Crystals of the reaction center (RC) from RCs from purple photosynthetic bacteria contain three subunits, L, M, and H (present in a 1:1:1 stoichiometry) and a number of cofactors: four bacteriochlorophylls (BChls), two bacteriopheophytins, two quinones, QA (primary electron acceptor), and QB (secondary electron acceptor), and one nonheme iron (for reviews, see refs. 1 and 2). Although RCs from different species exhibit many similarities in structure, there are some significant structural differences.The RCs from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis that are the subject of this investigation show the following differences. In R. sphaeroides the secondary, water-soluble cytochrome is not present in purified RCs. In contrast, RCs from R. viridis contain a fourth subunit, a cytochrome, that has four heme groups associated with it. The two species contain different types of BChl: R. sphaeroides has BChl-a whereas R. viridis contains BChl-b. The primary quinone in R. sphaeroides is a ubiquinone, whereas in R. viridis it is a menaquinone. Furthermore, the two quinones that serve as acceptors are retained in purified RCs from R. sphaeroides, but one is apparently lost from R. viridis during the purification.Although extensive work has been done during the past two decades to characterize RCs, until recently there was very little information available on their three-dimensional structure. The reason was the lack of crystals suitable for x-ray diffraction studies. This situation changed with the successful crystallization of RCs from R. viridis (3) and R. sphaeroides (4, §). These crystals are of sufficient size and quality to obtain good x-ray diffraction data. The structure of the RCs from R. viridis has been reported recently at a resolution of 3 A (5, 6).In this work we describe the use of the Patterson search (molecular replacement) method (for reviews, see refs. 7 and 8) to obtain a low-resolution electron density map of the RC from R. sphaeroides and to show the homology between the structures of the RCs from the two bacterial species. A preliminary account of this work has been presented (9).EXPERIMENTAL PROCEDURES Crystallization. The RC from R. sphaeroides was crystallized by using the vapor diffusion technique. Different crystallization conditions produced a variety of forms as reported (4,10,11). The crystal form used for these structural studies was grown under the following conditions. The initial protein solution consisted of 5 mg of RC per ml, 0.36 M NaCl, 3.9%