Three datasets were obtained from crystals prepared under different substrate soak conditions. Each structure was obtained in the I213 space group and featured two monomers of LlNDT-2 in the asymmetric unit. We first obtained an apo structure of LlNDT-2, which had not been soaked with substrate ligands, and featured no ligand density in the active sites. The second structure was obtained from crystals soaked with 3 (EdU). Both active sites featured density between the side chains of E98 and D92 in a 'closed' conformation of the enzyme corresponding to that observed previously (Figure ). This density was modelled as the covalent 2'-deoxyribosyl enzyme complex 16, evidenced by continuous density from the side chain of E98 to the C1ʹ atom of the deoxyribose sugar. Although crystallographic evidence for this intermediate in DRTase-I Class enzymes has previously been reported, the structure of a covalent 2'-deoxyribosyl adduct (Figure ) has not been observed in a Class II enzyme.