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1sl4 redone
Crystal Structure of DC-SIGN carbohydrate recognition domain complexed with Man4

This information was created with PDB-REDO version 7.32. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 43 a: 55.660 Å b: 55.660 Å c: 53.330 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.55 Å Reflections 23752 Test set 1219 (5.1%)
R 0.2230 R-free 0.2550
According to PDB-REDO
Resolution 1.55 Å Reflections 23752 Test set 1219 (5.1%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.2184 0.1412
R-free 0.2389 0.1691
Bond length RMS Z-score 0.237 0.391
Bond angle RMS Z-score 0.584 0.631
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.740 61 0.251 85
Rotamer normality -1.109 75 0.686 97
Coarse packing -0.489 37 -0.440 39
Fine packing -1.939 16 -1.534 30
Bump severity 0.013 51 0.013 51
Hydrogen bond satisfaction 0.870 22 0.862 18
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 2
Side chains flipped 0
Waters removed 32
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 92
Residues fitting density worse 0
Change in density map fit (RSCC)