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PDB-REDO Databank

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3zwe redone
Structure of BambL, a lectin from Burkholderia ambifaria, complexed with blood group B epitope

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

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 47.980 Å b: 49.140 Å c: 102.710 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.75 Å Reflections 24088 Test set 1218 (5.1%)
R 0.2080 R-free 0.2660
According to PDB-REDO
Resolution 1.75 Å Reflections 24088 Test set 1218 (5.1%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.2059 0.1878
R-free 0.2598 0.2253
Bond length RMS Z-score 0.701 0.445
Bond angle RMS Z-score 0.740 0.690
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.928 55 -0.299 73
Rotamer normality -1.972 58 -0.271 89
Coarse packing 1.136 95 1.194 96
Fine packing -1.875 18 -1.771 21
Bump severity 0.007 67 0.003 82
Hydrogen bond satisfaction 0.884 32 0.878 27
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 1
Side chains flipped 0
Waters removed 22
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)