The complex between Saccharomyces cerevisiae flavocytochrome b2 and the sulfite anion has been analyzed by x-ray diffraction. A map of the difference in electron density between the complex and the native protein has been computed. One positive peak of electron density is visible at the active site of each of the two subunits in the asymmetric unit, very close to the N-5 of the flavin. The molecular fragment SO3(2-) can account for the shape of this difference in electron density. A third peak is visible in the subunit containing pyruvate, the reaction product. It is a peak of negative electron density localized at the position where the pyruvate usually is in the native form. These results are interpreted on the basis of the mechanism defined in solution for the reaction between flavins and sulfite.