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| Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 |
| This entry was created with PDB-REDO version 7.34. |
| 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 | 0.2270 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.45 Å | Reflections | 47591 | Test set | 2426 (5.1%) | Twin | false |
| 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 | 0.2096 | 0.2004 |
| R-free | 0.2387 | 0.2376 |
| Bond length RMS Z-score | 0.347 | 0.488 |
| Bond angle RMS Z-score | 0.633 | 0.716 |
| Model quality | ||
| Ramachandran plot normality | -2.316 24 | -2.615 20 |
| Rotamer normality | -2.844 42 | -2.652 46 |
| Coarse packing | -0.382 42 | -0.493 36 |
| Fine packing | -0.930 56 | -0.923 56 |
| Bump severity | 0.304 3 | 0.325 3 |
| Hydrogen bond satisfaction | 0.898 48 | 0.878 27 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 33 |
| Peptides flipped | 5 |
| Chiralities fixed | 0 |
| Residues fitting density better | 14 |
| Residues fitting density worse | 1 |