International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 25.2, pp. 716-717   | 1 | 2 |

Section 25.2.4.1. Scope and function of the package

D. E. Tronrudm* and L. F. Ten Eycky

25.2.4.1. Scope and function of the package

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TNT (Tronrud et al., 1987[link]) is a computer program package that optimizes the parameters of a molecular model given a set of observations and indicates the location of errors that it cannot correct. Its authors presume the principal set of observations to be the structure factors observed in a single-crystal diffraction experiment. To complement such a data set, which for most macromolecules has limitations, stereochemical restraints such as standard bond lengths and angles are also used as observations.

A molecule is parameterized as a set of atoms, each with a position in space, an isotropic B factor and an occupancy. The complete model also includes an overall scale factor, which converts the arbitrary units of the measured structure factors to e Å−3, and a two-parameter model of the electron density of the bulk solvent.

Because a TNT model of a macromolecule does not allow anisotropic B factors, TNT cannot be used to finish the refinement of any structure that diffracts to high enough resolution to justify the use of these parameters. If one has a crystal that diffracts to 1.4 Å or better, the final model should probably include these parameters and TNT cannot be used. One may still use TNT in the early stages of such a refinement because one usually begins with only isotropic B's.

At the other extreme of resolution, TNT begins to break down with data sets limited to only about 3.5 Å data. This breakdown occurs for two reasons. First, at 3.5 Å resolution, the maps can no longer resolve β-sheet strands or α-helices. The refinement of a model against data of such low resolution requires strong restraints on dihedral angles and hydrogen bonds – tasks for which TNT is not well suited. Second, the errors in an initial model constructed with only 3.5 Å data are usually of such a magnitude and quality that the function minimizer in TNT cannot correct them.

References

Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Cryst. A43, 489–501.Google Scholar








































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