Calcium ATPase (Calcium pump) from sarcoplasmic reticulum is an integral membrane protein of Mr 110 K and a representative member of P-type ATPase involved in the active transports of ions with the energy from ATP hydrolysis. This ion pump regulates muscle relaxation by up-taking calcium ions from muscle cells into sarcoplasmic reticulum against the concentration gradient of the calcium. This ion pump has been successfully crystallized into ultra-thin plate crystals (<20 micron) by a dialysis method. Through the multiple-isomorphous replacement experiments at cryogenic temperature, the three-dimensional structure of this pump has been determined at a resolution of 2.6Å. The crystal structure is the first to reveal the structural architecture of P-type ATPase. Here, we describe the methods used for solving the phase problem in the crystal structure analysis for such ultra-thin plate crystal: combination of cryogenic X-ray diffraction experiments and cryogenic electron microscopy.