We describe the quantitative refinement of nanoparticle structures from gold nanoparticles probed by ultrafast electron crystallography (UEC). We establish the equivalence between the modified radial distribution function employed in UEC and the atomic pair distribution function (PDF) used in x-ray and neutron powder diffraction analysis. By leveraging PDF refinement techniques, we demonstrate that UEC data are of sufficient quality to differentiate between cuboctahedral, decahedral and icosahedral nanoparticle models. Furthermore, we identify the signatures of systematic errors that may occur during data reduction and show that atomic positions refined from UEC are robust to these errors. This work serves as a foundation for reliable quantitative structural analysis of time-resolved laser-excited nanoparticle states.