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PDB-REDO Databank

The PDB-REDO databank contains optimised versions of existing PDB entries with electron density maps, a description of model changes, and a wealth of model validation data. It is a good starting point for any structural biology project.

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4xtp redone
Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen

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

Crystallographic data
From PDB header
Spacegroup I 2 2 2 a: 56.093 Å b: 86.024 Å c: 128.877 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.97 Å Reflections 21798 Test set 1075 (4.9%)
R 0.1980 R-free 0.2540
According to PDB-REDO
Resolution 1.97 Å Reflections 21798 Test set 1075 (4.9%) 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 0.1999 0.1870
R-free 0.2354 R-free was considered biased, the estimated unbiased R-free was used. 0.2106
Bond length RMS Z-score 0.651 0.686
Bond angle RMS Z-score 0.737 0.821
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.153 49 -0.459 69
Rotamer normality -1.992 58 -1.551 67
Coarse packing 1.058 95 1.106 95
Fine packing -0.195 79 -0.180 79
Bump severity 0.004 78 0.005 74
Hydrogen bond satisfaction 0.880 28 0.880 28
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 2
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 2
Residues fitting density worse 0
Change in density map fit (RSCC)