Crystals of the EmrE membrane-protein imposed several technical challenges for X-ray crystallography, including high mosaicity, poor diffraction and a relatively large number of heavy atoms. Consequently, the heavy-atom substructure solution was difficult to obtain. By removing the histidine tag for protein purification, the mosaicity and the diffraction quality were greatly improved. The direct-methods Shake-and-Bake program SnB was successful in locating the heavy-atom sites from a mutant of EmrE which lacks a cysteine and therefore has a reduction in the number of heavy-atom sites. The substructure solution was solved from data with anomalous difference at a resolution of 5.5 A and the structure was determined to 3.8 A.