/rstb.2013.0497.
  Garman, E.F. and Murray, J.W. 2003. Heavy‐atom derivatization. Acta Cryst. D 59:1903‐1913. doi: 10.1107/S0907444903012794.
  Garman, E.F. and Owen, R.L. 2006. Cryocooling and radiation damage in macromolecular crystallography. Acta Cryst. D 62:32‐47. doi: 10.1107/S0907444905034207.
  Hajdu, J. 2000. Single‐molecule X‐ray diffraction. Curr. Opin. Struct. Biol. 10:569‐573. doi: 10.1016/S0959‐440X(00)00133‐0.
  Hanson, B.L., Langan, P., Katz, A., Li, X., Harp, J.M., Glusker, J.P., Schoenborn, B.P., and Bunick, G.J. 2004. A preliminary time‐of‐flight neutron diffraction study of S. rubiginosus D‐xylose isomerase. Acta Cryst. D 60:241‐249. doi: 10.1107/S0907444903025873.
  Harp, J.M., Timm, D.E., and Bunick, G.J. 1998. Macromolecular crystal annealing: Overcoming increased mosaicity associated with cryocrystallography. Acta Cryst. D 54:622‐628. doi: 10.1107/S0907444997019008.
  Helliwell, J.R. 1992. Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press, Cambridge, UK.
  Hendrickson, W.A. 2000. Synchrotron crystallography. Trends Biochem. Sci. 25:637‐643. doi: 10.1016/S0968‐0004(00)01721‐7.
  Hendrickson, W.A., Horton, J.R., and LeMaster, D.M. 1990. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): A vehicle for direct determination of three‐dimensional structure. EMBO J. 9:1665‐1672.
  Holbrook, S.R. and Kim, S.‐H. 1985. Crystallization and heavy‐atom derivatives of polynucleotides. Methods Enzymol. 114:167‐176. doi: 10.1016/0076‐6879(85)14017‐6.
  Hura, G.L., Budworth, H., Dyer, K.N., Rambo, R.P., Hammel, M., McMurray, C.T., and Tainer, J.A. 2013. Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat. Methods 10:453‐454. doi: 10.1038/nmeth.2453.
  Jancarik, J. and Kim, S.‐H. 1991. Sparse matrix sampling: A screening method for crystallization of proteins. J. Appl. Cryst. 24:409‐411. doi: 10.1107/S0021889891004430.
  Johnson, C.H., Egli, M., and Stewart, P.L. 2008. Structural insights into a circadian oscillator. Science 322:697‐701. doi: 10.1126/science.1150451.
  Kang, Y., Zhou, X.E., Gao, X., He, Y., Liu, W., Ishchenko, A., Barty, A., White, T.A., Yefanov, O., Han, G.W., Xu, Q., de Waal, P.W., Ke, J., Tan, M.H., Zhang, C., Moeller, A., West, G.M., Pascal, B.D., Van Eps, N., Caro, L.N., Vishnivetskiy, S.A., Lee, R.J., Suino‐Powell, K.M., Gu, X., Pal, K., Ma, J., Zhi, X., Boutet, S,. Williams, G.J., Messerschmidt, M., Gati, C., Zatsepin, N.A., Wang, D., James, D., Basu, S., Roy‐Chowdhury, S., Conrad, C.E., Coe, J., Liu, H., Lisova, S., Kupitz, C., Grotjohann, I., Fromme, R., Jiang, Y., Tan, M., Yang, H., Li, J., Wang, M., Zheng, Z., Li, D., Howe, N., Zhao, Y., Standfuss, J., Diederichs, K., Dong, Y., Potter, C.S., Carragher, B., Caffrey, M., Jiang, H., Chapman, H.N., Spence, J.C., Fromme, P., Weierstall, U., Ernst, O.P., Katritch, V., Gurevich, V.V., Griffin, P.R., Hubbell, W.L., Stevens, R.C., Cherezov, V., Melcher, K., and Xu, H.E. 2015. Crystal structure of rhodopsin bound to arrestin by femtosecond X‐ray laser. Nature 523:561‐567. doi: 10.1038/nature14656.
