| Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 1.6 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 64.693 Å | b: 68.611 Å | c: 80.085 Å | α: 90.00° | β: 98.08° | γ: 90.00° |
| Resolution | 2.30 Å | Reflections | 27923 | Test set | 1339 (4.8%) | ||
| R | 0.1990 | R-free | 0.2610 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.29 Å | Reflections | 27923 | Test set | 1339 (4.8%) | ||
| Twin | false | Radiation damage | 45 | ||||
| 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 | 0.2018 | 0.1829 |
| R-free | 0.2518 | 0.2330 |
| Bond length RMS Z-score | 0.565 | 0.424 |
| Bond angle RMS Z-score | 0.745 | 0.616 |
| Model quality | ||
| Ramachandran plot normality | -2.115 29 | -1.262 48 |
| Rotamer normality | -2.296 45 | -1.487 62 |
| Coarse packing | -0.371 32 | -0.320 34 |
| Fine packing | -0.625 67 | -0.402 74 |
| Bump severity | 0.097 10 | 0.088 11 |
| Hydrogen bond satisfaction | 0.855 15 | 0.874 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 49 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |