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1sl6 redone
Crystal Structure of a fragment of DC-SIGNR (containg the carbohydrate recognition domain and two repeats of the neck) complexed with Lewis-x.

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

Crystallographic data
From PDB header
Spacegroup P 32 2 1 a: 153.750 Å b: 153.750 Å c: 128.702 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.25 Å Reflections 73013 Test set 6102 (8.4%)
R 0.2190 R-free 0.2560
According to PDB-REDO
Resolution 2.25 Å Reflections 73013 Test set 6102 (8.4%) 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 0.2165 0.2019
R-free 0.2491 0.2263
Bond length RMS Z-score 0.265 0.512
Bond angle RMS Z-score 0.566 0.681
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.745 19 -1.430 42
Rotamer normality -1.928 59 -0.988 78
Coarse packing -0.131 55 -0.015 61
Fine packing -1.298 40 -0.688 65
Bump severity 0.011 56 0.004 78
Hydrogen bond satisfaction 0.862 18 0.857 16
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 13
Side chains flipped 10
Waters removed 26
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 11
Residues fitting density worse 2
Change in density map fit (RSCC)