  Kato, T., Goodman, R.P., Erben, C.M., Turberfield, A.J., and Namba, K. 2009. High‐resolution structural analysis of a DNA nanostructure by cryoEM. Nano Lett. 9:2747‐2750. doi: 10.1021/nl901265n.
  Keel, A.Y., Rambo, R.P., Batey, R.T., and Kieft, J.S. 2007. A general strategy to solve the phase problem in RNA crystallography. Structure 15:761‐772. doi: 10.1016/j.str.2007.06.003.
  Keeler, J. 2011. Understanding NMR Spectroscopy, 2nd edition. John Wiley & Sons, Hoboken, N.J.
  Kemp, M. 2003. The Mona Lisa of modern science. Nature 421:416‐420. doi: 10.1038/nature01403.
  Kim, S.‐H., Shin, W.‐C., and Warrant, R.W. 1985. Heavy metal ion‐nucleic acid interaction. Methods Enzymol. 114:156‐167. doi: 10.1016/0076‐6879(85)14016‐4.
  Konermann, L., Pan, J., and Liu, Y.H. 2011. Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem. Soc. Rev. 40:1224‐1234. doi: 10.1039/C0CS00113A.
  Leal, R.M.F., Callow, S., Callow, P., Blakeley, M.P., Cardin, C.J., Denny, W.A., Teixeira, S.C.M., Mitchell, E.P., and Forsyth, V.T. 2010. Combined neutron and X‐ray diffraction studies of DNA in crystals and solution. Acta Cryst. D 66:1244‐1248. doi: 10.1107/S0907444910017713.
  Lei, L. and Egli, M. 2016. In situ proteolysis for crystallization of membrane‐bound cytochrome P450 17A1 and 17A2 proteins from zebrafish. Curr. Protoc. Protein Sci. In press. doi: 10.1002/0471140864.ps2916s84.
  Lilley, D.M.J. and Wilson, T.J. 2000. Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr. Opin. Chem. Biol. 4:507‐517. doi: 10.1016/S1367‐5931(00)00124‐1.
  Liu, H., Jin, L., Koh, S.B., Atanasov, I., Schein, S., and Zhou, Z.H. 2010. Atomic structure of human adenovirus by cryo‐EM reveals interactions among protein networks. Science 329:1038‐1043. doi: 10.1126/science.1187433.
  Lovell, S.C., Davis, I.W., Arendall, W.B.III, de Bakker, P.I.W., Word, J.M., Prisant, M.G., Richardson, J.S., and Richardson, D.C. 2003. Structure validation by C alpha geometry: 18 phi, psi and C beta deviation. Proteins Struct. Funct. Genet. 50:437‐450. doi: 10.1002/prot.10286.
  Mchaourab, H.S., Steed, P.R., and Kazmier, K. 2011. Toward the fourth dimension of membrane protein structure: Insight into dynamics from spin‐labeling EPR spectroscopy. Structure 19:1549‐1561. doi: 10.1016/j.str.2011.10.009.
  McPherson, A. 1998. Crystallization of Biological Macromolecules. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  McRee, D.E. 1999. Practical Protein Crystallography, 2nd edition. Academic Press, San Diego.
  McSweeney, S. 2014. Sophisticated synchrotrons. Nature 505:620‐621. doi: 10.1038/505620a.
  Milligan, J.F. and Uhlenbeck, O.C. 1989. Synthesis of small RNAs using T7 RNA‐polymerase. Methods Enzymol. 180:51‐62. doi: 10.1016/0076‐6879(89)80091‐6.
  Moffat, K. 2014. Time‐resolved crystallography and protein design: Signalling photoreceptors and optogenetics. Phil. Trans. R. Soc. B 369:20130568. doi: 10.1098/rstb.2013.0568.
  Murshudov, G.N., Vagin, A.A., and Dodson, E.J. 1999. Refinement of macromolecular structures by the maximum‐likelihood method. Acta Cryst. D 53:240‐255. doi: 10.1107/S0907444996012255.
