MAD and MIR

Smith, J. L.; Hendrickson, W. A.; Terwilliger, T. C.; Berendzen, J.

doi:10.1107/97809553602060000686

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

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International Tables for Crystallography (2006). Vol. F. ch. 14.2, pp. 299-309 | 1 | 2 |
https://doi.org/10.1107/97809553602060000686

Chapter 14.2. MAD and MIR

J. L. Smith,^a W. A. Hendrickson,^b T. C. Terwilliger^c and J. Berendzen^d

^aDepartment of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA, ^bDepartment of Biochemistry, College of Physicians & Surgeons of Columbia University, 630 West 168th Street, New York, NY 10032, USA, ^cBioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA, and ^dBiophysics Group, Mail Stop D454, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

References

Abrahams, J. P., Leslie, A. G. W., Lutter, R. & Walker, J. E. (1994). Structure at 2.8-angstrom resolution of f1-ATPase from bovine heart-mitochondria. Nature (London), 370, 621–628.Google Scholar

Als-Nielsen, J. & McMorrow, D. F. (2001). Elements of modern X-ray physics. New York: John Wiley & Sons.Google Scholar

Baker, D., Krukowski, A. E. & Agard, D. A. (1993). Uniqueness and the ab initio phase problem in macromolecular crystallography. Acta Cryst. D49, 186–192.Google Scholar

Bellizzi, J. J. III, Widom, J., Kemp, C. W. & Clardy, J. (1999). Producing selenomethionine-labeled proteins with a baculovirus expression vector system. Structure, 7, R263–R267.Google Scholar

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein data bank: computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.Google Scholar

Bijvoet, J. M. (1949). Phase determination in direct Fourier-synthesis of crystal structures. Proc. Acad. Sci. Amst. B52, 313–314.Google Scholar

Blow, D. M. (1958). The structure of haemoglobin. VII. Determination of phase angles in the non-centrosymmetric [100] zone. Proc. R. Soc. London Ser. A, 247, 302–335.Google Scholar

Blundell, T. L. & Johnson, L. N. (1976). Protein crystallography. p. 368. New York: Academic Press.Google Scholar

Burling, F. T., Weis, W. I., Flaherty, K. M. & Brünger, A. T. (1996). Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science, 271, 72–77.Google Scholar

Chang, G. & Lewis, M. (1994). Using genetic algorithms for solving heavy-atom sites. Acta Cryst. D50, 667–674.Google Scholar

Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.Google Scholar

Crick, F. H. C. & Magdoff, B. S. (1956). The theory of the method of isomorphous replacement for protein crystals. I. Acta Cryst. 9, 901–908.Google Scholar

Cromer, D. T. & Liberman, D. (1970a). Relativistic calculation of anomalous scattering factors for X-rays. J. Chem. Phys. 53, 1891–1898.Google Scholar

Cromer, D. T. & Liberman, D. (1970b). Relativistic calculation of anomalous scattering factors for X-rays. Report LA-4403. Los Alamos National Laboratory, USA.Google Scholar

Dickerson, R. E., Kendrew, J. C. & Strandberg, B. E. (1961). The crystal structure of myoglobin: phase determination to a resolution of 2 Å by the method of isomorphous replacement. Acta Cryst. 14, 1188–1195.Google Scholar

Doublié, S. (1997). Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276, 523–530.Google Scholar

Fanchon, E. & Hendrickson, W. A. (1990). Effect of the anisotropy of anomalous scattering on the MAD phasing method. Acta Cryst. A46, 809–820.Google Scholar

Goldstein, A. & Zhang, K. Y. J. (1998). The two-dimensional histogram as a constraint for protein phase improvement. Acta Cryst. D54, 1230–1244.Google Scholar

Hendrickson, W. A. (1985). Analysis of protein structure from diffraction measurement at multiple wavelengths. Trans. Am. Crystallogr. Assoc. 21, 11–21.Google Scholar

Hendrickson, W. A., Horton, J. R. & 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.Google Scholar

