We have cooled a two-ion-crystal to the ground state of its collective modes of motion. Laser cooling, more specific resolved sideband cooling is performed sympathetically by illuminating only one of the two $^{40}$Ca$^+$ ions in the crystal. The heating rates of the motional modes of the crystal in our linear trap have been measured, and we found them considerably smaller than those previously reported by Q. Turchette {em et. al.} Phys. Rev. A 61, 063418 (2000) in the case of trapped $^9$Be$^+$ ions. After the ground state is prepared, coherent quantum state manipulation of the atomic population can be performed. Within the coherence time, up to 12 Rabi oscillations are observed, showing that many coherent manipulations can be achieved. Coherent excitation of each ion individually and ground state cooling are important tools for the realization of quantum information processing in ion traps.