The first four carbohydrates of the N-linked glycan in PDB entry 2qc1
with four negative mFo − DFc 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.