[28] Phase determination from multiwavelength anomalous diffraction measurements.

Publisher Summary This chapter discusses phase determination from multiwavelength anomalous diffraction (MAD) measurements. The MAD approach to macromolecular structure determination has potential advantages for accuracy and convenience in phase evaluation. Isomorphism is intrinsically perfect; an algebraically exact analysis is possible; relative scattering strength and phasing power increase with scattering angle; and all required diffraction data can be measured from a single crystal. The virtual immortalization of crystals through freezing makes these advantages real and practical. Although many of the procedures in MAD phasing are in common with crystallographic practice, there are also a number of practical steps unique to this methodology. The chapter discusses the basic foundations of the method, presents the design and execution of experiments, and describes the steps and alternatives for data analysis.

[1]  V. Ramakrishnan,et al.  X‐ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha‐helix. , 1995, The EMBO journal.

[2]  W A Hendrickson,et al.  Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. , 1992, Science.

[3]  K. Hodgson,et al.  Phase determination by multiple-wavelength x-ray diffraction: crystal structure of a basic "blue" copper protein from cucumbers. , 1988, Science.

[4]  R. Kahn,et al.  X-ray curved-crystal monochromator system at the storage ring DCI , 1978 .

[5]  A. Engelman,et al.  Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. , 1994, Science.

[6]  John Kuriyan,et al.  Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA , 1994, Cell.

[7]  E. Getzoff,et al.  Sulfite Reductase Structure at 1.6 Å: Evolution and Catalysis for Reduction of Inorganic Anions , 1995, Science.

[8]  Peter D. Kwong,et al.  Structural basis of cell-cell adhesion by cadherins , 1995, Nature.

[9]  J. Helliwell,et al.  Optimized anomalous dispersion in crystallography: a synchrotron X-ray polychromatic simultaneous profile method , 1982, Nature.

[10]  J. Risler,et al.  Crystal structure study of Opsanus tau parvalbumin by multiwavelength anomalous diffraction , 1985, FEBS letters.

[11]  Wayne A. Hendrickson,et al.  Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur , 1981, Nature.

[12]  J. Hurley,et al.  Crystal structure of the Cys2 activator-binding domain of protein kinase Cδ in complex with phorbol ester , 1995, Cell.

[13]  Reginald W. James,et al.  The Optical principles of the diffraction of X-rays , 1948 .

[14]  P. Beachy,et al.  A potential catalytic site revealed by the 1.7-Å crystal structure of the amino-terminal signalling domain of Sonic hedgehog , 1995, Nature.

[15]  Peter D. Kwong,et al.  Crystal structure of an HIV-binding recombinant fragment of human CD4 , 1990, Nature.

[16]  E. Merritt,et al.  Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation , 1988, Proteins.

[17]  Janet L. Smith Determination of three-dimensional structure by multiwavelength anomalous diffraction: Current Opinion in Structural Biology 1991, 1:1002–1011 , 1991 .

[18]  J. L. Smith,et al.  Structure of the allosteric regulatory enzyme of purine biosynthesis. , 1994, Science.

[19]  Y. Satow,et al.  Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. , 1990, Science.

[20]  W. Weis,et al.  Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. , 1991, Science.

[21]  S. Darst,et al.  Crystal structure of the GreA transcript cleavage factor from Escherichia coli , 1995, Nature.

[22]  D. Filman,et al.  An enzyme–substrate complex involved in bacterial cell wall biosynthesis , 1995, Nature Structural Biology.

[23]  W. Hendrickson,et al.  Crystal structure of dimeric human ciliary neurotrophic factor determined by MAD phasing. , 1995, The EMBO journal.

[24]  V. Ramakrishnan,et al.  Crystal structure of globular domain of histone H5 and its implications for nucleosome binding , 1993, Nature.

[25]  J. L. Smith,et al.  A probability representation for phase information from multiwavelength anomalous dispersion. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[26]  Y. Satow,et al.  Crystal Structure Analysis of Cytochrome c' by the Multiwavelength Anomalous Diffraction Method Using Synchrotron Radiation , 1986 .

[27]  W. Hendrickson Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. , 1991, Science.

[28]  Y. Satow,et al.  Structure of interleukin 1 alpha at 2.7-A resolution. , 1990, Biochemistry.

[29]  W. Hendrickson,et al.  Crystal structure of Clostridium acidi-urici ferredoxin at 5-A resolution based on measurements of anomalous X-ray scattering at multiple wavelengths. , 1988, The Journal of biological chemistry.

