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| Ricin bound to VHH antibody V5E4 |
| This entry was created with PDB-REDO version 7.35. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 45.281 Å | b: 76.494 Å | c: 101.440 Å | α: 90.00° | β: 90.92° | γ: 90.00° |
| Resolution | 2.81 Å | Reflections | 16830 | Test set | 879 (5.2%) | ||
| R | 0.2370 | R-free | 0.2940 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.81 Å | Reflections | 16830 | Test set | 879 (5.2%) | Twin | false |
| 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 | 0.2654 | 0.2631 |
| R-free | 0.3078 | 0.3553 |
| Bond length RMS Z-score | 0.259 | 0.583 |
| Bond angle RMS Z-score | 0.539 | 0.847 |
| Model quality | ||
| Ramachandran plot normality | -3.384 13 | -4.484 7 |
| Rotamer normality | -3.039 39 | -5.376 12 |
| Coarse packing | -0.897 19 | -1.205 11 |
| Fine packing | -1.260 42 | -1.586 28 |
| Bump severity | 0.354 3 | 0.370 2 |
| Hydrogen bond satisfaction | 0.783 4 | 0.804 5 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains flipped | 1 |
| Waters removed | 23 |
| Peptides flipped | 17 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |