Fig. 8. Weighting of raw atomic displacements by the propagated errors of atoms provides a more accurate representation of structural change. (a) An overlay of a segment of two GFP structures (Y145C, blue, and T203C, Y145C, gold) reveals excellent overall agreement but shows large observed displacements of several atomic centroids. Two atoms are highlighted, K162 (Ne ) and H148 (Ne ), with positional errors calculated by the method of Stroud and Fauman (1) indicated. (b) Raw displacements of atoms in this region for the two structures () show greater displacement of K162 Ne than H148 Ne (indicated by arrows), but weighting of the atomic displacements by the propagated error of the two atomic centroids () indicates the opposite conclusion (c) H148 Ne is more significantly displaced than K162 Ne , a result consistent with the fact the K162 Ne centroid is less well determined. (d) As an independent check for consistency of this weighting scheme, we integrated the electron density over one atomic radius around centroid positions of atoms in the Y145C (Upper) and Y145C, T203C (Lower) structures (F_obs, a _calc). The data show that while positions of most atoms (including H148 atoms) are well supported by electron density, the terminal K162 atoms are only poorly represented. Thus, the calculation of the normalized displacement parameter (D r_norm) appropriately down-weights atoms whose centroids are experimentally not well determined. Maps were calculated by using cns (2) and integration was performed by using mapman (3). Bars for each residue in b-d represent atoms in the following order: main chain (Ca , N, C, O) and then side-chain atoms as in standard PDB format.

1. Stroud, R. M. & Fauman, E. B. (1995) Protein Sci. 4, 2392-2404.

2. Brunger, A. T. (1992) Nature 355, 472-474.

3. Kleywegt, G. J. & Jones, T. A. (1996) Acta Crystallogr. D 52, 826-828.