TABLE 1.
Shown are improvements in JNK1 and JNK2 protein-inhibitor structural models using Ewald refinement. The R/Rfree statistics for the deposited PDB structures are shown as originally reported and after recalculation using the Force Field X program. After Ewald refinement, the final structural models improved the mean Rfree value relative to the recalculated Rfree by 1.4% on average. In addition, the mean MolProbity score was improved from the 51rst percentile to the 97th percentile (see the text for a description of the MolProbity structure validation tool).
| PDB / Ligand | Original Refinements
|
Ewald Refinements
|
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Res (Å) | R / Rfree | MolProbity
|
Recalculated R / Rfree | Final R / Rfree | MolProbity
|
RMSD (Å) | |||
| Score | % | Score | % | ||||||
| 3O17 / Apo | 3.0 | 26.3 / 30.8 | 3.9 | 17 | 25.5 / 30.6 | 22.9 / 27.9 | 2.3 | 97 | 0.38 |
| 3O2M / 46A | 2.7 | 23.3 / 26.6 | 3.3 | 30 | 22.8 / 26.4 | 19.7 / 24.9 | 2.3 | 94 | 0.25 |
| 3NEW / 3NE | 2.5 | 21.9 / 30.6 | 3.0 | 42 | 22.0 / 30.6 | 21.6 / 29.2 | 1.6 | 99 | 0.40 |
| 3E7O / 35F | 2.1 | 21.9 / 25.0 | 2.1 | 77 | 21.7 / 24.6 | 18.4 / 23.0 | 1.6 | 97 | 0.39 |
| 3NPC / B96 | 2.4 | 21.4 / 25.4 | 2.1 | 88 | 21.0 / 24.7 | 18.8 / 25.0 | 1.7 | 98 | 0.16 |
|
| |||||||||
| Mean | 2.5 | 23.0 / 27.7 | 2.9 | 51 | 22.7 / 27.4 | 20.3 / 26.0 | 1.9 | 97 | 0.31 |