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Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 56.093 Å | b: 86.024 Å | c: 128.877 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.97 Å | Reflections | 21798 | Test set | 1075 (4.9%) | ||
R | 0.1980 | R-free | 0.2540 | ||||
According to PDB-REDO | |||||||
Resolution | 1.97 Å | Reflections | 21798 | Test set | 1075 (4.9%) | 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 | 0.1999 | 0.1870 |
R-free |
0.2354
|
0.2106 |
Bond length RMS Z-score | 0.651 | 0.686 |
Bond angle RMS Z-score | 0.737 | 0.821 |
Model quality | ||
Ramachandran plot normality | -1.153 49 | -0.459 69 |
Rotamer normality | -1.992 58 | -1.551 67 |
Coarse packing | 1.058 95 | 1.106 95 |
Fine packing | -0.195 79 | -0.180 79 |
Bump severity | 0.004 78 | 0.005 74 |
Hydrogen bond satisfaction | 0.880 28 | 0.880 28 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 2 |
Side chains flipped | 0 |
Waters removed | 2 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |