The chalcogenide Bi$_2$Se$_3$ can attain the three dimensional (3D) Dirac semimetal state under the influence of strain and microstrain. Here we report the presnece of large linear magnetoresistance in such a Bi$_2$Se$_3$ crystal. The magnetoresistance has quadratic form at low fields which crossovers to linear above 4 T. The temperature dependence of magnetoresistance scales with carrier mobility and the crossover field scales with inverse of mobility. Our analysis suggest that the linear magnetoresistance in our system has a classical origin and arises from the scattering of high mobility 3D Dirac electrons from crystalline inhomogeneities. We observe that the charged selenium vacancies are strongly screened by high mobility Dirac electrons and the neutral crystalline defects are the main scattering center for transport mechanism. Our analysis suggests that both the resistivity and the magnetoresistance have their origin in scattering of charge carriers from neutral defects.
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