International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 19.3, pp. 428-437   | 1 | 2 |
https://doi.org/10.1107/97809553602060000700

Chapter 19.3. Small-angle X-ray scattering

H. Tsurutaa and J. E. Johnsonb*

a SSRL/SLAC & Department of Chemistry, Stanford University, PO Box 4349, MS69, Stanford, California 94309-0210, USA, and bDepartment of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
Correspondence e-mail:  jackj@scripps.edu

References

First citation Arai, M., Ikura, T., Semisotnov, G. V., Kihara, H., Amemiya, Y. & Kuwajima, K. (1998). Kinetic refolding of β-lactoglobulin. Studies by synchrotron X-ray scattering, and circular dichroism, absorption and fluorescence spectroscopy. J. Mol. Biol. 275, 149–162.Google Scholar
 First citation Bonneté, F., Malfois, M., Finet, S., Tardieu, A., Lafont, S. & Veesler, S. (1997). Different tools to study interaction potentials in γ-crystallin solutions: relevance to crystal growth. Acta Cryst. D53, 438–447.Google Scholar
 First citation Boulin, C. J., Kempf, A., Gabriel, A. & Koch, M. H. J. (1988). Data acquisition systems for linear and area X-ray detectors using delay line readout. Nucl. Instrum. Methods Phys. Res. A, 269, 312–320.Google Scholar
 First citation Bu, Z., Perlo, A., Johnson, G. E., Olack, G., Engelman, D. M. & Wyckoff, H. W. (1998). A small-angle X-ray scattering apparatus for studying biological macromolecules in solution. J. Appl. Cryst. 31, 533–543.Google Scholar
 First citation Chacón, P., Morán, F., Díaz, J. F., Pantos, E. & Andreu, J. M. (1998). Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys. J. 74, 2760–2775.Google Scholar
 First citation Chen, L., Hodgson, K. O. & Doniach, S. (1996). A lysozyme folding intermediate revealed by solution X-ray scattering. J. Mol. Biol. 261, 658–671.Google Scholar
 First citation Chen, L., Wildegger, G., Kiefhaber, T., Hodgson, K. O. & Doniach, S. (1998). Kinetics of lysozyme refolding: structural characterization of a non-specifically collapsed state using time-resolved X-ray scattering. J. Mol. Biol. 276, 225–237.Google Scholar
 First citation Cipriani, F., Gabriel, A. & Koch, M. H. J. (1994). Alternative approaches to delay line readout for multiwire proportional chambers. Nucl. Instrum. Methods A, 346, 286–291.Google Scholar
 First citation Czeslik, C., Malessa, R., Winter, R. & Rapp, G. (1996). High pressure synchrotron X-ray diffraction studies of biological molecules using the diamond anvil technique. Nucl. Instrum. Methods Phys. Res. A, 368, 847–851.Google Scholar
 First citation Dubuisson, J.-M., Decamps, T. & Vachette, P. (1997). Improved signal-to-background ratio in small-angle X-ray scattering experiments with synchrotron radiation using an evacuated cell for solutions. J. Appl. Cryst. 30, 49–54.Google Scholar
 First citation Feigin, L. A. & Svergun, D. I. (1987). Structure analysis by small-angle X-ray and neutron scattering. New York: Plenum Press.Google Scholar
 First citation Genick, U., Borgstahl, G. E. O., Ng, K., Ren, Z., Pradervand, C., Burke, P. M., Srajer, V., Teng, T.-Y., Schildkamp, W., McRee, D. E., Moffat, K. & Getzoff, E. D. (1997). Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science, 275, 1471–1475.Google Scholar
 First citation Glatter, O. (2004). X-ray techniques. In International tables for crystallography, Vol. C. Mathematical, physical and chemical tables, edited by E. Prince, Section 2.6.1. Dordrecht: Kluwer Academic Publishers.Google Scholar
 First citation Glatter, O. & Kratky, O. (1982). Editors. Small angle X-ray scattering. London: Academic Press.Google Scholar
 First citation Griffith, J. P., Griffith, D. L., Rayment, I., Murakami, W. T. & Caspar, D. L. D. (1992). Inside polyomavirus at 25-Å resolution. Nature (London), 355, 652–654.Google Scholar
 First citation Grossman, J. G., Hasnain, S. S., Yousafzai, F. K., Smith, B. E. & Eady, R. R. (1997). The first glimpse of a complex of nitrogenase component proteins by solution X-ray scattering: conformation of the electron transfer transition state complex of Klebsiella pneumonia nitrogenase. J. Mol. Biol. 266, 642–648.Google Scholar
 First citation Guinier, A. & Fournet, G. (1955). Small-angle scattering of X-rays. New York: John Wiley & Sons.Google Scholar
 First citation Harrison, S. C. (1969). Structure of tomato bushy stunt virus. I. The spherically averaged electron density. J. Mol. Biol. 42, 457–483.Google Scholar
 First citation Heidorn, D. B. & Trewhella, J. (1988). Comparison of the crystal and solution structures of calmodulin and troponin C. Biochemistry, 27, 909–915.Google Scholar
 First citation Henderson, S. J. (1995). Comparison of parasitic scattering from window materials used for small-angle X-ray scattering: a better beryllium window. J. Appl. Cryst. 28, 820–826.Google Scholar
 First citation Hiragi, Y., Nakatani, H., Kajiwara, K., Inoue, H., Sano, Y. & Kataoka, M. (1988). Temperature-jump apparatus and measuring system for synchrotron solution X-ray scattering experiments. Rev. Sci. Instrum. 59, 64–66.Google Scholar
 First citation Improta, S., Krueger, J. K., Gautel, M., Atkinson, R. A., Lefevre, J. F., Moulton, S., Trewhella, J. & Pastore, A. (1998). The assembly of immunoglobulin-like modules in titin: implications for muscle elasticity. J Mol. Biol. 284, 761–777.Google Scholar
 First citation Inouye, H., Tsuruta, H., Sedzik, J., Uyemura, K. & Kirschner, D. A. (1999). Tetrameric assembly of full-sequence protein zero myelin glycoprotein by synchrotron X-ray scattering. Biophys. J. 76, 423–437.Google Scholar
 First citation Jack, A. & Harrison, S. C. (1975). On the interpretation of small-angle X-ray solution scattering from spherical viruses. J. Mol. Biol. 99, 15–25.Google Scholar
 First citation Johnson, J. E. & Hollingshead, C. (1981). Crystallographic studies of cowpea mosaic virus by electron microscopy and X-ray diffraction. J. Ultrastruct. Res. 74, 223–231.Google Scholar
 First citation Kataoka, M., Head, J. F., Seaton, B. A. & Engelman, D. M. (1989). Melittin binding causes a large calcium-dependent conformational change in calmodulin. Proc. Natl Acad. Sci. USA, 86, 6944–6948.Google Scholar
 First citation Kihara, H. (1994). Stopped-flow apparatus for X-ray scattering and XAFS. J. Synchrotron Rad. 1, 74–77.Google Scholar
 First citation Koch, M. H. J. (1988). Instruments and methods for small-angle scattering with synchrotron radiation. Makromol. Chem. Macromol. Symp. 15, 79–90.Google Scholar
 First citation Koch, M. H. J. (1991). Scattering from non-crystalline systems. In Handbook on synchrotron radiation, Vol. 4, edited by S. Ebashi, M. Koch & E. Rubenstein. Amsterdam: Elsevier Science Publishers.Google Scholar
 First citation Koch, M. H. J. & Svergun, D. I. (1992). Unpublished result.Google Scholar
 First citation König, S., Svergun, D., Koch, M. H. J., Höbner, G. & Schellenberger, A. (1992). Synchrotron radiation solution X-ray scattering study of the pH dependence of the quaternary structure of yeast pyruvate decarboxylase. Biochemistry, 31, 8726–8731.Google Scholar
 First citation Kozin, M. B., Volkov, V. V. & Svergun, D. I. (1997). ASSA, a program for three-dimensional rendering in solution scattering from biopolymers. J. Appl. Cryst. 30, 811–815.Google Scholar
 First citation Krueger, J. K., Glah, G. A., Rokop, S. E., Zhi, G., Stull, J. T. & Trewhella, J. (1997). Structures of calmodulin and a functional myosin light chain kinase in the activated complex: a neutron scattering study. Biochemistry, 36, 6017–6023.Google Scholar
 First citation Lattman, E. E. (1989). Rapid calculation of the solution scattering profile from a macromolecule of known structure. Protein Struct. Funct. Genet. 5, 149–155.Google Scholar
 First citation Mandelkow, E., Lange, G. & Mandelkow, E. M. (1989). Applications of synchrotron radiation to the study of biopolymers in solution time-resolved X-ray scattering of microtubule self-assembly and oscillations. Top. Curr. Chem. 151, 2–30.Google Scholar
 First citation Miller, S. T., Genova, J. D. & Hogle, J. M. (1999). Collection of very low resolution protein data. J. Appl. Cryst. 32, 1183–1185.Google Scholar
 First citation Moffat, K. (1997). Laue diffraction. Methods Enzymol. 277, 433–447.Google Scholar
 First citation Moore, P. B. (1980). Small-angle scattering. Information content and error analysis. J. Appl. Cryst. 13, 168–175.Google Scholar
