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6cbp redone
Crystal structure of the single chain variable fragment of the DH270.6 bnAb in complex with the Man9-V3 glycopeptide

This information was created with PDB-REDO version 7.31. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 41 2 2 a: 68.005 Å b: 68.005 Å c: 128.835 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.17 Å Reflections 15873 Test set 813 (5.1%)
R 0.2210 R-free 0.2780
According to PDB-REDO
Resolution 2.17 Å Reflections 15873 Test set 813 (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 0.2448 0.2186
R-free 0.2896 0.2705
Bond length RMS Z-score 0.272 0.709
Bond angle RMS Z-score 0.495 0.897
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.994 53 -1.469 41
Rotamer normality -0.663 83 -2.636 46
Coarse packing -0.977 17 -1.008 16
Fine packing -1.048 51 -0.967 54
Bump severity 0.390 2 0.549 1
Hydrogen bond satisfaction 0.868 20 0.885 33
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 1
Waters removed 3
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 4
Residues fitting density worse 0
Change in density map fit (RSCC)