The polarized Raman scattering spectra from freshly cleaved $ab$, $ac$, and $bc$ surfaces of high quality twin free YBa$_2$Cu$_3$O$_{6.5}$ (Ortho-II) single crystals ($T_c$=57.5 K and $Delta T = 0.6$ K) were studied between 80 and 300 K. All eleven $A_g$ Raman modes expected for the Ortho-II structure as well some modes of $B_{2g}$ and $B_{3g}$ symmetry were identified in close comparison with predictions of lattice dynamical calculations. The electronic scattering from the $ab$ planes is strongly anisotropic and decreases between 200 and 100 K within the temperature range of previously reported pseudogap opening. The coupling of phonons to Raman active electronic excitations manifested by asymmetric (Fano) profiles of several modes also decreases in the same range. Among the new findings that distinguish the Raman scattering of Ortho-II from that of Ortho-I phase is the unusual relationship ($alpha_{xx} approx -alpha_{yy}$) between the elements of the Raman tensor of the apex oxygen $A_g$ mode.
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