 First citation Mourey, L., Pédelacq, J.-D., Fabre, C., Causse, H., Rougé, P. & Samama, J.-P. (1997). Small-angle X-ray scattering and crystallographic studies of arcelin-1: an insecticidal lectin-like glycoprotein from Phaseolus vulgaris L. Proteins, 29, 433–442.Google Scholar
 First citation Olah, G. A., Gray, D. M., Gray, C. W., Kergil, D. L., Sosnick, T. R., Mark, B. L., Vaughan, M. R. & Trewhella, J. (1995). Structures of fd gene 5 protein–nucleic acid complexes: a combined solution scattering and electron microscopy study. J. Mol. Biol. 249, 576–594.Google Scholar
 First citation Petitpas, I., Lepault, J., Vachette, P., Charpilienne, A., Mathieu, M., Kohli, E., Pothier, P., Cohen, J. & Reyl, F. A. (1998). Crystallization and preliminary X-ray analysis of rotavirus protein VP6. J. Virol. 72, 7615–7619.Google Scholar
 First citation Petrascu, A.-M., Koch, M. H. J. & Gabriel, A. (1998). A beginners' guide to gas-filled proportional detectors with delay line readout. J. Macromol. Sci. Phys. B37, 463–483.Google Scholar
 First citation Pilz, I., Glatter, O. & Kratky, O. (1979). Small-angle X-ray scattering. Methods Enzymol. 61, 148–249.Google Scholar
 First citation Pollack, L., Tate, M. W., Darnton, N. C., Knight, J. B., Gruner, S. M., Eaton, W. A. & Austin, R. H. (1999). Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle X-ray scattering. Proc. Natl Acad. Sci. USA, 96, 10115–10117.Google Scholar
 First citation Potschka, M., Koch, M. H. J., Adams, M. L. & Schuster, T. M. (1988). Time-resolved solution X-ray scattering of tobacco mosaic virus coat protein: kinetics and structure of intermediates. Biochemistry, 27, 8481–8491.Google Scholar
 First citation Schindelin, H., Kisker, C., Schlessman, J. L., Howard, J. B. & Rees, D. C. (1997). Structure of ADP. AIF-4-stabilized nitrogenase complex and its implications for signal transduction. Nature (London), 387, 370–376.Google Scholar
 First citation Schmidt, T., Johnson, J. E. & Phillips, W. (1983). The spherically averaged structures of cowpea mosaic virus components by X-ray solution scattering. Virology, 127, 65–73.Google Scholar
 First citation Schuster, M. & Göbel, H. (1995). Parallel-beam coupling into channel-cut monochromators using curved graded multilayers. J. Phys. D, 28, A270–A275.Google Scholar
 First citation Seaton, B. A., Head, J. F., Engelman, D. M. & Richards, F. M. (1985). Calcium-induced increase in the radius of gyration and maximum dimension of calmodulin measured by small-angle X-ray scattering. Biochemistry, 24, 6740–6743.Google Scholar
 First citation Sousa, M. C. & McKay, D. B. (1998). The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change. Biochemistry, 37, 15392–15399.Google Scholar
 First citation Srajer, V., Teng, T.-Y., Ursby, T., Pradervand, C., Ren, Z., Adachi, S., Bourgeois, D., Wulff, M. & Moffat, K. (1996). Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography [see Comments]. Science, 274, 1726.Google Scholar
 First citation Stuhrmann, H. B. (1970). Interpretation of small-angle scattering functions of dilute solutions and gases. A representation of the structures related to a one-particle-scattering function. Acta Cryst. A26, 297–306.Google Scholar
 First citation Sunnerhagen, M., Olah, G. A., Stenflo, J., Forsen, S., Drakenberg, T. & Trewhella, J. (1996). The relative orientation of Gla and EGF domains in coagulation factor X is altered by Ca-2+ binding to the first EGF domain. A combined NMR–small angle X-ray scattering study. Biochemistry, 35, 11547–11559.Google Scholar
 First citation Svergun, D. I. (1992). Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Cryst. 25, 495–503.Google Scholar
 First citation Svergun, D. I. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76, 2879–2886.Google Scholar
 First citation Svergun, D. I., Aldag, I., Sieck, T., Altendorf, K., Koch, M. H. J., Kane, D. J., Kozin, M. B. & Grueber, G. (1998). A model of the quaternary structure of the Escherichia coli F1 ATPase from X-ray solution scattering and evidence for structural changes in the Delta subunit during ATP hydrolysis. Biophys. J. 75, 2212–2219. Google Scholar
