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Crystal Structure of DC-SIGN carbohydrate recognition domain complexed with LNFP III (Dextra L504). |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 2 | a: 72.570 Å | b: 55.370 Å | c: 29.630 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.80 Å | Reflections | 11105 | Test set | 911 (8.2%) | ||
R | 0.1790 | R-free | 0.2230 | ||||
According to PDB-REDO | |||||||
Resolution | 1.80 Å | Reflections | 11105 | Test set | 909 (8.2%) New test set, PDB-REDO compensated for this | ||
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 | |
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Crystallographic refinement | ||
R | 0.1774 | 0.1655 |
R-free | 0.2111 R-free was considered biased, the estimated unbiased R-free was used | 0.2145 |
Bond length RMS Z-score | 0.236 | 0.376 |
Bond angle RMS Z-score | 0.586 | 0.621 |
Model quality | ||
Ramachandran plot normality | -1.617 37 | -1.273 46 |
Rotamer normality | -0.715 82 | 0.277 95 |
Coarse packing | -0.624 30 | -0.509 36 |
Fine packing | -1.966 15 | -1.855 18 |
Bump severity | 0.184 6 | 0.178 6 |
Hydrogen bond satisfaction | 0.849 13 | 0.830 9 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 23 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |