| Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 |
| This entry was created with PDB-REDO version 8.12. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 41 21 2 | a: 104.670 Å | b: 104.670 Å | c: 228.720 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.45 Å | Reflections | 47591 | Test set | 2426 (5.1%) | ||
| R | 0.1920 | R-free | 0.2269 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.45 Å | Reflections | 47591 | Test set | 2426 (5.1%) | ||
| Twin | false | Radiation damage | 13 | ||||
| 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 | 0.2106 | 0.1982 |
| R-free | 0.2390 | 0.2381 |
| Bond length RMS Z-score | 0.908 | 0.445 |
| Bond angle RMS Z-score | 0.776 | 0.621 |
| Model quality | ||
| Ramachandran plot normality | -2.155 28 | -2.040 30 |
| Rotamer normality | -2.844 35 | -2.524 40 |
| Coarse packing | 1.037 86 | 0.989 85 |
| Fine packing | -0.894 57 | -0.870 58 |
| Bump severity | 0.304 3 | 0.308 3 |
| Hydrogen bond satisfaction | 0.875 25 | 0.875 25 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 38 |
| Peptides flipped | 3 |
| Chiralities fixed | 0 |
| Residues fitting density better | 19 |
| Residues fitting density worse | 0 |