The three-dimensional structure of deoxyhemoglobin San Diego has been solved to 3.5 Å resolution using mixed crystals of the variant hemoglobin and hemoglobin A. The site of the amino acid replacement can be clearly located in the difference electron density map and is consistent with the chemical result (β109 Val→Met) discussed in the preceding paper. The abnormally high oxygen affinity and impaired cooperativity appear to result from perturbations of the α₁β₁-subunit interface.