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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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3n9k redone
F229A/E292S Double Mutant of Exo-beta-1,3-glucanase from Candida albicans in Complex with Laminaritriose at 1.7 A

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: 58.725 Å b: 64.397 Å c: 94.866 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.70 Å Reflections 40191 Test set 2014 (5.0%)
R 0.1520 R-free 0.1970
According to PDB-REDO
Resolution 1.70 Å Reflections 40191 Test set 2014 (5.0%) 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 0.1485 0.1426
R-free 0.1875 0.1735
Bond length RMS Z-score 1.002 0.760
Bond angle RMS Z-score 0.973 0.866
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.957 54 -0.600 65
Rotamer normality -0.961 78 -0.547 85
Coarse packing -0.467 38 -0.512 35
Fine packing -1.811 20 -1.701 24
Bump severity 0.005 74 0.012 53
Hydrogen bond satisfaction 0.878 27 0.887 35
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 14
Side chains flipped 0
Waters removed 42
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)