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![[Figure 3]](von5002fig3mag.jpg)
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Figure 3
Structures refined in Servalcat using the updated monomer library and restraints from MetalCoord. The metal-containing compounds are highlighted in ball-and-stick representation. Water molecules are shown as red spheres. Coordination of other surrounding metal atoms and selected interactions are depicted as dashed lines. Atoms are coloured by their element: carbon, grey; nitrogen, blue; oxygen, red; sulfur, yellow; phosphorus, light orange; iron, dark orange; fluorine, light green; magnesium, dark green; sodium, purple. The figures were prepared using PyMOL 3.0 (Schrödinger). The refinement statistics are reported in Supplementary Table S1 and the relevant restraints are listed in Supplementary Table S2. (a, b) The cryo-EM SPA structure of monomeric photosystem II from Synechocystis (PDB entry 6wj6; Gisriel et al., 2020  ). The originally deposited structure model is shown in magenta. The new monomer library in concert with refinement by Servalcat improved the modelling of the coordination of the magnesium cation in chlorophyll A (monomer code CLA) (a) as well as the coordination of the iron cation in haem (monomer code HEM) (b). The density was resampled (rate 1.5) and sharpened in Coot (Emsley et al., 2010). (c) The hybrid iron–sulfur–oxygen cluster (monomer code FS2) in the hybrid cluster protein crystal structure (PDB entry 1w9m; Aragão et al., 2008). mCys denotes S-mercaptocysteine. The 2mFo − DFc density map is contoured at a 2σ level. (d) Trigonal bipyramidal aluminium coordination in aluminium trifluoride (monomer code AF3) in the crystal structure of nitrogenase-like dark-operative protochlorophyllide oxidoreductase complex, chain A (PDB entry 2ynm; Moser et al., 2013). The 2mFo − DFc density map is contoured at a 1σ level. (e) Octahedral aluminium coordination in aluminium trifluoride (monomer code AF3) in the crystal structure of dUTPase (PDB entry 4dl8; Hemsworth et al., 2013). The 2mFo − DFc density map is contoured at a 1σ level. (f) Ferricyanide [Fe(CN)6]3− (monomer code FC6) modelled with a partial occupancy of 0.8 in the crystal structure of bilirubin oxidase, chain A (PDB entry 6i3j; Koval', Švecová et al., 2019). The 2mFo − DFc density map is contoured at a 0.9σ level. |
![[Figure 3]](von5002fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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