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Volumn 364, Issue , 2007, Pages 95-120

Characterizing a crystal from an initial native dataset

(1)  Sawaya, M R a  

a NONE

Author keywords

Matthew's coefficient; Merohedral twinning; Native Patterson map; Noncrystallographic symmetry; Self rotation function

Indexed keywords

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLIZATION; DIMERIZATION; MACROMOLECULE; METHODOLOGY; STATISTICS; X RAY DIFFRACTION;

EID: 36549053563     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-266-1:95     Document Type: Article
Times cited : (12)

References (46)
  • 1
    • 0032924978 scopus 로고    scopus 로고
    • Locating proper non-crystallographic symmetry in low-resolution electron-density maps with the program GETAX
    • Vonrhein, C. and Schulz, G. E. (1999) Locating proper non-crystallographic symmetry in low-resolution electron-density maps with the program GETAX. Acta Cryst. D55, 225-229.
    • (1999) Acta Cryst , vol.D55 , pp. 225-229
    • Vonrhein, C.1    Schulz, G.E.2
  • 2
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews, B. W (1968) Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
    • (1968) J. Mol. Biol , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 3
    • 0030841590 scopus 로고    scopus 로고
    • Collaborative computational project, number 4: Providing programs for protein crystallography
    • Dodson, E. J., Winn, M., and Ralph, A. (1997) Collaborative computational project, number 4: providing programs for protein crystallography. Methods Enzymol. 277, 620-633.
    • (1997) Methods Enzymol , vol.277 , pp. 620-633
    • Dodson, E.J.1    Winn, M.2    Ralph, A.3
  • 4
    • 0042011224 scopus 로고    scopus 로고
    • Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals
    • Kantardjieff, K. A. and Rupp, B. (2003) Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Science 12, 1865-1871.
    • (2003) Protein Science , vol.12 , pp. 1865-1871
    • Kantardjieff, K.A.1    Rupp, B.2
  • 5
    • 0022272119 scopus 로고
    • Determination of protein molecular weight, hydration, and packing from crystal density
    • Matthews, B. W. (1985) Determination of protein molecular weight, hydration, and packing from crystal density. Methods Enzymol. 114, 176-187.
    • (1985) Methods Enzymol , vol.114 , pp. 176-187
    • Matthews, B.W.1
  • 6
    • 0022307511 scopus 로고
    • Crystal density measurements using aqueous ficoll solutions
    • Westbrook, E. M. (1985) Crystal density measurements using aqueous ficoll solutions. Methods Enzymol. 114, 187-196.
    • (1985) Methods Enzymol , vol.114 , pp. 187-196
    • Westbrook, E.M.1
  • 7
    • 0008950857 scopus 로고    scopus 로고
    • An improved method for protein crystal density measurements
    • Leung, A. K. W., Park, M. M. V., and Borhani, D. W. (1999) An improved method for protein crystal density measurements. J. Appl. Cryst. 32, 1006-1009.
    • (1999) J. Appl. Cryst , vol.32 , pp. 1006-1009
    • Leung, A.K.W.1    Park, M.M.V.2    Borhani, D.W.3
  • 8
    • 0000070408 scopus 로고
    • A Fourier series method for the determination of the components of interatomic distances in crystals
    • Patterson, A. L. (1934) A Fourier series method for the determination of the components of interatomic distances in crystals. Phys. Rev. 46, 372-376.
    • (1934) Phys. Rev , vol.46 , pp. 372-376
    • Patterson, A.L.1
  • 9
    • 0035788101 scopus 로고    scopus 로고
    • Implementation of molecular replacement in AMoRe
    • Navaza, J. (2001) Implementation of molecular replacement in AMoRe. Acta Cryst. D57, 1367-1372.
    • (2001) Acta Cryst , vol.D57 , pp. 1367-1372
    • Navaza, J.1
  • 10
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin, A. and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022-1025.
    • (1997) J. Appl. Cryst , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 11
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography and NMR system: A new software suite for macromolecular structure determination
    • Brunger, A. T., Adams, P. D., Clore, G. M., et al. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Cryst. D54, 905-921.
