The Mn4CaO5 cluster of photosystem II promotes a crucial step in the oxygenic photosynthesis, namely, the water-splitting reaction. The structure of such cluster in the S-1 state of the Kok-Joliot's cycle has been recently resolved by femtosecond X-ray free-electron laser (XFEL) measurements. However, the XFEL results are characterized by appreciable discrepancies with previous X-ray diffraction (XRD), as well as with S-1 models based on ab initio calculations. We provide here a unifying picture based on a combined set of DFT-based structures and molecular dynamics simulations of the S-0 and S-1 states. Our findings indicate that the XFEL results cannot be interpreted on the grounds of a single structure. A combination of two S-1 stable isomers together with a minority contribution of the S-0 state is necessary to reproduce XFEL results within 0.16 angstrom.