Fig. 3.

Determination of the ligand location in the ligand-bound SAM-IV cryo-EM map. a Ligand-bound SAM-IV cryo-EM map. b Map computed from the SAM-IV RNA-only model from a. c Difference map between a and b shown at two different thresholds. The insets show the prominent density in the difference map into which are fitted the ligand model derived from SAM-I crystal structure (PDB code: 3GX5). d Segmented SAM density from a is highlighted in a wire frame representation, fitted with the ligand model derived from SAM-I crystal structure (PDB code: 3GX5). Q-scores of the ligand components between the map and model are calculated.