| Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed with human-civet chimeric receptor ACE2 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 81.670 Å | b: 119.523 Å | c: 113.532 Å | α: 90.00° | β: 92.50° | γ: 90.00° |
| Resolution | 3.00 Å | Reflections | 41384 | Test set | 2066 (5.0%) | ||
| R | 0.2388 | R-free | 0.2918 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.00 Å | Reflections | 41384 | Test set | 2066 (5.0%) | ||
| Twin | false | Radiation damage | 21 | ||||
| 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 | 0.2496 | 0.2562 |
| R-free | 0.3059 | 0.2931 |
| Bond length RMS Z-score | 1.212 | 0.326 |
| Bond angle RMS Z-score | 0.772 | 0.570 |
| Model quality | ||
| Ramachandran plot normality | -6.582 1 | -4.601 6 |
| Rotamer normality | -5.479 7 | -4.784 11 |
| Coarse packing | -0.299 35 | -0.121 43 |
| Fine packing | -2.467 6 | -2.277 8 |
| Bump severity | 0.038 22 | 0.146 7 |
| Hydrogen bond satisfaction | 0.795 5 | 0.583 0 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 39 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 41 |
| Chiralities fixed | 0 |
| Residues fitting density better | 11 |
| Residues fitting density worse | 40 |