[30]  Y. Okaya,et al.  New Formulation and Solution of the Phase Problem in X-Ray Analysis of Noncentric Crystals Containing Anomalous Scatterers , 1956 .

[31]  John Kuriyan,et al.  Crystal structure of the DsbA protein required for disulphide bond formation in vivo , 1993, Nature.

[32]  D. T. Cromer,et al.  Calculation of anomalous scattering factors at arbitrary wavelengths , 1983 .

[33]  T. Steitz,et al.  Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA , 1995, Nature.

[34]  A T Brünger,et al.  Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases , 1996, Science.

[35]  W. Hendrickson,et al.  Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. , 1995, Structure.

[36]  L. K. Templeton,et al.  X-RAY DICHROISM AND POLARIZED ANOMALOUS SCATTERING OF THE URANYL ION , 1982 .

[37]  A. Aggarwal,et al.  Structure of restriction endonuclease BamHI and its relationship to EcoRI , 1994, Nature.

[38]  Structure determination and refinement of homotetrameric hemoglobin from Urechis caupo at 2.5 A resolution. , 1992, Acta crystallographica. Section B, Structural science.

[39]  M. Wall,et al.  High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation. , 1995, Structure.

[40]  E. Fanchon,et al.  Effect of the anisotropy of anomalous scattering on the MAD phasing method. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[41]  A. Aggarwal,et al.  Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis. , 1994, Structure.

[42]  W A Hendrickson,et al.  Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase. , 1995, Structure.

[43]  Nigel M. Allinson,et al.  SR instrumentation for optimized anomalous scattering and high resolution structure studies of proteins and nucleic acids (invited) , 1995 .

[44]  E. Lattman,et al.  Representation of phase probability distributions for simplified combination of independent phase information , 1970 .

[45]  M. Hatada,et al.  Bio–incorporation of telluromethionine into buried residues of dihydrofolate reductase , 1994, Nature Structural Biology.

[46]  T. Prangé,et al.  The catalytic site of serine proteinases as a specific binding cavity for xenon. , 1995, Structure.

[47]  N. Watanabe,et al.  Macromolecular crystallography station BL‐18B at the Photon Factory , 1995 .

[48]  W. Lovenberg,et al.  Structure of rubredoxin: an x-ray study to 2.5 A resolution. , 1970, Journal of molecular biology.

[49]  N. Yasuoka,et al.  S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method. , 1990, Journal of biochemistry.

[50]  G N Murshudov,et al.  The structural basis of sequence-independent peptide binding by OppA protein. , 1994, Science.

[51]  M. Jaskólski,et al.  High-resolution structure of the catalytic domain of avian sarcoma virus integrase. , 1995, Journal of molecular biology.

[52]  T. Steitz,et al.  Crystal structure of lac repressor core tetramer and its implications for DNA looping. , 1995, Science.

[53]  Keith O. Hodgson,et al.  The use of anomalous scattering effects to phase diffraction patterns from macromolecules , 1980 .

[54]  S. Hubbard,et al.  Crystal structure of the tyrosine kinase domain of the human insulin receptor , 1994, Nature.

[55]  P. Reinemer,et al.  Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate. , 1995, Journal of molecular biology.

[56]  W A Hendrickson,et al.  Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis of the selenomethionyl protein. , 1994, Structure.

[57]  R. Liddington,et al.  Crystal structure of the A domain from the a subunit of integrin CR3 (CD11 b/CD18) , 1995, Cell.

[58]  F. D. Michaud,et al.  Performance of beamline X8C at the NSLS , 1995 .

[59]  F. Zanini,et al.  THE MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE AT ELETTRA , 1995 .

[60]  W A Hendrickson,et al.  Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three‐dimensional structure. , 1990, The EMBO journal.

[61]  E. W. Czerwinski,et al.  Local scaling: a method to reduce systematic errors in isomorphous replacement and anomalous scattering measurements , 1975 .

[62]  S. Hasnain Synchrotron radiation and biophysics , 1990 .

[63]  Gregory L. Verdine,et al.  Structure of the NF-κB p50 homodimer bound to DNA , 1995, Nature.

[64]  D. Cromer,et al.  Relativistic Calculation of Anomalous Scattering Factors for X Rays , 1970 .

[65]  Paul Greengard,et al.  Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1 , 1995, Nature.

[66]  C. J. Sparks,et al.  Resonant anomalous X-ray scattering : theory and applications , 1994 .