Hendrickson, W. A. & Lattman, E. E. (1970). Representation of phase probability distributions for simplified combination of independent phase information. Acta Cryst. B26, 136–143.Google Scholar

Hendrickson, W. A. & Ogata, C. M. (1997). Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. 276, 494–523.Google Scholar

Hendrickson, W. A., Smith, J. L., Phizackerley, R. P. & Merritt, E. A. (1988). Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. Proteins Struct. Funct. Genet. 4, 77–88.Google Scholar

Hendrickson, W. A. & Teeter, M. M. (1981). Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur. Nature (London), 290, 107–113.Google Scholar

Hoppe, W. & Jakubowski, U. (1975). The determination of phases of erythrocruorin using the two-wavelength method with iron as anomalous scatterer. In Anomalous scattering, edited by S. Ramaseshan & S. C. Abrahams, 3–11. Copenhagen: Munksgaard.Google Scholar

James, R. W. (1948). The optical principles of the diffraction of X-rays. Reprinted (1982) Ox Bow Press, Woodbridge, CT.Google Scholar

Karle, J. (1980). Some developments in anomalous dispersion for the structural investigation of macromolecular systems in biology. Int. J. Quantum Chem. Quantum Biol. Symp. 7, 357–367.Google Scholar

Krahn, J. M., Sinha, S. & Smith, J. L. (1999). Successes and prospects for SeMet MAD and large structures. Trans. Am. Crystallogr. Assoc. 35, 27–38.Google Scholar

La Fortelle, E. de & Bricogne, G. (1997). Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494.Google Scholar

Lustbader, J. W., Wu, H., Birken, S., Pollak, S., Kolks-Gawinowicz, M. A., Pound, A. M., Austen, D., Hendrickson, W. A. & Canfield, R. E. (1995). The expression, characterization and crystallization of wild-type and selenomethionyl human chorionic gonadotropin. Endocrinology, 136, 640–650.Google Scholar

Matthews, B. W. (1966a). The extension of the isomorphous replacement method to include anomalous scattering measurements. Acta Cryst. 20, 82–86.Google Scholar

Matthews, B. W. (1966b). The determination of the position of anomalously scattering heavy atom groups in protein crystals. Acta Cryst. 20, 230–239.Google Scholar

Matthews, B. W. & Czerwinski, E. W. (1975). Local scaling: a method to reduce systematic errors in isomorphous replacement and anomalous scattering measurements. Acta Cryst. A31, 480–487.Google Scholar

Miller, R., Gallo, S. M., Khalak, H. G. & Weeks, C. M. (1994). SnB: crystal structure determination via shake-and-bake. J. Appl. Cryst. 27, 613–621.Google Scholar

North, A. C. T. (1965). The combination of isomorphous replacement and anomalous scattering data in phase determination of non-centrosymmetric reflexions. Acta Cryst. 18, 212–216.Google Scholar

Okaya, Y. & Pepinsky, R. (1956). New formulation and solution of the phase problem in X-ray analysis of noncentric crystals containing anomalous scatterers. Phys. Rev. 103, 1645–1647.Google Scholar

Pähler, A., Smith, J. L. & Hendrickson, W. A. (1990). A probability representation for phase information from multiwavelength anomalous dispersion. Acta Cryst. A46, 537–540.Google Scholar

Podjarny, A. D., Bhat, T. N. & Zwick, M. (1987). Improving crystallographic macromolecular images: the real-space approach. Annu. Rev. Biophys. Biophys. Chem. 16, 351–373.Google Scholar

Ramakrishnan, V. & Biou, V. (1997). Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. Methods Enzymol. 276, 538–557.Google Scholar

Rossmann, M. G. (1961). The position of anomalous scatterers in protein crystals. Acta Cryst. 14, 383–388.Google Scholar

Sharff, A. J., Koronakis, E., Luisi, B. & Koronakis, V. (2000). Oxidation of selenomethionine: some MADness in the method! Acta Cryst. D56, 785–788.Google Scholar

