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C-type carbohydrate-recognition domain 4 of the mannose receptor complexed with Fuc-(alpha1-3)-GlcNAc |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 34.120 Å | b: 54.245 Å | c: 35.805 Å | α: 90.00° | β: 94.99° | γ: 90.00° |
Resolution | 1.20 Å | Reflections | 40253 | Test set | 1987 (4.9%) | ||
R | 0.1485 | R-free | 0.1784 | ||||
According to PDB-REDO | |||||||
Resolution | 1.20 Å | Reflections | 40253 | Test set | 1987 (4.9%) | ||
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 | 0.1509 | 0.1304 |
R-free | 0.1727 | 0.1605 |
Bond length RMS Z-score | 0.533 | 0.902 |
Bond angle RMS Z-score | 0.753 | 0.867 |
Model quality | ||
Ramachandran plot normality | -1.251 46 | -1.209 47 |
Rotamer normality | 0.711 97 | 0.552 96 |
Coarse packing | -0.268 48 | -0.267 48 |
Fine packing | -2.451 6 | -2.383 7 |
Bump severity | 0.161 7 | 0.179 6 |
Hydrogen bond satisfaction | 0.875 25 | 0.882 30 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 2 |
Side chains flipped | 0 |
Waters removed | 32 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 20 |
Residues fitting density worse | 0 |