Figure 2
Electron density of original 3k78
model. 2mFo − DFc electron density contoured at 0.8σ (blue), 5σ mFo − DFc difference density (positive light green, negative red). The left panel shows the misplaced residues in the original 3k78
model (yellow carbon stick model) and in the original electron density, reconstructed as described in the text. No refinement has been conducted, but the correct placement of the residues can be easily recognized. The right panels show the same electron density, but now additionally with the starting model 1fm4
(not a re-refined 3k78
model) loaded into COOT. The starting model 1fm4
(orange carbon stick model) fits the electron density better than the deposited model, which indicates that the 3k78
model has not been properly refined (or that the structure factors do not match the model). |