    • (1998) Acta Cryst , vol.D54 , pp. 905-921
    • Brunger, A.T.1    Adams, P.D.2    Clore, G.M.3
  • 12
    • 0031058884 scopus 로고    scopus 로고
    • Rotation function calculations with GLRF program
    • Tong, L. and Rossmann, M. G. (1997) Rotation function calculations with GLRF program. Methods Enzymol. 276, 594-611.
    • (1997) Methods Enzymol , vol.276 , pp. 594-611
    • Tong, L.1    Rossmann, M.G.2
  • 13
    • 0002660809 scopus 로고
    • The detection of subunits within the crystallographic asymmetric unit
    • Rossmann, M. G. and Blow, D. M. (1962) The detection of subunits within the crystallographic asymmetric unit. Acta Cryst. 15, 24-31.
    • (1962) Acta Cryst , vol.15 , pp. 24-31
    • Rossmann, M.G.1    Blow, D.M.2
  • 14
    • 0035788369 scopus 로고    scopus 로고
    • Molecular replacement-historical background
    • Rossmann, M. G. (2001) Molecular replacement-historical background. Acta Cryst. D57, 1360-1366.
    • (2001) Acta Cryst , vol.D57 , pp. 1360-1366
    • Rossmann, M.G.1
  • 15
    • 0002815512 scopus 로고
    • D-glyceraldehyde-3-phosphate dehydrogenase: Three-dimensional structure and evolutionary significance
    • Buehner, M., Ford, G. C., Moras, D., Olsen, K. W., and Rossmann, M. G. (1973). D-glyceraldehyde-3-phosphate dehydrogenase: three-dimensional structure and evolutionary significance. Proc. Natl Acad. Sci. USA 70, 3052-3054.
    • (1973) Proc. Natl Acad. Sci. USA , vol.70 , pp. 3052-3054
    • Buehner, M.1    Ford, G.C.2    Moras, D.3    Olsen, K.W.4    Rossmann, M.G.5
  • 17
    • 0029949156 scopus 로고    scopus 로고
    • Symmetry, stability, and dynamics of multidomain and multicomponent protein systems
    • Blundell, T. L. and Srinivasan, N. (1996) Symmetry, stability, and dynamics of multidomain and multicomponent protein systems. Proc. Natl. Acad. Sei. USA 93, 14,243-14,248.
    • (1996) Proc. Natl. Acad. Sei. USA , vol.93
    • Blundell, T.L.1    Srinivasan, N.2
  • 18
    • 36549031147 scopus 로고    scopus 로고
    • Padilla, J. E. and Yu, T. (2002) Self-assembling symmetric protein materials. In: Biopolymers 7: Polyamides and Complex Proteinaceous Materials I, (Steinbuchel, A. and Fahnestock, S. R., eds.), Wiley-VCH, Weinheim, Germany, pp. 261-284.
    • Padilla, J. E. and Yu, T. (2002) Self-assembling symmetric protein materials. In: Biopolymers Vol. 7: Polyamides and Complex Proteinaceous Materials I, (Steinbuchel, A. and Fahnestock, S. R., eds.), Wiley-VCH, Weinheim, Germany, pp. 261-284.
  • 19
    • 0034517589 scopus 로고    scopus 로고
    • An approach to multi-copy search in molecular replacement
    • Vagin, A. and Teplyakov, A. (2000) An approach to multi-copy search in molecular replacement. Acta Cryst. D56, 1622-1624.
    • (2000) Acta Cryst , vol.D56 , pp. 1622-1624
    • Vagin, A.1    Teplyakov, A.2
  • 20
    • 0031059039 scopus 로고    scopus 로고
    • Detecting and overcoming crystal twinning
    • Yeates, T. O. (1997) Detecting and overcoming crystal twinning. Methods Enzymol. 276, 344-358.
    • (1997) Methods Enzymol , vol.276 , pp. 344-358
    • Yeates, T.O.1
  • 21
    • 13044254231 scopus 로고    scopus 로고
    • Analysis and characterization of data from twinned crystals
    • Chandra, N., Acharya, K. R., and Moody, P. C. E. (1999) Analysis and characterization of data from twinned crystals. Acta Cryst. D55, 1750-1758.
    • (1999) Acta Cryst , vol.D55 , pp. 1750-1758
    • Chandra, N.1    Acharya, K.R.2    Moody, P.C.E.3
  • 22
    • 0033607003 scopus 로고    scopus 로고
    • Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit
    • Ban, N., Nissen, P., Hansen, J., Capel, M., Moore, P. B., and Steitz, T. A. (1999) Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400, 841-847.
    • (1999) Nature , vol.400 , pp. 841-847
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Capel, M.4    Moore, P.B.5    Steitz, T.A.6
  • 23
    • 0033876912 scopus 로고    scopus 로고
    • Effects of crystal twinning on the ability to solve a macromolecular structure using multiwavelength anomalous diffraction
    • Yang, F., Dauter, Z., and Wlodawer, A. (2000) Effects of crystal twinning on the ability to solve a macromolecular structure using multiwavelength anomalous diffraction. Acta Cryst. D56, 959-964.