Sheldrick, G. M. (1990). Phase annealing in SHELX-90: direct methods for larger structures. Acta Cryst. A46, 467–473.Google Scholar

Smith, J. L. (1998). Multiwavelength anomalous diffraction in macromolecular crystallography. In Direct methods for solving macromolecular structures, edited by S. Fortier, pp. 221–225. The Netherlands: CCLRC.Google Scholar

Smith, J. L. & Thompson, A. (1998). Reactivity of selenomethionine – dents in the magic bullet? Structure, 15, 815–819.Google Scholar

Templeton, L. K. & Templeton, D. H. (1988). Biaxial tensors for anomalous scattering of X-rays in selenolanthionine. Acta Cryst. A44, 1045–1051.Google Scholar

Templeton, L. K., Templeton, D. H., Phizackerley, R. P. & Hodgson, K. O. (1982). L₃-edge anomalous scattering by gadolinium and samarium measured at high resolution with synchrotron radiation. Acta Cryst. A38, 74–78.Google Scholar

Terwilliger, T. C. (1994a). MAD phasing: Bayesian estimates of $[F_{A}]$ . Acta Cryst. D50, 11–16.Google Scholar

Terwilliger, T. C. (1994b). MAD phasing: treatment of dispersive differences as isomorphous replacement information. Acta Cryst. D50, 17–23.Google Scholar

Terwilliger, T. C. (1997). Multiwavelength anomalous diffraction phasing of macromolecular structures: analysis of MAD data as single isomorphous replacement with anomalous scattering data using the MADMRG program. Methods Enzymol. 276, 530–537.Google Scholar

Terwilliger, T. C. & Berendzen, J. (1996). Correlated phasing of multiple isomorphous replacement data. Acta Cryst. D52, 749–757.Google Scholar

Terwilliger, T. C. & Berendzen, J. (1997). Bayesian correlated MAD phasing. Acta Cryst. D53, 571–579.Google Scholar

Terwilliger, T. C. & Berendzen, J. (1999a). Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods. Acta Cryst. D55, 501–505.Google Scholar

Terwilliger, T. C. & Berendzen, J. (1999b). Automated MIR and MAD structure solution. Acta Cryst. D55, 849–861.Google Scholar

Terwilliger, T. C. & Berendzen, J. (1999c). Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density. Acta Cryst. D55, 1872–1877.Google Scholar

Terwilliger, T. C. & Eisenberg, D. (1983). Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions. Acta Cryst. A39, 813–817.Google Scholar

Terwilliger, T. C. & Eisenberg, D. (1987). Isomorphous replacement: effects of errors on the phase probability distribution. Acta Cryst. A43, 6–13.Google Scholar

Terwilliger, T. C., Kim, S.-H. & Eisenberg, D. (1987). Generalized method of determining heavy-atom positions using the difference Patterson function. Acta Cryst. A43, 1–5.Google Scholar

Tesmer, J. J. G., Klem, T. J., Deras, M. L., Davisson, V. J. & Smith, J. L. (1996). The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nature Struct. Biol. 3, 74–86.Google Scholar

Vagin, A. & Teplyakov, A. (1998). A translation-function approach for heavy-atom location in macromolecular crystallography. Acta Cryst. D54, 400–402.Google Scholar

Wang, B.-C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90–112.Google Scholar

Weis, W. I., Kahn, R., Fourme, R., Drickamer, K. & Hendrickson, W. A. (1991). Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science, 254, 1608–1615.Google Scholar

Wilson, A. J. C. (1942). Determination of absolute from relative X-ray intensity data. Nature (London), 150, 151–152.Google Scholar

Xiang, S., Carter, C. W. Jr, Bricogne, G. & Gilmore, C. J. (1993). Entropy maximization constrained by solvent flatness: a new method for macromolecular phase extension and map improvement. Acta Cryst. D49, 193–212.Google Scholar

Zhang, K. Y. J. & Main, P. (1990). The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Cryst. A46, 377–381.Google Scholar