| 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 8.12 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | 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 | 46127 | Test set | 0 (0.0%) | ||
| R | 0.2240 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.89 Å | Reflections | 46127 | Test set |
2327 (5.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 22 | ||||
| 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 | 0.2503 | 0.2199 |
| R-free |
0.3032
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2648 |
| Bond length RMS Z-score | 0.759 | 0.458 |
| Bond angle RMS Z-score | 0.727 | 0.687 |
| Model quality | ||
| Ramachandran plot normality | -5.883 2 | -4.681 6 |
| Rotamer normality | -4.757 11 | -3.968 19 |
| Coarse packing | 0.225 59 | 0.372 65 |
| Fine packing | -1.879 17 | -1.490 32 |
| Bump severity | 0.029 28 | 0.039 22 |
| Hydrogen bond satisfaction | 0.830 9 | 0.826 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 39 |
| Side chains flipped | 0 |
| Waters removed | 15 |
| Peptides flipped | 41 |
| Chiralities fixed | 0 |
| Residues fitting density better | 44 |
| Residues fitting density worse | 8 |