  Narayanan, B.C., Westbrook, J., Ghosh, S., Petrov, A.I., Sweeney, B., Zirbel, C.L., Leontis, N.B., and Berman, H.M. 2013 The nucleic acid database: New features and capabilities. Nucleic Acids Res. 42: D114‐D122. doi: 10.1093/nar/gkt980.
  Pallan, P.S. and Egli, M. 2007a. Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures. Nat. Protocols 2:640‐646. doi: 10.1038/nprot.2007.74.
  Pallan, P.S. and Egli, M. 2007b. Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2′‐SeMe‐uridine for crystallographic phasing of nucleic acid structures. Nat. Protocols 2:647‐651. doi: 10.1038/nprot.2007.75.
  Pallan, P.S., Wang, X., Lei, L., Yoshimoto, F.K., Auchus, R.J., Waterman, M.R., Guengerich, F.P., and Egli, M. 2015. Human cytochrome P450 21A2, the major steroid 21‐hydroxylase. Structure of the enzyme‐progesterone substrate complex and rate‐limiting C‐H bond cleavage. J. Biol. Chem. 290:13128‐13143. doi: 10.1074/jbc.M115.646307.
  Pattanayek, R. and Egli, M. 2015. Protein‐protein interactions in the cyanobacterial circadian clock: Structure of KaiA dimer in complex with C‐terminal KaiC peptides at 2.8 Å resolution. Biochemistry 54:4575‐4578. doi: 10.1021/acs.biochem.5b00694.
  Pattanayek, R., Williams, D.R., Rossi, G., Weigand, S., Mori, T., Johnson, C.H., Stewart, P.L., and Egli, M. 2011. Combined SAXS/EM based models of the S. elongatus post‐translational circadian oscillator and its interactions with the output His‐kinase SasA. PLoS One 6:e23697. doi: 10.1371/journal.pone.0023697.
  Petsko, G.A. 1985. Preparation of isomorphous heavy‐atom derivatives. Methods Enzymol. 114:147‐156. doi: 10.1016/0076‐6879(85)14015‐2.
  Pitsch, S., Weiss, P.A., Jenny, L., Stutz, A., and Wu, X. 2001. Reliable chemical synthesis of oligoribonucleotides (RNA) with 2′‐O‐[(triisopropylsilyl)oxy]methyl(2′‐O‐tom)‐protected phosphoramidites. Helv. Chim. Acta 84:3773‐3795. doi: 10.1002/1522‐2675 (20011219)84:12<3773::AID‐HLCA3773>3.0.CO;2‐E.
  Potrzebowski, W. and André, I. 2015. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement. Nat. Methods 12:697‐684. doi: 10.1038/nmeth.3399.
  Putnam, C.D., Hammel, M., Hura, G.L., and Tainer, J.A. 2007. X‐ray solution scattering (SAXS) combined with crystallography and computation: Defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 40:191‐285. doi: 10.1017/S0033583507004635.
  Radaev, S. and Sun, P.D. 2002. Crystallization of protein‐protein complexes. J. Appl. Cryst. 35:674‐676. doi: 10.1107/S0021889802013973.
  Rasmussen, S.G., 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., Weis, W.I., and Kobilka, B.K. 2007. Crystal structure of the human β2 adrenergic G‐protein‐coupled receptor. Nature 450:383‐387. doi: 10.1038/nature06325.
  Reddy, V.S., Natchiar, S.K., Stewart, P.L., and Nemerov, G.R. 2010. Crystal structure of human adenovirus at 3.5 Å resolution. Science 329:1071‐1075. doi: 10.1126/science.1187292.
  Reddy, V.S. and Nemerow, G.R. 2014. Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection. Proc. Natl. Acad. Sci. U.S.A. 111:11715‐11720. doi: 10.1073/pnas.1408462111.
  Rhodes, G. 2006. Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, 3rd edition. Academic Press, San Diego.
