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| Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 |
| This entry was created with PDB-REDO version 7.31. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 | a: 80.424 Å | b: 119.823 Å | c: 109.772 Å | α: 90.00° | β: 95.50° | γ: 90.00° |
| Resolution | 2.90 Å | Reflections | 46190 | Test set | 0 (0.0%) | ||
| R | 0.2240 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.89 Å | Reflections | 46190 | Test set |
2227 (4.8%)
New test set, PDB-REDO compensated for this
|
Twin | false |
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2499 | 0.2202 |
| R-free |
0.3027
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2569 |
| Bond length RMS Z-score | 0.475 | 0.385 |
| Bond angle RMS Z-score | 0.610 | 0.669 |
| Model quality | ||
| Ramachandran plot normality | -5.922 3 | -3.978 9 |
| Rotamer normality | -4.778 17 | -3.565 31 |
| Coarse packing | -1.410 8 | -0.931 18 |
| Fine packing | -1.939 16 | -1.253 42 |
| Bump severity | 0.032 28 | 0.092 11 |
| Hydrogen bond satisfaction | 0.831 9 | 0.841 11 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 30 |
| Side chains flipped | 0 |
| Waters removed | 7 |
| Peptides flipped | 21 |
| Chiralities fixed | 0 |
| Residues fitting density better | 36 |
| Residues fitting density worse | 6 |