| Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 80.435 Å | b: 118.034 Å | c: 112.075 Å | α: 90.00° | β: 93.12° | γ: 90.00° |
| Resolution | 2.68 Å | Reflections | 58223 | Test set | 2675 (4.6%) | ||
| R | 0.1970 | R-free | 0.2288 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.68 Å | Reflections | 58223 | Test set | 2675 (4.6%) | ||
| Twin | false | Radiation damage | 52 | ||||
| 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 | 0.2144 | 0.1971 |
| R-free | 0.2393 | 0.2375 |
| Bond length RMS Z-score | 0.482 | 0.425 |
| Bond angle RMS Z-score | 0.652 | 0.612 |
| Model quality | ||
| Ramachandran plot normality | -1.844 34 | -3.083 16 |
| Rotamer normality | -2.661 38 | -3.290 28 |
| Coarse packing | 0.729 78 | 0.679 76 |
| Fine packing | -1.124 48 | -1.382 37 |
| Bump severity | 0.485 2 | 0.508 1 |
| Hydrogen bond satisfaction | 0.857 16 | 0.838 11 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 8 |
| Peptides flipped | 16 |
| Chiralities fixed | 0 |
| Residues fitting density better | 63 |
| Residues fitting density worse | 6 |