  Ringe, D. and Petsko, G.A. 1996. A consumer's guide to protein crystallography. In Protein Engineering and Design (P.R. Carey, ed.) pp. 205‐229. Academic Press, San Diego.
  Rodriguez, J.A., Ivanova, M., Sawaya, M.R., Cascio, D., Reyes, F., Shi, D., Johnson, L., Guenther, E., Sangwan, S., Hattne, J., Nannenga, B., Brewster, A.S., Messerschmidt, M., Boutet, S., Sauter, N.K., Gonen, T., and Eisenberg, D.S. 2015. Structure of the amyloid forming segment, GAVVTGVTAVA, from the NAC domain of Parkinson's disease protein α‐synuclein, residues 68‐78, determined by electron diffraction. Nature 525:486‐490. doi: 10.1038/nature15368.
  Romainczyk, O., Elduque, X., and Engels, J.W. 2012. Attachment of nitroxide spin labels to nucleic acids for EPR. Curr. Protoc. Nucleic Acid Chem. 49:7.17.1‐7.17.40. doi: 10.1002/0471142700.nc0717s49.
  Rose, P.W., Prlic, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J.D., Woo, J., Young, J., Zardecki, C., Berman, H.M., Bourne, P.E., and Burley, S.K. 2015. The RCSB Protein Data Bank: Views of structural biology for basic and applied research and education. Nucleic Acids Res. 43:D345‐D356. doi: 10.1093/nar/gku1214.
  Rould, M.A. 1997. Screening for heavy‐atom derivatives and obtaining accurate isomorphous differences. Methods Enzymol. 276:461‐472. doi: 10.1016/S0076‐6879(97)76072‐5.
  Rupp, B. 2010. Biomolecular Crystallography, 1st Edition. Garland Science, New York.
  Saibil, H.R. 2000. Macromolecular structure determination by cryo‐electron microscopy. Acta Cryst. D 56:1215‐1222. doi: 10.1107/S0907444900010787.
  Scaringe, S.A., Francklyn, C., and Usman, N. 1990. Chemical synthesis of biologically active oligoribonucleotides using β‐cyanoethyl protected ribonucleoside phosphoramidites. Nucleic Acids Res. 18:5433‐5441. doi: 10.1093/nar/18.18.5433.
  Scaringe, S.A., Wincott, F.E., and Caruthers, M.H. 1998. Novel RNA synthesis method using 5′‐silyl‐2′‐orthoester protecting groups. J. Am. Chem. Soc. 120:11820‐11821. doi: 10.1021/ja980730v.
  Schneidman‐Duhovny, D., Rossi, A., Avila‐Sakar, A., Kim, S.J., Velazquez‐Muriel, J., Strop, P., Liang, H., Krukenberg, K.A., Liao, M., Kim, H.M., Sobhanifar, S., Dötsch, V., Rajpal, A., Pons, J., Agard, D.A., Cheng, Y., and Sali, A. 2012. A method for integrative structure determination of protein‐protein complexes. Bioinformatics 28:3282‐3289. doi: 10.1093/bioinformatics/bts628.
  Schuler, B. and Eaton, W.A. 2008. Protein folding studied by single‐molecule FRET. Curr. Opin. Struct. Biol. 18:16‐26. doi: 10.1016/j.sbi.2007.12.003.
  Scott, W.G., Finch, J.T., Grenfell, R., Fogg, J., Smith, T., Gait, M.J., and Klug, A. 1995. Rapid crystallization of chemically synthesized hammerhead RNAs using a double screening procedure. J. Mol. Biol. 250:327‐332. doi: 10.1006/jmbi.1995.0380.
  Sheldrick, G.M. 2010. Experimental phasing with SHELXC/D/E: Combining chain tracing with density modification. Acta Cryst. D 66:479‐485. doi: 10.1107/S0907444909038360.
  Smyth, D.R., Mrozkiewicz, M.K., McGrath, W.J., Listwan, P., and Kobe, B. 2003. Crystal structures of fusion proteins with large‐affinity tags. Protein Sci. 12:1313‐1322. doi: 10.1110/ps.0243403.
