Crystal structures of linker-PDE (PDB code: 7D7P) and TMD-linker (PDB code: 7D7Q) of Rhodopsin phosphodiesterase (Rh-PDE). For TMD (PDB code: 7CJ3) please refer to CXIDB ID 171. TMD-linker: 91 small-wedge (10 or 5°/crystal) datasets collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. Beam size was around 15×10 or 5×5 µm2 and oscillation step was 0.1°. The crystals belonged to space group I222 with unit cell parameters a~76, b~137, c~207 Å. 74 datasets were indexed and integrated using XDS with KAMO pipeline. Finally 58 integrated results were merged at 3.5 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result. Linker-PDE: 128 small-wedge (10°/crystal) datasets collected from different potions of a few large crystals broken in cryoloops using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. Beam size was around 15×10 µm2 and oscillation step was 0.1°. The crystals belonged to space group C2 with unit cell parameters a~117, b~68, c~57 Å, β~111°. 109 datasets were indexed and integrated using XDS with KAMO pipeline. Finally 64 integrated results were merged at 2.1 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result.