    • (2000) Acta Cryst , vol.D56 , pp. 959-964
    • Yang, F.1    Dauter, Z.2    Wlodawer, A.3
  • 24
    • 0037162554 scopus 로고    scopus 로고
    • A structural basis for the activity of retro-Diels-Alder catalytic antibodies: Evidence for a catalytic aromatic residue
    • Hugot, M., Bensel, N., Vogel, M., et al. (2002) A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue. Proc. Natl. Acad. Sci. USA 99, 9674-9678.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9674-9678
    • Hugot, M.1    Bensel, N.2    Vogel, M.3
  • 25
    • 0036901174 scopus 로고    scopus 로고
    • Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal
    • Larsen, N. A., Heine, A., de Prada, P., et al. (2002) Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal. Acta Cryst. D58, 2055-2059.
    • (2002) Acta Cryst , vol.D58 , pp. 2055-2059
    • Larsen, N.A.1    Heine, A.2    de Prada, P.3
  • 26
    • 0001420692 scopus 로고
    • The interpretation of pseudo-orthorhombic diffraction patterns
    • Dunitz, J. D. (1964) The interpretation of pseudo-orthorhombic diffraction patterns. Acta Cryst. 17, 1299-1304.
    • (1964) Acta Cryst , vol.17 , pp. 1299-1304
    • Dunitz, J.D.1
  • 27
    • 0035208082 scopus 로고    scopus 로고
    • A twinned monoclinic form of human peroxiredoxin 5 with eight molecules in the asymmetric unit
    • Declercq, J. -P. and Evrard, C. (2001) A twinned monoclinic form of human peroxiredoxin 5 with eight molecules in the asymmetric unit. Acta Cryst. D57, 1829-1835.
    • (2001) Acta Cryst , vol.D57 , pp. 1829-1835
    • Declercq, J.-P.1    Evrard, C.2
  • 28
    • 0013670239 scopus 로고    scopus 로고
    • Refinement of twinned structures with SHELXL97
    • Herbst-Irmer, R. and Sheldrick, G. M. (1998) Refinement of twinned structures with SHELXL97. Acta Cryst. B54, 443-449.
    • (1998) Acta Cryst , vol.B54 , pp. 443-449
    • Herbst-Irmer, R.1    Sheldrick, G.M.2
  • 29
    • 0000026146 scopus 로고    scopus 로고
    • Application and comparison of different tests on twinning by merohedry
    • Kahlenberg, V. (1999) Application and comparison of different tests on twinning by merohedry. Acta Cryst. B55, 745-751.
    • (1999) Acta Cryst , vol.B55 , pp. 745-751
    • Kahlenberg, V.1
  • 31
    • 0346432075 scopus 로고    scopus 로고
    • Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning
    • Lee, S., Sawaya, M. R., and Eisenberg, D. (2003) Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning. Acta Cryst. D59, 2191-2199.
    • (2003) Acta Cryst , vol.D59 , pp. 2191-2199
    • Lee, S.1    Sawaya, M.R.2    Eisenberg, D.3
  • 32
    • 0346432066 scopus 로고    scopus 로고
    • 1 obscured by pseudo-translational NCS
    • 1 obscured by pseudo-translational NCS. Acta Cryst. D59, 2237-2241.
    • (2003) Acta Cryst , vol.D59 , pp. 2237-2241
    • Barends, T.R.1    Dijkstra, B.W.2
  • 33
    • 0037779022 scopus 로고    scopus 로고
    • A statistic for local intensity differences: Robustness to anisotropy and pseudo-centering and utility for detecting twinning
    • Padilla, J. E. and Yeates, T. O. (2003) A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Cryst. D59, 1124-1130.
    • (2003) Acta Cryst , vol.D59 , pp. 1124-1130
    • Padilla, J.E.1    Yeates, T.O.2
  • 34
    • 0037322013 scopus 로고    scopus 로고
    • Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1b
    • Rudolph, M. G., Kelker, M. S., Schneider, T. R., et al. (2003) Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1b. Acta Cryst. D59, 290-298.
    • (2003) Acta Cryst , vol.D59 , pp. 290-298
    • Rudolph, M.G.1    Kelker, M.S.2    Schneider, T.R.3
  • 35
    • 0033410194 scopus 로고    scopus 로고
    • Methionine-141 directly influences the binding of 4-methylpyrazole in human σσ alcohol dehydrogenase
    • Xie, P. T. and Hurley, T. D. (1999) Methionine-141 directly influences the binding of 4-methylpyrazole in human σσ alcohol dehydrogenase. Protein Sci. 8, 2639-2644.
    • (1999) Protein Sci , vol.8 , pp. 2639-2644
    • Xie, P.T.1    Hurley, T.D.2
  • 36
    • 0034636799 scopus 로고    scopus 로고
    • Crystal structure of 4-methyl-5-β-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 Å resolution
    • Campobasso, N., Mathews, I. I., Begley, T. P., and Ealick, S. E. (2000) Crystal structure of 4-methyl-5-β-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 Å resolution. Biochem. 39, 7868-7877.
    • (2000) Biochem , vol.39 , pp. 7868-7877
    • Campobasso, N.1    Mathews, I.I.2    Begley, T.P.3    Ealick, S.E.4
  • 37
    • 0025874138 scopus 로고
    • Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants
    • Tulip, W. R., Varghese, J. N., Baker, A. T., et al. (1991) Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants. J. Mol. Biol. 221, 487-497.
    • (1991) J. Mol. Biol , vol.221 , pp. 487-497
    • Tulip, W.R.1    Varghese, J.N.2    Baker, A.T.3
  • 38
    • 0030839256 scopus 로고    scopus 로고
    • High-resolution structure of a Polyomavirus VP1-oligosaccharide complex: Implications for assembly and receptor binding
    • Stehle, T. and Harrison, S. C. (1997) High-resolution structure of a Polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding. EMBOJ. 16, 5139-5148.
    • (1997) EMBOJ , vol.16 , pp. 5139-5148
    • Stehle, T.1    Harrison, S.C.2
  • 39
    • 0032555745 scopus 로고    scopus 로고
    • Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein
    • Lenzen, C. U., Steinmann, D., Whiteheart, S. W., and Weis, W. I. (1998) Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein. Cell 94, 525-536.
    • (1998) Cell , vol.94 , pp. 525-536
    • Lenzen, C.U.1    Steinmann, D.2    Whiteheart, S.W.3    Weis, W.I.4
  • 40
    • 0032548495 scopus 로고    scopus 로고
    • The 2.3 Å X-ray crystal structure of S. cerevisiae phosphoglycerate mutase
    • Rigden, D. J., Alexeev, D., Phillips, S. E., and Fothergill-Gilmore, L. A. (1998) The 2.3 Å X-ray crystal structure of S. cerevisiae phosphoglycerate mutase. J. Mol. Biol. 276, 449-459.
    • (1998) J. Mol. Biol , vol.276 , pp. 449-459
    • Rigden, D.J.1    Alexeev, D.2    Phillips, S.E.3    Fothergill-Gilmore, L.A.4
  • 41
    • 0037066769 scopus 로고    scopus 로고
    • Zhou, T., Kurnasov, O., Tomchick, D. R., et al. (2002) Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. J. Biol. Chem. 277, 13, 148-13,154.
    • Zhou, T., Kurnasov, O., Tomchick, D. R., et al. (2002) Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. J. Biol. Chem. 277, 13, 148-13,154.
  • 42
    • 0033544926 scopus 로고    scopus 로고
    • Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase
    • Fraaije, M. W., van den Heuvel, R. H., van Berkel, W. J., and Mattevi, A. (1999) Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase. J. Biol. Chem. 214, 35,514-35,520.
    • (1999) J. Biol. Chem , vol.214
    • Fraaije, M.W.1    van den Heuvel, R.H.2    van Berkel, W.J.3    Mattevi, A.4
  • 43
    • 0034646571 scopus 로고    scopus 로고
    • Divergence in macromolecular assembly: X-ray crystallographic structure analysis of lumazine synthase from Brucella abortus
    • Braden, B. C., Velikovsky, C. A., Cauerhff, A. A., Polikarpov, I., and Goldbaum, F. A. (2000) Divergence in macromolecular assembly: X-ray crystallographic structure analysis of lumazine synthase from Brucella abortus. J. Mol. Biol. 297, 1031-1036.
    • (2000) J. Mol. Biol , vol.297 , pp. 1031-1036
    • Braden, B.C.1    Velikovsky, C.A.2    Cauerhff, A.A.3    Polikarpov, I.4    Goldbaum, F.A.5
  • 44
    • 0037031287 scopus 로고    scopus 로고
    • Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation
    • Gill, H. S., Pfluegl, G. M., and Eisenberg, D. (2002) Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation. Biochemistry 41, 9863-9872.
    • (2002) Biochemistry , vol.41 , pp. 9863-9872
    • Gill, H.S.1    Pfluegl, G.M.2    Eisenberg, D.3
  • 45
    • 0031959912 scopus 로고    scopus 로고
    • The crystal structure of Dps, a ferritin homolog that binds and protects DNA
    • Grant, R. A., Filman, D. J., Finkel, S. E., Kolter, R., and Hogle, J. M. (1998) The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat. Struct. Biol. 5, 294-303.
    • (1998) Nat. Struct. Biol , vol.5 , pp. 294-303
    • Grant, R.A.1    Filman, D.J.2    Finkel, S.E.3    Kolter, R.4    Hogle, J.M.5


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