| Ricin bound to VHH antibody V5E4 |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 1.2 |
| 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 | 0.2367 | R-free | 0.2937 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.81 Å | Reflections | 16830 | Test set | 879 (5.2%) | ||
| 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 | 0.2665 | 0.2753 |
| R-free | 0.3085 | 0.3478 |
| Bond length RMS Z-score | 0.965 | 0.535 |
| Bond angle RMS Z-score | 0.686 | 0.678 |
| Model quality | ||
| Ramachandran plot normality | -3.342 14 | -4.491 7 |
| Rotamer normality | -3.033 32 | -4.236 16 |
| Coarse packing | -0.286 36 | -0.369 32 |
| Fine packing | -0.915 57 | -1.169 46 |
| Bump severity | 0.351 3 | 0.347 3 |
| Hydrogen bond satisfaction | 0.786 4 | 0.792 5 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 95 |
| Peptides flipped | 11 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |