The structure of high quality $[{\mathrm{YBCO}}_{N}/{\mathrm{PBCO}}_{M}{]}_{1000\AA{}}$ superlattices, with $N$ ranging between 1 and 12 unit cells and $M\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}5$ unit cells, grown by high oxygen pressure sputtering, is analyzed. Intracell atomic structure of the layers along the $c$ axis and disorder at interfaces is investigated using an x-ray refinement technique. Negligible roughness, step disorder, and interdiffusion are found at the interfaces. Epitaxial mismatch strain results in a surprising reorganization of interatomic distances for the thinnest YBCO layers, which seems to correlated with the decrease in the critical temperature. Intracell structure is invoked as an additional source of ${T}_{c}$ changes in very thin YBCO layers.