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Ricin bound to VHH antibody V5E4 |
This entry was created with PDB-REDO version 7.35. |
From original header | |||||||
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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 |