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Ricin bound to VHH antibody V11B2 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 21 21 2 | a: 77.607 Å | b: 99.559 Å | c: 111.283 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.55 Å | Reflections | 28754 | Test set | 1456 (5.1%) | ||
R | 0.2265 | R-free | 0.2802 | ||||
According to PDB-REDO | |||||||
Resolution | 2.55 Å | Reflections | 28754 | Test set | 1456 (5.1%) | ||
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 | 0.2495 | 0.2563 |
R-free | 0.2938 | 0.2864 |
Bond length RMS Z-score | 0.904 | 0.193 |
Bond angle RMS Z-score | 0.784 | 0.418 |
Model quality | ||
Ramachandran plot normality | -2.937 17 | -2.902 17 |
Rotamer normality | -5.494 11 | -2.424 50 |
Coarse packing | 0.248 74 | 0.142 69 |
Fine packing | -1.219 44 | -0.985 54 |
Bump severity | 0.432 2 | 0.020 39 |
Hydrogen bond satisfaction | 0.851 14 | 0.849 13 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 10 |
Side chains flipped | 0 |
Waters removed | 10 |
Peptides flipped | 2 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |