To investigate the impact of impurities on properties of single crystals of rubrene (C48H24), we consider structural, charge transport and optical properties. We show that transport properties are strongly influenced by the presence of a bandgap acceptor state, commonly occurring in crystals of rubrene. The bandgap state is likely caused by incorporation of an oxygen-related impurity. We demonstrate that the impurity presence can be detected using optical spectroscopy. The impurity model explains commonly-observed variations of rubrene properties. The acceptor-like characteristics of the impurity suggests a possible approach for modification of the charge transport in molecular crystals.