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We report the existence of two distinct oxygen-radical-containing Mn 4 CaO 5/6 conformations with short O···O bonds in the crystal structures of the oxygen-evolving enzyme photosystem II (PSII), obtained using an X-ray free electron laser (XFEL). A short O···O distance of &lt;2.3 Å between the O4 site of the Mn 4 CaO 5 complex and the adjacent water molecule (W539) in the proton-conducting O4-water chain was observed in the second flash-induced (2F) XFEL structure (2F-XFEL), which may correspond to S 3 . By use of a quantum mechanical/molecular mechanical approach, the OH • formation at W539 and the short O4···O W539 distance (&lt;2.3 Å) were reproduced in S 2 and S 3 with reduced Mn1(III), which lacks the additional sixth water molecule O6. As the O •- formation at O6 and the short O5···O6 distance (1.9 Å) have been reported in another 2F-XFEL structure with reduced Mn4(III), two distinct oxygen-radical conformations exist in the 2F-XFEL crystals.

Two Distinct Oxygen-Radical Conformations in the X-ray Free Electron Laser Structures of Photosystem II