| Crystal structure of anti- SARS-CoV human neutralizing S230 antibody Fab fragment |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 37.823 Å | b: 104.406 Å | c: 108.710 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.50 Å | Reflections | 69719 | Test set | 3514 (5.0%) | ||
| R | 0.1285 | R-free | 0.1671 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.50 Å | Reflections | 69719 | Test set | 3514 (5.0%) | ||
| Twin | false | Radiation damage | 2 | ||||
| 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 | 0.1321 | 0.1981 |
| R-free | 0.1686 | 0.2199 |
| Bond length RMS Z-score | 1.225 | 0.543 |
| Bond angle RMS Z-score | 0.907 | 0.700 |
| Model quality | ||
| Ramachandran plot normality | 0.959 95 | 1.191 96 |
| Rotamer normality | 1.231 98 | 0.692 96 |
| Coarse packing | 0.623 74 | 0.585 73 |
| Fine packing | 1.042 95 | 0.971 95 |
| Bump severity | 0.003 81 | 0.002 85 |
| Hydrogen bond satisfaction | 0.905 57 | 0.912 66 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 18 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 163 |