The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinuset al.(2015).Acta Cryst.A71, 235–244] has been applied to a set of experimental data sets from five different samples – Ni₂Si, PrVO₃, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.