| Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 80.008 Å | b: 119.762 Å | c: 108.801 Å | α: 90.00° | β: 96.23° | γ: 90.00° |
| Resolution | 2.80 Å | Reflections | 48054 | Test set | 0 (0.0%) | ||
| R | 0.2140 | R-free | 0.2790 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.79 Å | Reflections | 48054 | Test set |
2342 (4.9%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 32 | ||||
| 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 | 0.2339 | 0.2085 |
| R-free |
0.2831
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2491 |
| Bond length RMS Z-score | 0.916 | 0.277 |
| Bond angle RMS Z-score | 0.735 | 0.511 |
| Model quality | ||
| Ramachandran plot normality | -5.267 4 | -3.389 13 |
| Rotamer normality | -4.970 10 | -3.090 31 |
| Coarse packing | 0.201 58 | 0.348 64 |
| Fine packing | -1.858 18 | -1.334 39 |
| Bump severity | 0.016 43 | 0.018 40 |
| Hydrogen bond satisfaction | 0.832 9 | 0.841 11 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 46 |
| Side chains flipped | 0 |
| Waters removed | 6 |
| Peptides flipped | 25 |
| Chiralities fixed | 0 |
| Residues fitting density better | 43 |
| Residues fitting density worse | 8 |