| Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CLpro |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 1.5 |
| 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 |
742 (9.9%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 35 | ||||
| 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 | 0.3204 | 0.2493 |
| R-free |
0.3891
R-free was considered biased, the
estimated unbiased R-free was used
|
0.3324 |
| Bond length RMS Z-score | 0.802 | 0.226 |
| Bond angle RMS Z-score | 0.651 | 0.485 |
| Model quality | ||
| Ramachandran plot normality | -3.763 11 | -3.388 13 |
| Rotamer normality | -5.320 8 | -4.304 15 |
| Coarse packing | -0.883 14 | -0.962 12 |
| Fine packing | -1.815 20 | -1.936 16 |
| Bump severity | 0.025 32 | 0.037 23 |
| Hydrogen bond satisfaction | 0.823 8 | 0.794 5 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 4 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 0 |