Fig 1.
Model and difference electron density maps.
Both panels A and B are from the same structure, PDB ID: 3B1Q, and are centered around the ligands B.330 (A) and P.33 (B). Blue meshes represent the model electron density. Green and red meshes represent discrepancies between experimental data and the structure model. The structure has very good overall quality, as demonstrated by a resolution of 1.7 Å, an R-factor value of 0.176, and an R-free value of 0.207. The panel A shows a high-quality region in the structure where the experimental data and model match very well. And the panel B shows that there are still low-quality regions within the structure, as demonstrated by the green and red blobs around the coordinating ligand residue (“ligand” refers to the coordination chemistry definition of this word).
Fig 2.
Workflow of the electron density analysis.
Fig 3.
Sina plots of density ratio for atoms, residues, and chains, before (Panels A-C) and after (Panels D-F) radii optimization.
PDB ID: 3UBK. The atom density ratios have the largest range, and chain density ratios have the smallest range, which can be used as internal standard to optimize the atom ratios to.
Fig 4.
Sina plot for the volumes of each atom type.
PDB ID: 3UBK.
Fig 5.
Correlation between chain deviation fractions and logarithm B-factors for each atom type.
PDB ID: 3UBK.
Fig 6.
Atom density ratios at each major step of improvement.
A) Original, B) After volume normalization, C) After B-factor correction, D) After radii optimization. PDB ID: 3UBK. After each major step, the overall distribution of the atom density ratios generally becomes less spread.
Table 1.
The atom radii before and after radii optimization.
Fig 7.
Histogram of the median chain deviation fraction for all structures in the PDB.
Fig 8.
Histogram of the mean value of electron density maps provided by PDBe.
The histogram illustrates that most of the electron density maps in the PDB are effectively zero-meaned. A) 2Fo-Fc density map, B) Fo-Fc density map.
Fig 9.
The absolute scale of the density ratio for all structures in the PDB.
Panel A shows the density ratios vs. inverse of voxel volume plot indicates that there is a consistent 1:3 ratio. Panel B is the histogram of the multiplication of the x and y axes values from Panel A. They both show that the density ratio is not affected much by adding an estimated F000 term.
Fig 10.
Evaluative use-case for the electron density conversion factor.
PDB id: 2P7Z, panel A highlighted residue: A.351, panel B highlighted residue: A.389. The blue lattice represents the significant density regions in the 2Fo-Fc map, while the green lattice represents the significant positive discrepant density blobs and the red lattice represents the significant negative discrepant density blobs, both from the Fo-Fc map.