| 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 8.13 using the deposited PDB model version 1.3 |
| 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 | 0.2296 | R-free | 0.2777 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.00 Å | Reflections | 37752 | Test set | 1926 (5.1%) | ||
| Twin | false | Radiation damage | 51 | ||||
| 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 | 0.2422 | 0.2198 |
| R-free | 0.2900 | 0.2668 |
| Bond length RMS Z-score | 0.968 | 0.344 |
| Bond angle RMS Z-score | 0.726 | 0.592 |
| Model quality | ||
| Ramachandran plot normality | -6.394 2 | -4.729 6 |
| Rotamer normality | -4.759 11 | -4.498 14 |
| Coarse packing | -0.103 44 | 0.341 64 |
| Fine packing | -2.292 8 | -1.759 21 |
| Bump severity | 0.035 24 | 0.065 14 |
| Hydrogen bond satisfaction | 0.792 5 | 0.825 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 52 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 31 |
| Chiralities fixed | 0 |
| Residues fitting density better | 61 |
| Residues fitting density worse | 6 |