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 them 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 performance of the proposed estimator is illustrated and compared to other methods using data from simulations and measurements, respectively. 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 additional degrees of freedom in the element factor model. We find that the penalty in SNR is 2.5 dB when introducing a model with two degrees of freedom relative to having zero degrees of freedom. Finally, the tradeoff between the number of degrees of freedom and the accuracy of the estimate is studied. A linear array is treated in more detail and the analysis provides a specific design tradeoff.