| Ricin bound to VHH antibody V5G6 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 44.345 Å | b: 77.438 Å | c: 101.577 Å | α: 89.97° | β: 90.18° | γ: 89.98° |
| Resolution | 2.30 Å | Reflections | 57474 | Test set | 2742 (4.8%) | ||
| R | 0.1870 | R-free | 0.2377 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.30 Å | Reflections | 57474 | Test set | 2742 (4.8%) | ||
| Twin | true | Radiation damage | 53 | ||||
| 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 | 0.2128 | 0.1710 |
| R-free | 0.2603 | 0.2454 |
| Bond length RMS Z-score | 1.636 | 0.601 |
| Bond angle RMS Z-score | 0.732 | 0.768 |
| Model quality | ||
| Ramachandran plot normality | -1.300 47 | -2.438 24 |
| Rotamer normality | -3.489 25 | -3.025 32 |
| Coarse packing | 0.537 71 | -0.015 48 |
| Fine packing | -0.278 77 | 0.546 91 |
| Bump severity | 0.371 2 | 0.498 2 |
| Hydrogen bond satisfaction | 0.864 19 | 0.830 9 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains built | 0 |
| Waters removed | 8 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1038 |
| Residues fitting density worse | 0 |