Native southern bean mosaic virus contains a significant number of Mg2+ and Ca2+ ions. These can be removed by treatment with EDTA causing the virus to swell by 7% in radius at alkaline pH values. The swollen virions are susceptible to protease and nuclease digestion. They are likely to be an intermediate during assembly and disassembly. Crystals of the metal-free virus have been grown and were found to be approximately isomorphous with the orthorhombic type III southern bean mosaic virus crystals (Akimoto, T., Wagner, M.A., Johnson, J.E., and Rossmann, M.G. (1975) J. Ultrastruct. Res. 53, 306-318), although the cell dimensions are longer by 2%. Native rhombohedral type II crystals disintegrate on changing the pH or increasing the ionic strength of the mother liquor. Damage can be prevented by addition of ethylene glycol. At alkaline pH values, these crystals also show a 2% increase in their cell dimensions as well as a significant alteration in their diffraction patterns. In the type II and III crystals, the viruses pack with only their 5-fold axes in contact. Thus, the difference of the apparent swelling in solution and in the crystals may be one of differential swelling over the virus surface.