For Y1-xCaxBa2Cu3Oy with varying oxygen and calcium content, the change of crystal structure at cooling from room temperature to 80 K has been investigated. The main change is associated with a shift of apical oxygen atoms. Using determined unit cell parameters as function of temperature, the coefficients of linear thermal expansion have been calculated as αX = 1/X·(dX/dT), where X = a, b, c - unit cell dimensions. For the compound without calcium all αX values demonstrate anomalous behavior such as growing at cooling in temperature interval T1 ÷ T2 ∼ 150 ÷ 225 K. The calculation of electronic structure at temperatures above, below and within this interval shows the appearance of the electronic states density peak for Ba and O4 atoms. It is explained by the localization of charge carriers with the participation of the lattice distortion in a form of apical Cu-O bond compression. As the material Y0.9Ca0.1Ba2Cu3Oy regardless of the oxygen content possess low and constant coefficient of thermal expansion along all crystallographic directions, that makes this material suitable for superconducting films and other composites.