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| Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2 |
| This entry was created with PDB-REDO version 7.31. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 | a: 80.008 Å | b: 119.762 Å | c: 108.801 Å | α: 90.00° | β: 96.22° | γ: 90.00° |
| Resolution | 2.80 Å | Reflections | 48071 | Test set | 0 (0.0%) | ||
| R | 0.2140 | R-free | 0.2790 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.79 Å | Reflections | 48071 | Test set |
2391 (5.0%)
New test set, PDB-REDO compensated for this
|
Twin | false |
| 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 | 0.2355 | 0.2188 |
| R-free |
0.2851
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2529 |
| Bond length RMS Z-score | 0.465 | 0.374 |
| Bond angle RMS Z-score | 0.634 | 0.630 |
| Model quality | ||
| Ramachandran plot normality | -5.348 4 | -3.484 12 |
| Rotamer normality | -4.969 15 | -3.199 37 |
| Coarse packing | -1.373 8 | -1.024 15 |
| Fine packing | -1.918 16 | -1.310 40 |
| Bump severity | 0.018 42 | 0.017 44 |
| Hydrogen bond satisfaction | 0.835 10 | 0.822 7 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 49 |
| Side chains flipped | 0 |
| Waters removed | 4 |
| Peptides flipped | 20 |
| Chiralities fixed | 0 |
| Residues fitting density better | 21 |
| Residues fitting density worse | 8 |