Abstract
The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of experimentally observed NOEs and the number of 'expected NOEs'. A practical definition of 'expected NOEs' based on inter-proton distances in the structures up to a given cut-off distance is proposed. The average completeness for the set of 97 structures is 68, 48, and 26% up to 3, 4, and 5 Å cut-off distances, respectively. For recent state-of-the-art structures these numbers are approximately 90, 75, and 45%. Almost 20% of the observed NOEs are between atoms that are further than 5 Å apart in the final structures. The completeness is independent of the relative surface accessibility and does not depend strongly on residue type, secondary structure or local precision, although the number of observed NOEs in these classes varies considerably. The completeness of NOE restraints is a useful quality criterion in the course of structure refinement. The completeness per residue is more informative than the number of NOEs per residue, which makes it a useful tool to assess the quality of the NMR data set in relation to the resulting structures.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.E., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535–542.
Clore, G.M., Robien, M.A.and Gronenborn, A.M. (1993) J. Mol. Biol., 231, 82–102.
Doreleijers, J.F., Rullmann, J.A.C. and Kaptein, R.(1998) J. Mol. Biol., 281, 149–164.
Folmer, R.H., Hilbers, C.W., Konings, R.N. and Nilges, M. (1997) J.Biomol. NMR, 9, 245–258.
Gardner, K.H., Rosen, M.K. and Kay, L.E. (1997) Biochemistry, 36, 1389–1401.
Garrett, D.S., Kuszewski, J., Hancock, T.J., Lodi, P.J., Vuister, G.W., Gronenborn, A.M. and Clore, G.M. (1994)J. Magn. Reson., B104, 99–103.
Hooft, R.W.W., Sander, C. and Vriend, G. (1997) Comput. Appl. Biosci.,13, 425–430.
Hyberts, S.G., Goldberg, M.S., Havel, T.F. and Wagner, G. (1992) Protein Sci., 1, 736–751.
Kleywegt, G.J. and Jones, T.A. (1996) Structure, 4, 1395–1400.
rKleywegt, G.J. and Jones, T.A. (1997)Methods Enzymol., 277, 208–230.
Kuszewski, J., Qin, J., Gronenborn, A.M. and Clore, G.M. (1995) J. Magn.Reson., 106, 92–96.
Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. and Thornton, J.M.(1996) J. Biomol. NMR, 8, 477–486.
Lodi, P.J., Garrett, D.S., Kuszewski, J., Tsang, M.L.S., Weatherbee, J.A., Leonard, W.J., Gronenborn, A.M. and Clore, G.M. (1994) Science, 263, 1762–1767.
Markley, J.L., Bax, A., Arata, Y., Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüthrich, K. (1998) J. Biomol. NMR, 12, 1–23.
Morris, A.L., MacArthur, M.W., Hutchinson, E.G. and Thornton, J.M. (1992) Proteins, 12, 345–364.
Neri, D., Szyperski, T., Otting, G., Senn, H. and Wüthrich, K. (1989) Biochemistry, 28, 7510–7516.
PalmerIII, A.G., Williams, J. and McDermott, A. (1996) J. Phys. Chem., 100, 13293–13310.
Pearlman, D.A. (1994)J. Biomol. NMR, 4, 1–16.
Pontius, J., Richelle, J. and Wodak, S.J. (1996) J. Mol. Biol., 264, 121–136.
Ramachandran, G.N., Ramakrishna, C. and Sasisekharan, V. (1963) J. Mol. Biol., 7, 95–99.
Rullmann, J.A.C. (1996) AQUA computer program, ftp://ftp.nmr.chem.uu.nl/pub/aqua.
Slijper, M., Bonvin, A.M.J.J., Boelens, R. and Kaptein, R. (1996) J. Mol. Biol., 259, 761–773.
Sutcliffe, M.J. (1993) Protein Sci., 2, 936–944.
Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M. and Bax, A. (1997) Nat. Struct. Biol., 4,732–738.
Vis, H., Mariani, M., Vorgias, C.E., Wilson, K.S., Kaptein, R. and Boelens, R. (1995) J. Mol. Biol.,254, 692–703.
Vis, H., Vageli, O., Nagel, J., Vorgia, C.E. and Wilson, K.S. (1996) Magn. Reson. Chem.,34, S81–S86.
Vriend, G. (1990) J. Mol. Graph., 8, 52–56.
rVriend, G. and Sander, C. (1993) J.Appl. Crystallogr., 26, 47–60.
Wagner, G., Braun, W., Havel, T.F., Schaumann, T., Go, N. and Wüthrich, K.(1987) J. Mol. Biol., 196, 611–639.
Wilson, K.S., Dauter, Z., Lamzin, V.S., Walsh, M., Wodak, S.J., Richelle, J., Pontius, J., Vaguine, A., Hooft, R.W.W., Sander, C., Vriend, G., Thornton, J.M., Laskowski, R.A., MacArthur, M.W., Dodson, E.J., Murshudov, G., Oldfield, T.J., Kaptein, R. and Rullmann, J.A.C. (1998) J. Mol. Biol., 276, 417–436.
Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY.
Wüthrich, K., Billeter, M. and Braun, W. (1983) J. Mol. Biol., 169, 949–961.
Author information
Authors and Affiliations
Electronic Supplementary Material
Rights and permissions
About this article
Cite this article
Doreleijers, J.F., Raves, M.L., Rullmann, T. et al. Completeness of NOEs in protein structures: A statistical analysis of NMR data. J Biomol NMR 14, 123–132 (1999). https://doi.org/10.1023/A:1008335423527
Issue Date:
DOI: https://doi.org/10.1023/A:1008335423527