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X-ray structure of the CCL2 lectin in complex with sialyl lewis X |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 61 2 2 | a: 121.680 Å | b: 121.680 Å | c: 144.907 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.95 Å | Reflections | 46081 | Test set | 2327 (5.0%) | ||
R | 0.1750 | R-free | 0.2043 | ||||
According to PDB-REDO | |||||||
Resolution | 1.95 Å | Reflections | 46081 | Test set | 2327 (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 | 0.1758 | 0.1605 |
R-free | 0.2063 | 0.1922 |
Bond length RMS Z-score | 1.214 | 0.978 |
Bond angle RMS Z-score | 0.919 | 0.900 |
Model quality | ||
Ramachandran plot normality | -0.227 77 | -0.065 81 |
Rotamer normality | 0.153 91 | -0.063 89 |
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 | 11 |
Side chains flipped | 22 |
Waters removed | 25 |
Peptides flipped | 1 |
Chiralities fixed | 0 |
Residues fitting density better | 20 |
Residues fitting density worse | 0 |