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C-type carbohydrate-recognition domain 4 of the mannose receptor complexed with Lewis-a |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 33.053 Å | b: 57.180 Å | c: 34.383 Å | α: 90.00° | β: 112.81° | γ: 90.00° |
Resolution | 1.35 Å | Reflections | 25698 | Test set | 1285 (5.0%) | ||
R | 0.1645 | R-free | 0.1984 | ||||
According to PDB-REDO | |||||||
Resolution | 1.35 Å | Reflections | 25698 | Test set | 1285 (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 | 0.1710 | 0.1515 |
R-free | 0.1963 | 0.1919 |
Bond length RMS Z-score | 0.523 | 0.568 |
Bond angle RMS Z-score | 0.728 | 0.709 |
Model quality | ||
Ramachandran plot normality | -1.286 45 | -1.783 34 |
Rotamer normality | 1.151 99 | 1.299 99 |
Coarse packing | 0.039 64 | -0.042 60 |
Fine packing | -2.576 5 | -2.343 7 |
Bump severity | 0.148 7 | 0.139 8 |
Hydrogen bond satisfaction | 0.868 20 | 0.865 19 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 1 |
Side chains flipped | 0 |
Waters removed | 15 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 3 |
Residues fitting density worse | 0 |