Not your average density

Structure

Volumn 5, Issue 12, 1997, Pages 1557-1569

  Kleywegt, Gerard J ^a   Read, Randy J ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031574325     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(97)00305-5     Document Type: Review

References (59)

1. Wang, X. & Janin, J. (1993). Orientation of non-crystallographic symmetry axes in protein crystals. Acta Cryst. D 49, 505-512.
2. Kleywegt, G.J. (1996). Use of non-crystallographic symmetry in protein structure refinement. Acta Cryst. D 52, 842-857.
3. Kleywegt, G.J. & Jones, T.A. (1995). Where freedom is given, liberties are taken. Structure 3, 535-540.
4. Brünger, A.T. (1997). X-ray crystallography and NMR: complementary views of structure and dynamics. Nat. Struct. Biol. 4, 862-865.
5. Bricogne, G. (1974). Geometric sources of redundancy in intensity data and their use for phase determination. Acta Cryst. A 30, 395-405.
6. Rossmann, M.G. & Blow, D.M. (1962). The detection of sub-units within the crystallographic asymmetric unit. Acta Cryst. 15, 24-31.
7. Main, P. (1967). Phase determination using non-crystallographic symmetry. Acta Cryst. 23, 50-54.
8. Colman, P.M. (1974). Noncrystallographic symmetry and the sampling theorem. Z. Krist. 140, 344-349.
9. Bricogne, G. (1976). Methods and programs for direct-space exploitation of geometric redundancies. Acta Cryst. A 32, 832-847.
10. Jones, T.A. (1992). A, yaap, asap, @#*? A set of averaging programs. In Molecular Replacement. (Dodson, E.J., Glover, S. & Wolf, W., eds.), pp 91-105, SERC Daresbury Laboratory, Daresbury, U.K.
11. Vellieux, F.M.D. & Read, R.J. (1997). Non-crystallographic symmetry averaging in phase refinement and extension. Methods Enzymol. 277, 18-53.
12. Wang, B.C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90-112.
13. Abrahams, J.P. (1997). Bias reduction in phase refinement by modified interference functions: introducing the gamma correction. Acta Cryst. D 53, 371-376.
14. Abrahams, J.P. & Leslie, A.G.W. (1996). Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst. D 52, 30-42.
15. Arnold, E., et al., & Rossmann, M.G. (1987). The structure determination of a common cold virus, human rhinovirus 14. Acta Cryst. A 43, 346-361.
16. Vellieux, F.M.D., et al., & Hol, W.G.J. (1993). Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data. Proc. Natl. Acad. Sci. USA 90, 2355-2359.
17. Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A 42, 140-149.
18. Matthews, B.W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
19. Leslie, A.G.W. (1987). A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang. Acta Cryst. A 43, 134-136.
20. Tête-Favier, F., Rondeau, J.M., Podjarny, A. & Moras, D. (1993). Structure determination of aldose reductase: joys and traps of local symmetry averaging. Acta Cryst. D 49, 246-256.
21. Ha, Y. & Allewell, N.M. (1997). Equivalence of pairs of enantiomorphic space groups in the presence of non-crystallographic symmetry. Acta Cryst. A 53, 400-401.
22. Colman, P.M., Fehlhammer, H. & Bartels, K. (1976). Patterson search methods in protein structure determination: β-trypsin and immunoglobulin fragments. In Crystallographic Computing Techniques. (Ahmed, F.R., Huml, K & Sedlacek, B., eds.), pp 248-258, Munksgaard, Copenhagen.
23. Read, R.J. & Schierbeek, A.J. (1988). A phased translation function. J. Appl. Cryst. 21, 490-495.
24. Stein, P.E., Boodhoo, A., Armstrong, G.D., Cockle, S.A., Klein, M.H. & Read, R.J. (1994). The crystal structure of pertussis toxin. Structure 2, 45-57.
25. Noble, M.E.M., Musacchio, A., Saraste, M., Courtneidge, S.A. & Wierenga, R.K. (1993). Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin. EMBO J. 12, 2617-2624.
26. Fletterick, R.J. & Steitz, T.A. (1976). The combination of independent phase information obtained from separate protein structure determinations of yeast hexokinase. Acta Cryst. A 32, 125-132.
27. Vellieux, F.M.D.A.P., Hunt, J.F., Roy, S. & Read, R.J. (1995). DEMON/ANGEL: a suite of programs to carry out density modification. J. Appl. Cryst. 28, 347-351.
28. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improvec methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
29. Kleywegt, G.J. & Jones, T.A. (1994). Halloween ... masks and bones. In From First Map to Final Model. (Bailey, S., Hubbard, R. & Waller, D.A., Eds.), pp 59-66, SERC Daresbury Laboratory, Daresbury, U.K.
30. Matthews, B.W., Sigler, P.B., Henderson, R. & Blow, D.M. (1967). Three-dimensional structure of tosyl-chymotrypsin. Nature 214, 652-656.
