view article
Figure 5
Electron density in the MT1 ligand-binding pocket. (a) Ligand electron density for MT1 (white cartoon) after ligand exchange of agomelatine (Ago) to 2-phenylmelatonin (2-PMT; orange). (b) Ligand electron density after incorrect placement of the transient ligand Ago (cyan) and refinement starting from the same molecular-replacement structure (see Section 2[link]). Both structural models are of comparable stereochemical quality, but the structure refined with Ago shows slightly worse refinement statistics (R and Rfree of 0.257 and 0.314 compared with 0.257 and 0.308, respectively). 2mFo − DFc maps (blue mesh) are contoured at 1σ. mFo − DFc electron-density difference maps contoured at ±3.5σ (green and red for positive and negative peaks, respectively) show strong (∼6.7σ) positive difference density for the missing phenyl ring in the structure refined with Ago.

IUCrJ
Volume 6| Part 6| November 2019| Pages 1106-1119
ISSN: 2052-2525
https://doi.org/10.1107/S2052252519013137