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Room temperature X-ray structure of perdeuterated 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: 72.620 Å | b: 89.070 Å | c: 159.200 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.55 Å | Reflections | 74700 | Test set | 3735 (5.0%) | ||
R | 0.1446 | R-free | 0.1621 | ||||
According to PDB-REDO | |||||||
Resolution | 1.55 Å | Reflections | 74700 | Test set | 3735 (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 | |
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Crystallographic refinement | ||
R | 0.1436 | 0.1111 |
R-free | 0.1591 | 0.1341 |
Bond length RMS Z-score | 0.594 | 0.831 |
Bond angle RMS Z-score | 0.702 | 0.786 |
Model quality | ||
Ramachandran plot normality | -0.222 77 | -0.422 72 |
Rotamer normality | -0.738 77 | 0.018 90 |
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 | 160 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 216 |
Residues fitting density worse | 0 |