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Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 43 21 2 | a: 85.675 Å | b: 85.675 Å | c: 257.073 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.36 Å | Reflections | 40409 | Test set | 2028 (5.0%) | ||
R | 0.2280 | R-free | 0.2520 | ||||
According to PDB-REDO | |||||||
Resolution | 2.36 Å | Reflections | 40409 | Test set | 2028 (5.0%) | ||
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 | 0.2347 | 0.2233 |
R-free | 0.2572 | 0.2349 |
Bond length RMS Z-score | 0.394 | 0.470 |
Bond angle RMS Z-score | 0.605 | 0.662 |
Model quality | ||
Ramachandran plot normality | -0.648 63 | -0.591 65 |
Rotamer normality | -0.999 77 | 0.657 97 |
Coarse packing | 1.218 96 | 1.097 95 |
Fine packing | 0.429 89 | 0.559 91 |
Bump severity | 0.002 87 | 0.003 82 |
Hydrogen bond satisfaction | 0.889 37 | 0.888 36 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 24 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |