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Figure 4
An N-linked glycan attached to Asn35 of human Toll-like receptor 4 (PDB entry 2z62; Kim et al., 2007BB23). Electron density is contoured at 1σ for the 2mFo − DFc map (grey) and 3σ for the mFo − DFc difference density map (green, positive; red, negative). (a) Model as found in the PDB with the (1–6)-linked fucose incorrectly modelled as FUL. The density near the O6 atom of asparagine-linked NAG is partially filled by four water molecules in a symmetry-related copy of the model (purposely not shown), which reduces the amount of positive difference density. (b) PDB-REDO model and map. The fucose residue is renamed FUC. Subsequent refinement improves the fit to the electron density, but distorts the ring conformation and flattens the hand of the C1 atom. (c) Manually rebuilt model after refinement by PDB-REDO. The (1,6)-linked fucose is flipped to correctly fit the density, as is the acetylamino group of the second NAG residue. Together with adding a (1–3)-linked fucose, these corrections remove all strong difference density. (d) The CARP plot for (1–6)-linked fucose shows the distribution of FUC-(1–6)-NAG glycosidic linkage torsion angles in the PDB. The relevant bonds in the glycosidic linkage are marked in (a). The models are marked as follows: PDB, P; PDB-REDO, R; manually rebuilt, M. Only the manually rebuilt model has common glycosidic torsion angles.

ISSN: 2053-230X
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