| 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 8.12 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 80.352 Å | b: 119.841 Å | c: 109.420 Å | α: 90.00° | β: 95.88° | γ: 90.00° |
| Resolution | 3.10 Å | Reflections | 38250 | Test set | 0 (0.0%) | ||
| R | 0.2210 | R-free | 0.3020 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.05 Å | Reflections | 38250 | Test set |
1896 (5.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2445 | 0.2342 |
| R-free |
0.2861
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2721 |
| Bond length RMS Z-score | 0.781 | 0.374 |
| Bond angle RMS Z-score | 0.748 | 0.600 |
| Model quality | ||
| Ramachandran plot normality | -6.401 2 | -5.043 4 |
| Rotamer normality | -5.557 6 | -4.437 14 |
| Coarse packing | 0.085 53 | 0.306 63 |
| Fine packing | -2.179 10 | -1.702 23 |
| Bump severity | 0.028 29 | 0.040 21 |
| Hydrogen bond satisfaction | 0.812 7 | 0.821 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 43 |
| Side chains flipped | 0 |
| Waters removed | 7 |
| Peptides flipped | 32 |
| Chiralities fixed | 0 |
| Residues fitting density better | 12 |
| Residues fitting density worse | 3 |