Crystal structures of the Asp$^{96}$ to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle-that is, after proton transfer to Asp$^{85}$ and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-cis, 15-anti and an extensive rearrangement of the three-dimensional network of hydrogenbonded residues and bound water that accounts for the changed pK$_a$ values (where K$_a$ is the acid constant) of the Schiff base and Asp$^{85}$. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.