Numerous projects of macromolecular structure-function studies involve soaking and/or co-crystallization of ligands. Their presence is afterwards expected to be observed in 2mFo-DFc electron density map and mainly in mFo-DFc (omit) map. However, computation of the electron density map may be distorted by additional factors. In less clear cases (e.g. lower occupancy of the ligand), the initial observed electron density may not contain information on localization of the ligand and further validation procedures are necessary: composite omit map, feature-enhanced map, polder map [1], etc. Current methods are briefly reviewed and their application is shown on a single case of an enzyme:substrate complex.
This publication was supported by project BIOCEV (CZ.1.05/1.1.00/02.0109) and CIISB4HEALTH (CZ.02.1.01/0.0/0.0/16_013/0001776) from the ERDF fund and by the Grant Agency of the Czech Technical University in Prague, grant No. SGS16/246/OHK4/3T/14.