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| Crystal structure of SARS-CoV main protease with authentic N and C-termini |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 108.406 Å | b: 81.750 Å | c: 81.750 Å | α: 90.00° | β: 104.70° | γ: 90.00° |
| Resolution | 1.60 Å | Reflections | 54588 | Test set | 5530 (10.1%) | ||
| R | 0.2010 | R-free | 0.2140 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.60 Å | Reflections | 54588 | Test set | 5530 (10.1%) | ||
| Twin | false | Radiation damage | 65 | ||||
| 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 | 0.2652 | 0.1560 |
| R-free |
0.2189
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1833 |
| Bond length RMS Z-score | 0.653 | 0.935 |
| Bond angle RMS Z-score | 0.870 | 0.923 |
| Model quality | ||
| Ramachandran plot normality | -1.070 53 | -0.381 73 |
| Rotamer normality | -1.017 72 | -0.037 89 |
| Coarse packing | 0.038 51 | 0.075 52 |
| Fine packing | -1.410 36 | -1.321 39 |
| Bump severity | 0.007 65 | 0.005 72 |
| Hydrogen bond satisfaction | 0.892 40 | 0.901 51 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 16 |
| Side chains flipped | 0 |
| Waters removed | 38 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 65 |
| Residues fitting density worse | 0 |