Small-angle neutron scattering (SANS) of aggregated protein in an aqueous solution is simulated based on the crystallographic data of the protein. After obtaining the crystallographic data of the target protein, hydrogen atoms are added to the data and then some hydrogen atoms are replaced with deuterium atoms. The structure models are made with this data and then their gyration radii and SANS intensities are calculated. Compared the calculated SANS data with the experimental one, the most probable structure is determined. With this analysis method, the aggregate structure of proteasome α7-subunit (PRSα) in an aqueous solution was investigated. Three structural models, a simple monomer and two types of dimers, were supposed as the aggregated structure of PRSα. The analysis showed that the best compromised structure was the dimer, which was consistent with electron microscopy observation. © 2008 Elsevier B.V. All rights reserved.