Since longer carboxylate ligands do not allow for crystallization, the question becomes how to purify and structurally characterize such objects. Recently, a purification method based on resins with amine groups was developed for oxo clusters with mixed (but still short) ligand shells. About 20 % free acid persisted in the final product. Regarding characterization, the oxo clusters in MOFs have been studied by X-ray total scattering and Pair Distribution Function analysis (PDF). Structural changes upon heating have been observed, usually by a model-free analysis. On the other hand, X-ray PDF has been often used to study the structure of nanocrystals. In this case, the organic ligands have usually been neglected in the structural models because the organic ligands scatter quite little compared to the inorganic core. In the case of larger clusters (Bi38, Cd35, Au144, Cd37) PDF could confirm the structure of the core, again by largely neglecting the organic ligands. However, to our knowledge, PDF has not yet been applied to the small discrete oxo clusters capped with organic ligands, as discussed here.