| Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus human 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: 81.362 Å | b: 118.332 Å | c: 111.937 Å | α: 90.00° | β: 93.06° | γ: 90.00° |
| Resolution | 2.90 Å | Reflections | 39951 | Test set | 2003 (5.0%) | ||
| R | 0.2259 | R-free | 0.2826 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.90 Å | Reflections | 39951 | Test set | 2003 (5.0%) | ||
| 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 | 0.2367 | 0.2577 |
| R-free | 0.2922 | 0.2812 |
| Bond length RMS Z-score | 0.890 | 0.300 |
| Bond angle RMS Z-score | 0.723 | 0.540 |
| Model quality | ||
| Ramachandran plot normality | -6.534 1 | -4.444 7 |
| Rotamer normality | -5.646 6 | -4.392 15 |
| Coarse packing | -0.181 40 | -0.029 47 |
| Fine packing | -2.475 6 | -1.853 18 |
| Bump severity | 0.035 24 | 0.043 20 |
| Hydrogen bond satisfaction | 0.803 6 | 0.815 7 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 39 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 42 |
| Chiralities fixed | 0 |
| Residues fitting density better | 16 |
| Residues fitting density worse | 14 |