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| Crystal structure of native SARS CLpro |
| This entry was created with PDB-REDO version 8.08. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 2 | a: 107.190 Å | b: 45.060 Å | c: 53.990 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.80 Å | Reflections | 9205 | Test set | 692 (7.5%) | ||
| R | 0.2410 | R-free | 0.2880 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.51 Å | Reflections | 9205 | Test set | 692 (7.5%) | ||
| Twin | false | Radiation damage | 5 | ||||
| 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 | 0.3164 | 0.2291 |
| R-free |
0.3849
R-free was considered biased, the
estimated unbiased R-free was used
|
0.3120 |
| Bond length RMS Z-score | 1.833 | 0.422 |
| Bond angle RMS Z-score | 1.229 | 0.634 |
| Model quality | ||
| Ramachandran plot normality | -6.197 2 | -5.047 4 |
| Rotamer normality | -5.615 6 | -4.876 11 |
| Coarse packing | -1.214 8 | -0.980 12 |
| Fine packing | -2.793 3 | -2.215 10 |
| Bump severity | 0.131 8 | 0.022 35 |
| Hydrogen bond satisfaction | 0.768 3 | 0.819 7 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 11 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |