| The octameric SARS-CoV main protease |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 41 21 2 | a: 161.930 Å | b: 161.930 Å | c: 166.435 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 3.20 Å | Reflections | 34933 | Test set | 1849 (5.3%) | ||
| R | 0.2204 | R-free | 0.2721 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.20 Å | Reflections | 34933 | Test set |
1772 (5.1%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 83 | ||||
| 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 | 0.2601 | 0.1775 |
| R-free |
0.2736
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2491 |
| Bond length RMS Z-score | 1.097 | 0.636 |
| Bond angle RMS Z-score | 0.936 | 0.887 |
| Model quality | ||
| Ramachandran plot normality | -6.603 1 | -4.321 7 |
| Rotamer normality | -7.232 1 | -5.690 6 |
| Coarse packing | -1.340 6 | -0.619 23 |
| Fine packing | -2.659 4 | -2.001 14 |
| Bump severity | 0.125 8 | 0.181 6 |
| Hydrogen bond satisfaction | 0.759 3 | 0.821 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 15 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 27 |
| Chiralities fixed | 0 |
| Residues fitting density better | 86 |
| Residues fitting density worse | 1 |