Extended Data Fig. 3: Evaluation of ions in submitted models (stereo images).
From: Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

(a) Target 1 6cvm reference model Mg A2002 (gray sphere) with water ligands (orange spheres), located near the PETG ligand, with density for classic octahedral coordination. Only six of 23 submitted Target 1 models included the Mg2+ and all three coordinating waters. Others had either only Mg2+, Mg2+ plus one or two waters, Mg2+ plus waters with zero occupancy, no atoms modeled, or atoms significantly displaced. (b) Some groups placed metal ions with weak justification, as exemplified by the Na+ (grey sphere) shown here in model EM005_1 for Target 3.