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fucose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain |
This entry was created with PDB-REDO version 7.35. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 45.120 Å | b: 50.670 Å | c: 79.370 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 0.97 Å | Reflections | 106862 | Test set | 5344 (5.0%) | ||
R | 0.1220 | R-free | 0.1370 | ||||
According to PDB-REDO | |||||||
Resolution | 0.96 Å | Reflections | 106862 | Test set | 5344 (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 | 0.1335 | 0.1331 |
R-free | 0.1470 | 0.1460 |
Bond length RMS Z-score | 0.676 | 0.552 |
Bond angle RMS Z-score | 0.977 | 0.844 |
Model quality | ||
Ramachandran plot normality | -1.579 38 | -1.677 36 |
Rotamer normality | -0.395 87 | -0.052 92 |
Coarse packing | -0.214 51 | -0.223 50 |
Fine packing | -1.749 22 | -1.646 26 |
Bump severity | 0.000 96 | 0.000 96 |
Hydrogen bond satisfaction | 0.882 30 | 0.871 22 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 4 |
Side chains flipped | 0 |
Waters removed | 33 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 5 |
Residues fitting density worse | 4 |