We combine off-axis electron holography and electron shadow imaging to accurately determine the specimen thickness and the incident electron beam direction over the illuminated area of a crystal. We, furthermore, quantify the variations in diffraction intensity with position over the same area. This unique solution to the experimental boundary condition problem enables us to make precise measurements of mean inner electrostatic potentials and structure factors that are sensitive to the bonding characteristics of materials. In this paper, we present the results of mean-inner potential determination from silicon and the newly discovered magnesiumdiboride superconductor.