A novel method is proposed for estimation of the mutual coupling matrix of an antenna array. The method extends previous work by incorporating an unknown phase center and the element factor (antenna radiation pattern) in the model, and treating these as nuisance parameters during the estimation of coupling. To facilitate this, a parametrization of the element factor based on a truncated Fourier series is proposed. The Cramer-Rao bound (CRB) for the estimation problem is derived and used to analyze how the required amount of measurement data increases when introducing a more and more flexible model for the element factor. Finally, the performance of the proposed estimator is illustrated using data from measurements on an 8-element antenna array.