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| Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77 |
| This entry was created with PDB-REDO version 7.29 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 2 | a: 45.050 Å | b: 63.840 Å | c: 106.588 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.10 Å | Reflections | 18524 | Test set | 1852 (10%) | ||
| R | 0.1500 | R-free | 0.2210 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.10 Å | Reflections | 18524 | Test set |
1869 (10.1%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.1597 | 0.1697 |
| R-free |
0.2083
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2403 |
| Bond length RMS Z-score | 0.437 | 0.501 |
| Bond angle RMS Z-score | 0.724 | 0.727 |
| Model quality | ||
| Ramachandran plot normality | -0.323 72 | -0.700 62 |
| Rotamer normality | -2.238 53 | -2.069 57 |
| Coarse packing | -0.544 34 | -0.585 32 |
| Fine packing | -1.518 31 | -1.323 39 |
| Bump severity | 0.010 58 | 0.002 87 |
| Hydrogen bond satisfaction | 0.895 44 | 0.899 49 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains built | 0 |
| Waters removed | 34 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |