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Joint X-ray/neutron room temperature structure of perdeuterated PLL lectin in complex with perdeuterated L-fucose |
This entry was created with PDB-REDO version 7.36. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 72.665 Å | b: 89.210 Å | c: 159.235 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.84 Å | Reflections | 45276 | Test set | 2265 (5.0%) | ||
R | 0.1210 | R-free | 0.1400 | ||||
According to PDB-REDO | |||||||
Resolution | 1.84 Å | Reflections | 45276 | Test set | 2265 (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 | 0.2008 | 0.1824 |
R-free | 0.2323 R-free was considered biased, the estimated unbiased R-free was used | 0.2037 |
Bond length RMS Z-score | 0.581 | 0.667 |
Bond angle RMS Z-score | 0.759 | 0.804 |
Model quality | ||
Ramachandran plot normality | -0.322 72 | -0.378 71 |
Rotamer normality | -0.523 85 | -0.875 80 |
Coarse packing | 0.661 87 | 0.597 86 |
Fine packing | 0.864 94 | 0.714 93 |
Bump severity | 0.003 82 | 0.004 78 |
Hydrogen bond satisfaction | 0.880 28 | 0.879 28 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 12 |
Side chains flipped | 0 |
Waters removed | 1001 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 3 |
Residues fitting density worse | 0 |