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Crystal structure of the 5F-tryptophan RSL lectin in complex with Lewis x tetrasaccharide |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | F 2 3 | a: 129.883 Å | b: 129.883 Å | c: 129.883 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.28 Å | Reflections | 46835 | Test set | 2369 (5.1%) | ||
R | 0.1224 | R-free | 0.1476 | ||||
According to PDB-REDO | |||||||
Resolution | 1.28 Å | Reflections | 46835 | Test set | 2369 (5.1%) | ||
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 | 0.1229 | 0.1209 |
R-free | 0.1487 | 0.1481 |
Bond length RMS Z-score | 1.259 | 0.711 |
Bond angle RMS Z-score | 1.052 | 0.813 |
Model quality | ||
Ramachandran plot normality | -0.035 81 | 0.127 85 |
Rotamer normality | -0.012 89 | 0.321 93 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.351 3 | 0.355 3 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 5 |
Side chains flipped | 3 |
Waters removed | 23 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 4 |