A new intermediate in the water-oxidizing reaction has been observed in spinach photosystem II (PSII) membranes that are depleted of Ca2+ from the site which is conformationally coupled to the manganese cluster comprising the water-oxidizing complex (WOC). It gives rise to a recently identified EPR signal (symmetric line shape with width 163 +/- 5 G, g = 2.004 +/- 0.005), which forms in samples inhibited either by depletion of Ca2+ [Boussac, A., Zimmerman, J.-L., & 28, 8984-8989; Sivaraja, M., Tso, J., & Dismukes, G.C. (1989) Biochemistry 28 9459-9464] or by substitution of Cl- by F- (Baumgarten, Philo, and Dismukes, submitted for publication). Further characterization of this EPR signal has revealed the following: (1) it forms independently of the local structure of the PSII acceptors; (2) it arises from photooxidation of a PSII species that donates an electron to Tyr-Z+ or to the Mn cluster in competition with an exogenous donor (DPC); (3) the Curie temperature dependence of the intensity suggests an isolated doublet ground state, attributable to a spin S = 1/2 radical; (4) the electron spin orientation relaxes 1000-fold more rapidly than typical for a free radical, exhibiting a strong temperature dependence of P1/2 (half-saturation power approximately T3.4) and a broad inhomogeneous line width; (5) it yields an undetectable change in the magnetic susceptibility upon formation by a laser flash; (6) it disappears in parallel with release of Mn during reduction with NH2OH, indicating that it forms only in the presence of the modified Mn cluster. (ABSTRACT TRUNCATED AT 250 WORDS)