| Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of SARS-CoV Main Protease |
| This entry was created with PDB-REDO version 8.10 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 108.195 Å | b: 82.419 Å | c: 53.609 Å | α: 90.00° | β: 104.98° | γ: 90.00° |
| Resolution | 2.17 Å | Reflections | 25625 | Test set | 1306 (5.1%) | ||
| R | 0.2090 | R-free | 0.2480 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.10 Å | Reflections | 25625 | Test set | 1306 (5.1%) | ||
| Twin | false | Radiation damage | 31 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2089 | 0.1818 |
| R-free | 0.2436 | 0.2189 |
| Bond length RMS Z-score | 0.819 | 0.446 |
| Bond angle RMS Z-score | 0.733 | 0.629 |
| Model quality | ||
| Ramachandran plot normality | -1.905 33 | -1.368 45 |
| Rotamer normality | -2.458 42 | -1.545 60 |
| Coarse packing | -0.113 44 | -0.125 43 |
| Fine packing | -1.328 39 | -0.943 55 |
| Bump severity | 0.010 56 | 0.003 81 |
| Hydrogen bond satisfaction | 0.898 47 | 0.898 47 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 17 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 21 |
| Residues fitting density worse | 0 |