 First citation Svergun, D. I., Barberato, C. & Koch, M. H. J. (1995). CRYSOL – a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Cryst. 28, 768–773.Google Scholar
 First citation Svergun, D. I., Barberato, C., Koch, M. H. J., Fetler, L. & Vachette, P. (1997). Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins Struct. Funct. Genet. 27, 110–117.Google Scholar
 First citation Svergun, D. I., Koch, M. H. & Serdyuk, I. N. (1994). Structural model of the 50 S subunit of Escherichia coli ribosomes from solution scattering. I. X-ray synchrotron radiation study. J. Mol. Biol. 240, 66–77.Google Scholar
 First citation Svergun, D. I., Konrad, S., Huss, M., Koch, M. H. J., Wieczorek, H., Altendorf, K., Volkov, V. V. & Grueber, G. (1998). Quaternary structure of V1 and F1 ATPase: significance of structural homologies and diversities. Biochemistry, 37, 17659–17663. Google Scholar
 First citation Svergun, D. I., Richard, S., Koch, M. H. J., Sayers, Z., Kuprin, S. & Zaccai, G. (1998). Protein hydration in solution: experimental observation by X-ray and neutron scattering. Proc. Natl Acad. Sci. USA, 95, 2267–2272. Google Scholar
 First citation Svergun, D. I., Volkov, V. V., Kozin, M. B. & Stuhrmann, H. B. (1996). New developments in direct shape determination from small-angle scattering. 2. Uniqueness. Acta Cryst. A52, 419–426.Google Scholar
 First citation Svergun, D. I., Volkov, V. V., Kozin, M. B., Stuhrmann, H. B., Barberato, C. & Koch, M. H. J. (1997). Shape determination from solution scattering of biopolymers. J. Appl. Cryst. 30, 798–802.Google Scholar
 First citation Thuman-Commike, P. A., Tsuruta, H., Greene, B., Prevelige, P. E., King, J. & Chiu, W. (1999). Solution X-ray scattering based estimation of electron cryomicroscopy imaging parameters for reconstruction of virus particles. Biophys. J. 76, 2249–2261.Google Scholar
 First citation Trewhella, J. (1998). Insights into biomolecular function from small-angle scattering. Curr. Opin. Struct. Biol. 7, 702–708.Google Scholar
 First citation Tsuruta, H., Reddy, V., Wikoff, W. & Johnson, J. (1998). Imaging RNA and dynamic protein segments with low resolution virus crystallography; experimental design, data processing and implications of electron density maps. J. Mol. Biol. 284, 1439–1452.Google Scholar
 First citation Tsuruta, H., Vachette, P., Sano, T., Moody, M. F., Amemiya, Y., Wakabayashi, K. & Kihara, H. (1994). Kinetics of the quaternary structure change of aspartate transcarbamylase triggered by succinate, a competitive inhibitor. Biochemistry, 33, 10007–10012.Google Scholar
 First citation Uversky, V. N., Segel, D. J., Doniach, S. & Fink, A. L. (1998). Association-induced folding of globular proteins. Proc. Natl Acad. Sci. USA, 95, 5480–5483.Google Scholar
 First citation Wang, J., Harting, J. A. & Flanagan, J. M. (1997). The structure of ClpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis. Cell, 91, 447–456.Google Scholar
 First citation Weik, M., Ravelli, R. B. G., Kryger, G., McSweeney, S., Raves, M. L., Harel, M., Gros, P., Silman, I., Kroon, J. & Sussman, J. L. (2000). Specific chemical and structural damage to proteins produced by synchrotron radiation. Proc. Natl Acad. Sci. USA, 97, 623–628.Google Scholar
 First citation Wikoff, W., Duda, R., Hendrix, R. & Johnson, J. (1998). Crystallization and preliminary X-ray analysis of the dsDNA bacteriophage HK97 mature empty capsid. Virology, 243, 113–118.Google Scholar
 First citation Wilbanks, S. M., Chen, L., Tsuruta, H., Hodgson, K. O. & McKay, D. B. (1995). Solution small-angle X-ray scattering study of the molecular chaperone Hsc70 and its subfragments. Biochemistry, 34, 12095–12106.Google Scholar
 First citation Yamashita, M. M., Almassy, R. J., Janson, C. A., Cascio, D. & Eisenberg, D. (1989). Refined atomic model of glutamine synthetase at 3.5 Å resolution. J. Biol. Chem. 264, 17681–17690.Google Scholar
 First citation Zheng, Y., Doerschuk, P. C. & Johnson, J. E. (1995). Determination of three-dimensional low-resolution viral structure from solution X-ray scattering data. Biophys. J. 69, 619–639.Google Scholar