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| Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CLpro |
| This entry was created with PDB-REDO version 7.00. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 2 | a: 106.668 Å | b: 45.160 Å | c: 53.967 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.70 Å | Reflections | 7522 | Test set | 0 (0.0%) | ||
| R | 0.2590 | R-free | 0.3630 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.70 Å | Reflections | 7522 | Test set |
743 (9.9%)
New test set, PDB-REDO compensated for this
|
Twin | false |
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.3202 | 0.2447 |
| R-free |
0.3842
R-free was considered biased, the
estimated unbiased R-free was used
|
0.3461 |
| Bond length RMS Z-score | 0.418 | 0.574 |
| Bond angle RMS Z-score | 0.592 | 0.824 |
| Model quality | ||
| Ramachandran plot normality | -3.080 11 | -3.481 8 |
| Rotamer normality | -6.315 1 | -6.156 1 |
| Coarse packing | -1.272 N/A | -1.379 N/A |
| Fine packing | -2.079 9 | -2.075 10 |
| Bump severity | 0.026 50 | 0.044 31 |
| Hydrogen bond satisfaction | 0.813 8 | 0.791 6 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 14 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 52 |
| Residues fitting density worse | 0 |