High resolution x-ray diffraction data from crystals of the Rhodobacter sphaeroides photosynthetic reaction center (RC) have been collected at cryogenic temperature in the dark and under illumination, and the structures were refined at 2.2 and 2.6 angstrom resolution, respectively. In the charge-separated D(+)Q(A)Q(B)(-) state (where D is the primary electron donor (a bacteriochlorophyll dimer), and Q(A) and Q(B) are the primary and secondary quinone accepters, respectively), Q(B)(-) is located approximately 5 angstroms from the Q(B) position in the charge-neutral (DQ(A)Q(B)) slate, and has undergone a 180 degrees propeller twist around the isoprene chain. A model based on the difference between the two structures is proposed to explain the observed kinetics of electron transfer from Q(A)-Q(B) to Q(A)Q(B)(-) and the relative binding affinities of the different ubiquinone species in the Q(B) pocket. In addition, several water channels (putative proton pathways) leading from the Q(B) pocket to the surface of the RC were delineated, one of which leads directly to the membrane surface.