| Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 3.0 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 82.299 Å | b: 119.429 Å | c: 113.237 Å | α: 90.00° | β: 91.97° | γ: 90.00° |
| Resolution | 2.90 Å | Reflections | 46095 | Test set | 2254 (4.9%) | ||
| R | 0.2180 | R-free | 0.2750 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.81 Å | Reflections | 46095 | Test set | 2254 (4.9%) | ||
| Twin | false | Radiation damage | 63 | ||||
| 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 | 0.2433 | 0.2188 |
| R-free | 0.2953 | 0.2640 |
| Bond length RMS Z-score | 1.044 | 0.294 |
| Bond angle RMS Z-score | 0.760 | 0.529 |
| Model quality | ||
| Ramachandran plot normality | -5.931 2 | -3.858 10 |
| Rotamer normality | -5.662 6 | -4.344 15 |
| Coarse packing | -0.072 45 | 0.138 55 |
| Fine packing | -2.360 7 | -1.891 17 |
| Bump severity | 0.326 3 | 0.357 3 |
| Hydrogen bond satisfaction | 0.815 7 | 0.619 1 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 45 |
| Side chains flipped | 0 |
| Waters removed | 30 |
| Peptides flipped | 42 |
| Chiralities fixed | 0 |
| Residues fitting density better | 75 |
| Residues fitting density worse | 14 |