| Crystal structure of SARS spike protein receptor binding domain |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 43 21 2 | a: 75.884 Å | b: 75.884 Å | c: 235.863 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.20 Å | Reflections | 36036 | Test set | 1798 (5.0%) | ||
| R | 0.1824 | R-free | 0.2131 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 36036 | Test set | 1798 (5.0%) | ||
| Twin | false | Radiation damage | 24 | ||||
| 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 | 0.2232 | 0.1747 |
| R-free | 0.2504 | 0.2118 |
| Bond length RMS Z-score | 1.070 | 0.732 |
| Bond angle RMS Z-score | 0.837 | 0.834 |
| Model quality | ||
| Ramachandran plot normality | -0.767 62 | -1.094 53 |
| Rotamer normality | -1.938 52 | -1.762 56 |
| Coarse packing | -0.777 17 | -0.870 15 |
| Fine packing | -1.546 30 | -1.698 24 |
| Bump severity | 0.003 81 | 0.008 62 |
| Hydrogen bond satisfaction | 0.851 14 | 0.862 18 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 21 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 95 |
| Residues fitting density worse | 0 |