| Complex structure of SARS-CoV 3C-like protease with TDT |
| This entry was created with PDB-REDO version 8.10 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 108.511 Å | b: 81.548 Å | c: 53.334 Å | α: 90.00° | β: 105.13° | γ: 90.00° |
| Resolution | 1.78 Å | Reflections | 38304 | Test set | 1929 (5.0%) | ||
| R | 0.1910 | R-free | 0.2240 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.78 Å | Reflections | 38304 | Test set | 1929 (5.0%) | ||
| Twin | false | Radiation damage | 58 | ||||
| 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 | 0.1873 | 0.1663 |
| R-free | 0.2128 | 0.1930 |
| Bond length RMS Z-score | 1.001 | 0.445 |
| Bond angle RMS Z-score | 0.922 | 0.640 |
| Model quality | ||
| Ramachandran plot normality | -1.424 44 | -0.864 59 |
| Rotamer normality | -1.584 60 | 0.062 90 |
| Coarse packing | -0.121 43 | -0.013 48 |
| Fine packing | -2.122 11 | -1.827 19 |
| Bump severity | 0.020 37 | 0.004 76 |
| Hydrogen bond satisfaction | 0.893 41 | 0.886 34 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 91 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 9 |
| Residues fitting density worse | 0 |