31. Muirhead, H., Cox, J.M., Mazzarella, L. & Perutz, M.F. (1967). Structure and function of haemoglobin. 3. A three-dimensional fourier synthesis of human deoxyhaemoglobin at 5.5 Angstrom resolution. J. Mol. Biol. 28, 117-156.
32. Buehner, M., Ford, G.C., Moras, D., Olsen, K.W. & Rossmann, M.G. (1974). Structure determination of crystalline lobster D-glyceraldehyde-3-phosphate dehydrogenase. J. Mol. Biol. 82, 563-585.
33. Bloomer, A.C., Champness, J.N., Bricogne, G., Staden, R. & Klug, A. (1978). Protein disk of tobacco mosaic virus at 2.8 A resolution showing the interactions within and between subunits. Nature 276, 362-368.
34. Harrison, S.C., Olson, A.J., Schutt, C.E., Winkler, F.K. & Bricogne, G. (1978). Tomato bushy stunt virus at 2.9 A resolution. Nature 276, 368-373.
35. Valegård, K., Liljas, L., Fridborg, K. & Unge, T. (1990). The three-dimensional structure of the bacterial virus MS2. Nature 345, 36-41.
36. Valegård, K., Liljas, L., Fridborg, K. & Unge, T. (1991). Structure determination of the bacteriophage MS2. Acta Cryst. B 47, 949-960
37. McKenna, R., Xia, D., Willingmann, P., Ilag, L.L. & Rossmann, M.G. (1992). Structure determination of the bacteriophage ΦX 174. Acta Cryst. 648, 499-511.
38. Speir, J.A., Munshi, S., Wang, G., Baker, T.S. & Johnson, J.E. (1995). Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. Structure 3, 63-78.
39. Gaykema, W.P.J., Hol, W.G J., Vereijken, J.M., Soeter, N.M., Bak, H.J. & Beintema, J.J. (1984). 3.2 A structure of the copper-containing, oxygen-carrying protein Panulirus interruptus haemocyanin. Nature 309, 23-29.
40. Braig, K., et al., & Sigler, P.B. (1994). The crystal structure of the bacterial chaperonin GroEL at 2.8 A. Nature 371, 578-586.
41. Esnouf, R., Ren, J., Jones, Y., Stammers, D. & Stuart, D. (1996). Removing bias from a model for HIV-1 reverse transcriptase by realspace averaging between different crystal forms. In Macromolecular Refinement. (Dodson, E., Moore, M., Ralph, A. & Bailey, S., Eds.), pp 153-161, CCLRC Daresbury Laboratory, Daresbury, U.K.
42. Rudenko, G., Bonten, E., d'Azzo, A. & Hol, W.G.J. (1996). Structure determination of the human protective protein: twofold averaging reveals the three-dimensional structure of a domain which was entirely absent in the initial model. Acta Cryst. D 52, 923-936.
43. Korolev, S., Nayal, M., Barnes, W.M., Di Cera, E. & Waksman, G. (1995). Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 Å resolution: structural basis for thermostability. Proc. Natl. Acad. Sci. USA 92, 9264-9268.
44. Stein, P.E., Boodhoo, A., Tyrrell, G.J., Brunton, J.L. & Read, R.J. (1992). Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli. Nature 355, 748-750.
45. 3. Biochemistry, in press.
46. Kleywegt, G.J., et al., & Jones, T.A. (1997). The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reeseiat 3.6 A resolution, and a comparison with related enzymes. J. Mol. Biol., 272, 383-397.
47. Kleywegt, G.J. & Brünger, A.T. (1996). Checking your imagination: applications of the free R value. Structure 4, 897-904.
48. Wilson, C. & Agard, D.A. (1993). PRISM: automated crystallographic phase refinement by iterative skeletonization. Acta Cryst. A 49, 97-104.
49. Zhang, K.Y.J. & Main, P. (1990). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A 46, 41-46.
50. Zhang, K.Y.J. & Main, P. (1990). The use of Sayres equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Cryst. A 46, 377-381.
51. Bolin, J.T., Smith, J.L. & Muchmore, S.W. (1993). Considerations in phase refinement and extension: experiments with a rapid and automatic procedure. Abstracts Am. Cryst. Assoc. Series 221, 51.
52. Cowtan, K. (1994). dm: an automated procedure for phase improvement by density modification. CCP4/ESF-EACBM Newsletter on Protein Crystallography 34-38.
53. Rossmann, M.G., et al., & Lynch, R.E. (1992). Molecular replacement real-space averaging. J. Appl. Cryst. 25, 166-180.
54. Grimes, J.M. (1995). Structural Studies of Bluetongue Virus. D. Phil. Thesis, University of Oxford.
55. Schuller, D.J. (1996). MAGICSQUASH: more versatile non-crystallographic symmetry averaging with multiple constraints. Acta Cryst. D 52, 425-434.
56. Turk, D. (1992). Weiterentwicklung eines Programms für Molekülgraphik und Elektronendichte-Manipulation und seine Anwendung auf verschiedene Protein-Strukturaufklärungen. Ph.D. Thesis, Technische Universität, München.
57. Furey, W. & Swaminathan, S. (1997). PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. Methods Enzymol. 277, 590-620.
58. Cowtan, K.D. & Main, P. (1993). Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta Cryst. D 49, 148-157.
59. Zhang, K.Y.J. (1993). SQUASH: combining constraints for macromolecular phase refinement and extension. Acta Cryst. D 49, 213-222.