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| Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human receptor ACE2 |
| This entry was created with PDB-REDO version 7.32. |
| 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 | 37752 | Test set | 1926 (5.1%) | ||
| R | 0.2300 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.00 Å | Reflections | 37752 | Test set | 1926 (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 | 0.2413 | 0.2394 |
| R-free | 0.2894 | 0.2729 |
| Bond length RMS Z-score | 0.454 | 0.347 |
| Bond angle RMS Z-score | 0.612 | 0.633 |
| Model quality | ||
| Ramachandran plot normality | -6.475 2 | -4.246 8 |
| Rotamer normality | -4.774 17 | -4.148 24 |
| Coarse packing | -1.652 5 | -1.164 12 |
| Fine packing | -2.285 8 | -1.539 30 |
| Bump severity | 0.035 26 | 0.254 4 |
| Hydrogen bond satisfaction | 0.792 4 | 0.821 7 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 39 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 26 |
| Chiralities fixed | 0 |
| Residues fitting density better | 35 |
| Residues fitting density worse | 2 |