Inhibitor APV (from AIDS reagent program) was dissolved in DMSO by vortex-mixing. The mixture was incubated on ice prior to centrifugation to remove any insoluble material. The inhibitor was mixed with 2.2 mg/ml protein in molar ratio of 5:1 in most cases. The two exceptions were: 3.5 mg/ml of PRI50V was used with inhibitor-protein ratio of 10:1, and 3.7 mg/ml of PRL90M. The crystallization trials employed the hanging drop method using equal volumes of enzyme-inhibitor and reservoir solution. PRWT-APV was crystallized from 0.1M MES, pH 5.6, and 0.6–0.8 M sodium chloride. Crystals of PRV32I-APV and PRI50V-APV were grown from 0.1M sodium acetate, pH 5.4, 0.4 M and 1.2 M sodium chloride, respectively. PRI54M-APV crystals were grown from 0.1M sodium acetate, pH 4.6, and 0.67 M sodium chloride. PRI54V-APV and PRI84V-APV crystals were grown from 0.1 M sodium acetate, pH 5.4 and 4.0, respectively, and 0.13 M sodium iodide, and PRL90M-APV crystals from 0.1 M sodium acetate, pH 4.8 and 0.2 M sodium iodide. Single crystals were mounted on fiber loops with 20 to 30 % (v/v) glycerol as cryoprotectant in the reservoir solution. X-ray diffraction data were collected at the SER-CAT beamline of the Advanced Photon Source, Argonne National Laboratories. Diffraction data were integrated, scaled, and merged using the HKL2000 package [54 ]. PRWT-APV, PRV32I-APV and PRI50V-APV were solved by molecular replacement program Phaser [55 (link)] with the protein atoms of structure 2QCI[32 (link)] as the starting model. The other complexes were solved by MOLREP [56 ], using the protein atoms of 2F8G as the starting model [19 (link)]. The crystal structures were refined using SHELX-97 [57 (link)], except that the lower resolution structure of PRI84V-APV was refined with REFMAC 5.2 [58 (link)]. The diffraction-data precision indicator (DPI) was used for determining the accuracy in the atomic positions [59 ]. The molecular graphics program COOT was used for map display and model building [60 (link)]. Structural figures were made by PyMol [61 ]. The structures were compared by superimposing their Cα atoms and using HIVAGENT [62 ] to calculate the distance between two atoms. The cut-off distances for different interactions were as described in [30 (link)].