Absence of electron density for the benzyl group of TBOA in the Glt_Ph structure (PDB code 2NWW ). Possible alternative orientation of the benzyl group of TBOA (shown with an arrow). The electron-density omit map is shown in gray mesh (1σ). The Fo-Fc map is colored in green (3σ) and red (−3σ). Cartoon representation. HP2 loop is shown in purple. TBOA (shown in black) and residues involved in its binding are presented as sticks. Omit maps are used to remove bias (largely introduced by molecular replacement, where phases are taken from the similar structure, or caused by erroneous modeling) and can be used to verify assignment of ligands in binding sites. This is achieved by excluding a part of the model from the refinement procedure followed by the calculation of a bias-free difference map.