  Southworth, D.R. and Agard, D.A. 2011. Client‐loading conformation of the Hsp90 molecular chaperone revealed in the cryo‐EM structure of the human Hsp90:Hop complex. Mol. Cell 42:771‐781. doi: 10.1016/j.molcel.2011.04.023.
  Spence, J.C.H. 2014. X‐ray lasers and crystallography. IUCrJ 1:151‐152. doi: 10.1107/S2052252514009567.
  Szulik, M.W., Voehler, M., and Stone, M.P. 2014. NMR analysis of base‐pair opening kinetics in DNA. Curr. Protoc. Nucleic Acid. Chem. 59:7.20.1‐7.20.18. doi: 10.1002/0471142700.nc0720s59.
  Structural Genomics Consortia. 2008. Protein production and purification. Nat. Methods 5:135‐146. doi: 10.1038/nmeth.f.202.
  Tereshko, V., Wilds, C.J., Minasov, G., Prakash, T.P., Maier, M.A., Howard, A., Wawrzak, Z., Manoharan, M., and Egli, M. 2001. Detection of alkali metal ions in DNA crystals using state‐of‐the‐art X‐ray diffraction experiments. Nucleic Acids Res. 29:1208‐1215. doi: 10.1093/nar/29.5.1208.
  Terwilliger, T.C. and Berendzen, J. 1999. Automated MAD and MIR structure solution. Acta Cryst. D 55:849‐861. doi: 10.1107/S0907444999000839.
  Terwilliger, T.C., Stuart, D., and Yokoyama, S. 2009. Lessons from structural genomics. Annu. Rev. Biophys. 38:371‐383. doi: 10.1146/annurev.biophys.050708.133740.
  Tsuruta, H. and Irving, T.C. 2008. Experimental approaches for solution X‐ray scattering and fiber diffraction. Curr. Opin. Struct. Biol. 18:601‐608. doi: 10.1016/j.sbi.2008.08.002.
  Weeks, C.M., Adams, P.D., Berendzen, J., Brunger, A.T., Dodson, E.J., Grosse‐Kunstleve, R.W., Schneider, T.R., Sheldrick, G.M., Terwilliger, T.C., Turkenburg, M.G., and Uson, I. 2003. Automatic solution of heavy‐atom substructures. Methods Enzymol. 374:37‐83. doi: 10.1016/S0076‐6879(03)74003‐8.
  Wilds, C.J., Pattanayek, R., Pan, C., Wawrzak, Z., and Egli, M. 2002. Selenium‐assisted nucleic acid crystallography: Use of DNA phosphoroselenoates for MAD phasing. J. Am. Chem. Soc. 124:14910‐14916. doi: 10.1021/ja021058b.
  Wilkins, S.W. 2013. Celebrating 100 years of X‐ray crystallography. Acta Cryst. A 69:1‐4. doi: 10.1107/S0108767312048490.
  Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S., and Usman, N. 1995. Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res. 23:2677‐2684. doi: 10.1093/nar/23.14.2677.
  Woolfson, M.M. 1997. An Introduction to X‐ray Crystallography, 2nd edition. Cambridge University Press, Cambridge, UK.
  Wüthrich, K. 1986. NMR of Proteins and Nucleic Acids, 1st edition. John Wiley & Sons, New York.
  Wyatt, J.R., Chastain, M., and Puglisi, J.D. 1991. Synthesis and purification of large amounts of RNA oligonucleotides. BioTechniques 11:764‐769.
  Zauberman, N., Mutsafi, Y., Ben Halevy, D., Shimoni, E., Klein, E., Xiao, C., Sun, S., and Minsky, A. 2008. Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus. PLoS Biol. 6:e114. doi: 10.1371/journal.pbio.0060114.
  Zhou, Z.H. 2008. Towards atomic resolution structural determination by single‐particle cryo‐electron microscopy. Curr. Opin. Struct. Biol. 18:218‐228. doi: 10.1016/j.sbi.2008.03.004.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library