The structure of pea lectin has been determined to 3.0-A resolution based on multiple isomorphous replacement phasing to 6.0-A resolution and a combination of single isomorphous replacement, anomalous scattering, and density modification to 3.0-A resolution. The pea lectin model has been optimized by restrained least squares refinement against the data between 7.0- and 3.0-A resolution. The final model at 3.0 A gives an R factor of 0.24 and a root mean square deviation from ideal bond distances of 0.02 A. The two monomers in the asymmetric unit are related by noncrystallographic 2-fold symmetry to form a dimer. Monomers were treated independently in modeling and refinement, but are found to be virtually identical at this resolution. The molecular structure of the pea lectin monomer is very similar to that of concanavalin A, the lectin from the jack bean. Similarities extend from secondary and tertiary structures to the occurrence of a cis-peptide bond and the pattern of coordination of the Ca2+ and Mn2+ ions. Differences between the two lectin structures are confined primarily to the loop regions and to the chain termini, which are different and give rise to the unusual permuted relationship between the pea lectin and concanavalin A protein sequences.