| Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 81.219 Å | b: 119.277 Å | c: 113.236 Å | α: 90.00° | β: 92.19° | γ: 90.00° |
| Resolution | 3.00 Å | Reflections | 33732 | Test set | 1725 (5.1%) | ||
| R | 0.2392 | R-free | 0.2853 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.99 Å | Reflections | 33732 | Test set | 1725 (5.1%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2516 | 0.2714 |
| R-free | 0.2965 | 0.3136 |
| Bond length RMS Z-score | 0.946 | 0.403 |
| Bond angle RMS Z-score | 0.767 | 0.664 |
| Model quality | ||
| Ramachandran plot normality | -7.268 1 | -6.029 2 |
| Rotamer normality | -5.073 9 | -5.506 7 |
| Coarse packing | -0.382 32 | -0.406 31 |
| Fine packing | -2.667 4 | -2.775 3 |
| Bump severity | 0.089 11 | 0.409 2 |
| Hydrogen bond satisfaction | 0.794 5 | 0.792 5 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 36 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 47 |
| Chiralities fixed | 0 |
| Residues fitting density better | 37 |
| Residues fitting density worse | 35 |