Custom geometry restraint files for Mn₄CaO₅ cluster refinement in extrinsic-protein-reconstituted photosystem II

This dataset contains the custom geometry restraint dictionary (OEX.cif) and the PHENIX geometry edits file (OEX_ligand.edits) used for refinement of the
extrinsic-protein-reconstituted Photosystem II (PSII) structure described in the manuscript:

“Structural Basis for Impaired Oxygen Evolution in Extrinsic-Protein-Reconstituted Photosystem II” by Yoshiki Nakajima, Koji Kato, Jian-Ren Shen, and Ryo Nagao.

The OEX.cif file defines the internal bonding and geometric parameters of the Mn₄CaO₅ oxygen-evolving complex, while the OEX_ligand.edits file specifies
coordination restraints between the cluster and surrounding protein residues and water molecules. These files were used directly in phenix.refine and are
provided to ensure complete transparency and reproducibility of the refinement procedure reported in the associated study.

Software used:

• PHENIX v1.21.1-5286

Both restraint files correspond exactly to those used for the final refined structure. Users should note that water residue numbers may change during
wwPDB deposition; the numbering in the .edits file may need to be updated to match the final deposited model.

Additional note:

This dataset is associated with the accepted manuscript entitled “Structural Basis for Impaired Oxygen Evolution in Extrinsic-Protein-Reconstituted Photosystem II.” The final publication details, including the DOI, are not yet available and will be added once assigned.