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. 2009 Jan 20;65(Pt 2):176–185. doi: 10.1107/S0907444908037591

Figure 4.

Figure 4

The first four carbohydrates of the N-linked glycan in PDB entry 2qc1 with four negative mF o − DF c difference density peaks at their O1 atoms. The difference density map is contoured at −3.0σ and waters are not shown for clarity. The O1 atom in NAG302B was placed in an axial conformation in the original PDB entry, but should have been removed completely before deposition. This superfluous oxygen hampers the detection of the link to Asn141B in Coot. The other O1 atoms are were left on top of other O atoms when creating links between the carbohydrates, which resulted in difference density peaks and numerous atomic overlap warnings in WHAT_CHECK (Hooft et al., 1996 ▶). Additionally, MAN304B is a β-d-mannose and must be named BMA instead of MAN.