Automated protein model building combined with iterative structure refinement (original) (raw)

References

  1. Bernstein, F.C. et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542 (1977).
    Article CAS Google Scholar
  2. Helliwell, J.R. Synchrotron radiation facilities. Nature Struct. Biol. 5, 614–617 (1998).
    Article CAS Google Scholar
  3. Ogata, C.M. MAD phasing grows up. Nature Struct. Biol. 5, 638–640 (1998).
    Article CAS Google Scholar
  4. Furey, W. & Swaminathan, S. PHASES-95: a program package for the processing and analyzing diffraction data from macromolecules. Methods Enzymol. 277, 590–620 (1997).
    Article CAS Google Scholar
  5. Otwinowski, Z, in Isomorphous replacement and anomalous scattering. Proceedings of the CCP4 study weekend, January 25–26, 1991 (eds Wolf, W., Evans, P.R. & Leslie, A.G.W.) 80–85 (Daresbury Laboratory, Warrington, UK; 1991).
    Google Scholar
  6. Fortelle de La, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276 , 590–620 (1997).
    Google Scholar
  7. Terwilliger, T.C. & Berendzen, J. Automated structure solution for MIR and MAD. Acta Crystallogr. D 55, 849–861 (1999).
    Article CAS Google Scholar
  8. Brünger, A.T. et al. Crystallography & NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 ( 1998).
    Article Google Scholar
  9. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 (1994).
    Article Google Scholar
  10. Miller, R., Gallo, S.M., DeTitta, G.T., Khalak, H.G. & Weeks, C.M. SnB, crystal structure determination via shake-and-bake. J. Appl. Crystallogr. 27, 613–621 (1994).
    Article CAS Google Scholar
  11. Sheldrick, G.M. Patterson superposition and ab initio phasing. Methods Enzymol. 276, 307–326 ( 1997).
    Article Google Scholar
  12. Lunin, V.Y., Lunina, N.L., Petrova, T.E., Urzhumtsev, A.G. & Podjarny, A.D. On the ab initio solution of the phase problem for macromolecules at very low resolution. II. Generalized likelihood based approach to cluster discrimination. Acta Crystallogr. D 54, 726–734 ( 1998).
    Article CAS Google Scholar
  13. Abrahams, J.P. & de Graaf, R.A.G. New developments in phase refinement Curr. Opin. Struct. Biol. 8, 601–605 (1998).
    Article CAS Google Scholar
  14. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).
    Article Google Scholar
  15. Oldfield, T.J. A Semi-Automated map fitting procedure. in Proceedings from the 1996 meeting of the International Union Of Crystallography Macromolecular Computing School (1996).
    Google Scholar
  16. Kleywegt, G.J. & Jones, T.A. Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta Crystallogr. D 53, 179– 185 (1997).
    Article CAS Google Scholar
  17. Schlagenhauf, E., Etges, R. & Metcalf, P. The crystal structure of Leishmania major surface proteinase leishmanolysin (gp63). Structure 6, 1035–1046 (1998).
    Article CAS Google Scholar
  18. Perrakis, A., Sixma, T.K., Wilson, K.S. & Lamzin, V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Crystallogr. D 53, 448–455 (1997).
    Article CAS Google Scholar
  19. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 ( 1994).
  20. Cowtan, K. & Main, P. Miscellaneous algorithms for density modification. Acta Crystallogr. D 54, 487 –493 (1998).
    Article CAS Google Scholar
  21. Lamzin, V.S. & Wilson, K.S. Automated refinement of protein models. Acta Crystallogr. D 49, 129– 147 (1993).
    Article CAS Google Scholar
  22. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240– 255 (1997).
    Article CAS Google Scholar
  23. Bricogne, G. Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta Crystallogr. D 49, 37–60 (1993).
    Article CAS Google Scholar
  24. Read, R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140 –149 (1986).
    Article Google Scholar
  25. Valegard, K. et al. Structure of a cephalosporin synthase. Nature 394, 805–809 (1998).
    Article CAS Google Scholar
  26. Hilge, M. et al. High resolution native and complex structures of thermostable β-mannanase from _Thermomonospora fusca—_substrate specificity in glycosyl hydrolase family 5. Structure, 6, 1433– 1444 (1998).
    Article CAS Google Scholar
  27. Perrakis, A. et al. Structure of a bacterial chitinase at 2.3 Å resolution. Structure 2, 1169–1180 (1994).
    Article CAS Google Scholar
  28. Brünger, A.T. Assessment of phase accuracy by cross validation: the free R value. Methods and application. Acta Crystallogr. D 49, 24–36 (1993).
    Article Google Scholar
  29. Lamzin, V.S. & Wilson, K.S. Automated refinement for protein crystallography. Methods Enzymol. 277, 269 –305 (1997).
    Article CAS Google Scholar
  30. Sussman, J.L., Holbrook, S.R., Church, G.M. & Kim, S.-H. A structure factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters. Acta Crystallogr. A 33, 800–804 ( 1977).
    Article Google Scholar
  31. Hendricksoon, W.A. & Konnert, J.H. in Computing in crystallography (eds Diamond, R., Ramasechan, S. & Venkatesan, K.), 13.01–13.25 (Indian Institute of Science, Bangalore, India; 1980).
    Google Scholar
  32. Zou, J.-Y. & Jones, A. Towards the automatic interpretation of macromolecular electron density maps: qualitative and quantitative matching of protein sequence to map. Acta Crystallogr. D 52, 833–841 (1996).
    Article CAS Google Scholar
  33. Deacon, A.M., Weeks, C.M., Miller, R. & Ealick, S.E. The shake-and bake structure determination of troclinic lysozyme. Proc. Natl. Acad. Sci. USA 16, 9284–9289 (1998).
    Article Google Scholar
  34. Dauter, Z., Sieker, L.C. & Wilson, K.S. Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 Å with and without restraints. Acta Crystallogr. B 48, 42–59 ( 1992).
    Article Google Scholar
  35. van Asselt, E.J., Perrakis, A., Kalk, K.H., Lamzin, V.S. & Dijkstra, B.W. Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP. Acta Crystallogr. D 54, 58–73 (1998).
    Article CAS Google Scholar
  36. Schmidt, A., Schlacher, A., Steiner, W., Schwab, H. & Kratky, K. Structure of the xylanase from Penicillium simplicissimum. Protein Sci. 7, 2081– 2088 (1998).
    Article CAS Google Scholar
  37. Becker, S., Groner, B. & Müller, C.W. Three dimensional structure of the Stat3β homodimer bound to DNA Nature 394, 145– 151 (1998).
    Article CAS Google Scholar
  38. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946 –950 (1991).
    Article Google Scholar
  39. Merrit, E.A. & Bacon, D.J. Raster3D photorealistic molecular graphics. Methods Enzymol. 277, 505– 524 (1997).
    Article Google Scholar

Download references