AU OR FES2? VALIDATION OF PROTEIN MODELS AND REFINEMENT PROTOCOLS. Gerard J. Kleywegt & T. Alwyn Jones, Department of Molecular Biology, Biomedical Centre, Uppsala University, Box 590, S-751 24 Uppsala, Sweden
At low resolution, it is often non-trivial to produce a model which is an accurate representation of the protein one has collected data on. Even data with a nominal resolution of ~2-2.5 A is no guarantee for a good model, or even a correctly traced one (1,2).
Methods that may help in preventing serious errors and over-fitting of the data while the refinement is in progress will be discussed. These include: the use of the free R-factor to monitor the refinement and to optimise the refinement protocol (3), the use of databases during model rebuilding (4,5), and the use of "quality control" as an integral part of the refinement process (6). In addition, a number of caveats with respect to the use of the free R-factor will be discussed.
Subsequently, a number of popular myths and wide-spread misconceptions with respect to the validation of final models will be debunked. These include:
* A low R-factor and small r.m.s. deviations from ideal geometry prove that a model is correct. In fact, these are necessary, but hopelessly insufficient conditions (2).
* If only the CA coordinates of a model are deposited, nobody will ever be able to validate the model. Actually, in some cases this is possible nowadays.
* One does not need to use non-crystallographic symmetry restraints. The examples to the contrary may make some want to re-do their most recent refinement (7).
* Ramachandran plots are stiflingly boring. On the contrary: they are extremely useful for model validation. We will show some highly entertaining examples from real-life models.
Considering the controversial nature of some aspects of this presentation, the audience is invited to disagree vehemently.
References:
(1) Branden, C.I., & Jones, T.A. (1990). Nature 343, 687-689.
(2) Kleywegt, G.J., & Jones, T.A. (1990). Structure 3, 535-540.
(3) Brunger, A.T. (1992). Nature 355, 472-475.
(4) Jones, T.A., Zou, J.Y., Cowan, S.W., & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
(5) Zou, J.Y., & Mowbray, S.L. (1994). Acta Cryst. D50, 237-249.
(6) Kleywegt, G.J., & Jones, T.A. (1996). Meth. Enzymol., in press.
(7) Kleywegt, G.J. (1996). Acta Cryst. D52, in press.