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Room temperature X-ray structure of H/D-exchanged PLL lectin in complex with L-fucose |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 72.600 Å | b: 89.240 Å | c: 159.280 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.60 Å | Reflections | 67576 | Test set | 3379 (5.0%) | ||
R | 0.1499 | R-free | 0.1728 | ||||
According to PDB-REDO | |||||||
Resolution | 1.60 Å | Reflections | 67576 | Test set | 3379 (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 | 0.1501 | 0.1196 |
R-free | 0.1674 | 0.1474 |
Bond length RMS Z-score | 0.612 | 0.627 |
Bond angle RMS Z-score | 0.702 | 0.672 |
Model quality | ||
Ramachandran plot normality | -0.355 74 | -0.222 77 |
Rotamer normality | -0.988 72 | -0.268 86 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 4 |
Side chains flipped | 0 |
Waters removed | 171 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 197 |
Residues fitting density worse | 0 |