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. 2023 May 23;79(Pt 6):462–472. doi: 10.1107/S2059798323003510

Figure 5.

Figure 5

Refinement of PDB entry 6s2g (Ramirez-Escudero et al., 2019 ▸) in PDB-REDO changes the torsion angle from an outlier in the PDB to an inlier in the PDB-REDO databank. The MAN (chain ID and sequence number F7)-1,6-BMA (chain ID and sequence number F3) linkage (red asterisk in the bottom panel) of PDB entry 6s2g (green) is identified as an outlier in the PDB (φ = −8.6°, ψ = −140.7°) but as an inlier in the PDB-REDO databank (φ = 71.5°, ψ = 169.0°): Δφ = 80.1°, Δψ = 50.3°. The change is brought on by moving the O6 atom (red asterisk in the top panel). BMA(F3) and MAN(F7) are represented by ball-and-stick models [C atoms in green (PDB model) or grey (PDB-REDO model)], whilst the rest of the attached glycan (PDB-REDO model) is represented in a faded grey ball-and-stick representation. 2F o − F c electron density (grey) is displayed for the linkage contoured to 1σ. The Z-scores for this linkage is −1.03 in the PDB model and 1.53 in the PDB-REDO model. The top image was produced using CCP4mg. Bottom: SNFG notation output from Privateer.