This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
| Crystal structure of spike protein receptor-binding domain from the 2002-2003 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: 80.352 Å | b: 119.841 Å | c: 109.420 Å | α: 90.00° | β: 95.89° | γ: 90.00° |
| Resolution | 3.10 Å | Reflections | 38289 | Test set | 0 (0.0%) | ||
| R | 0.2210 | R-free | 0.3020 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.05 Å | Reflections | 38289 | Test set |
1794 (4.7%)
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 | 0.2450 | 0.2487 |
| R-free |
0.2866
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2720 |
| Bond length RMS Z-score | 0.475 | 0.336 |
| Bond angle RMS Z-score | 0.638 | 0.607 |
| Model quality | ||
| Ramachandran plot normality | -6.431 2 | -3.954 9 |
| Rotamer normality | -5.551 11 | -3.659 30 |
| Coarse packing | -1.597 5 | -1.123 13 |
| Fine packing | -2.222 9 | -1.513 31 |
| Bump severity | 0.030 29 | 0.026 33 |
| Hydrogen bond satisfaction | 0.817 7 | 0.825 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 36 |
| Side chains flipped | 0 |
| Waters removed | 11 |
| Peptides flipped | 32 |
| Chiralities fixed | 0 |
| Residues fitting density better | 7 |
| Residues fitting density worse | 3 |