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Figure 3
Electron-density maps during light-state occupancy determination. The substrate, product and FAD cofactor are shown as sticks. (a) Light–dark difference density map, contoured at ±3.0σ (green/red). The de­carboxyl­ation of the fatty acid substrate and the change in conformation of the product alkyl chain are clearly visible. (b) Extrapolated electron-density map, contoured at 1.0σ, showing density for the photolyzed state only. (c) 2mFo − DFc electron-density map contoured at 0.8σ after ensemble refinement. The contribution of the photolyzed state (occupancy ∼0.44) can just be made out in the density of the alkyl chain of the product. (d) Plot of the residual density at the carboxyl­ate position for various assumed occupancies during occupancy determination. Circles show the data points and the straight line is fitted through these points. A clear zero-point crossing is observed at ∼0.44. Note that this graph shows the second of two searches for the zero-point crossing; initially, a much coarser search in terms of trial occupancies (0.05–0.9) is performed, leading to much higher absolute difference map values. The second, finer, search is performed around the zero-point crossing found in the initial, coarse, search. However, the results of the coarse and fine searches typically do not vary by more than 0.03 in occupancy.

IUCrJ
Volume 13| Part 5| September 2026|
ISSN: 2052-2525
https://doi.org/10.1107/S2052252526005403