Full Rietveld refinement of the crystal structure of the synthetic calcium-deficient carbonated apatite Cal_3.40[Ca2_5.90 (NH₄)_0.10] [(PO₄) _4.95(CO₃)_1.05(H ₂O)_0.30] [(OH) _1.65(H₂O)_0.45] (space group P6₃/m; a=9.437(1), c=6.888(1) Å; Z=1; R_wp=5.23%) was carried out using X-ray powder diffraction data. The use of the model with the split position of O3 atom made it possible to find two orientations of CO₃ triangles sharing one of their edges. They occupy randomly the adjacent faces of a PO₄ tetrahedron that are parallel to the c axis. O3c atoms coordinating carbon atoms are shifted by 0.37 Å from O3p atoms belonging to PO₄ tetrahedra. The charge unbalance occurring when [CO₃]^2- ions replace [PO₄]^3- groups is primarily compensated by vacancies in Ca1 sites. The studies of the sample thermal decomposition performed by simultaneous thermal analysis and by X-ray diffraction helped to analyze the localization and the amount of lattice water that enhanced the reliability of the structural model.