A new methodology of performing structural analysis of nanocrystals based on wide angle powder diffraction is proposed. It combines molecular dynamics simulations with the analysis of pair distribution function. The actual analysis was performed on CdSe quantum dots. MD simulations of nanocrystals with shapes defined by low-index atomic planes, (1 0 0), (1 1 0), and (1 1 1) introduced bulk and surface relaxation in initially perfect crystal lattice. In search for the best atomistic model of the actual CdSe nanocrystals, experimental structure functions S(Q) and interatomic distance functions G(r) were matched to those calculated with MD models. Eventually it was concluded that CdSe nanocrystals with dimensions of 2.5-3.5 nm assume the shape of octahedrons terminated by (1 1 1) surfaces.