A general method to deconvolute oscillation data sets from twinned protein crystals to a corresponding single-crystal data set has been developed and applied to diffraction data measured from crystals of a fragment containing the FAD- and NADH-binding domains of nitrate reductase. The procedure allows straightforward processing of diffraction data from twinned crystals. Typically, R(merge) values of reduced data sets from the nitrate reductase crystals after deconvolution are about 0.06 compared to 0.13 and higher before deconvolution. Based on these deconvoluted data sets, the structure of the FAD- and NADH-binding domains of nitrate reductase could be solved successfully. The result indicates that crystal twinning does not necessarily prevent crystallographic structure determination.