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3zw1 redone
Structure of Bambl lectine in complex with lewix x antigen

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 3 a: 81.440 Å b: 81.440 Å c: 81.440 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.60 Å Reflections 23119 Test set 1180 (5.1%)
R 0.1530 R-free 0.1890
According to PDB-REDO
Resolution 1.60 Å Reflections 23119 Test set 1180 (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 0.1495 0.1456
R-free 0.1842 0.1759
Bond length RMS Z-score 0.707 0.546
Bond angle RMS Z-score 0.771 0.730
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.490 68 -0.314 73
Rotamer normality 0.781 97 1.169 99
Coarse packing 0.750 89 0.747 89
Fine packing -1.327 39 -1.424 35
Bump severity 0.655 1 0.643 1
Hydrogen bond satisfaction 0.836 10 0.843 12
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 4
Side chains flipped 0
Waters removed 12
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)