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PDB-REDO Databank

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5xc2 redone
Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose

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

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 108.700 Å b: 99.020 Å c: 138.430 Å α: 90.00° β: 111.35° γ: 90.00°
Resolution 2.70 Å Reflections 74950 Test set 2005 (2.7%)
R 0.1760 R-free 0.2320
According to PDB-REDO
Resolution 2.70 Å Reflections 74950 Test set 2005 (2.7%) 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 0.2008 0.2246
R-free 0.2436 0.2489
Bond length RMS Z-score 0.435 0.420
Bond angle RMS Z-score 0.676 0.671
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.782 18 -2.890 17
Rotamer normality -3.018 39 -3.387 34
Coarse packing -1.085 14 -0.878 20
Fine packing -1.800 20 -1.442 34
Bump severity 0.026 33 0.035 26
Hydrogen bond satisfaction 0.875 25 0.867 20
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 37
Side chains flipped 69
Waters removed 295
Peptides flipped 7
Chiralities fixed 0
Residues fitting density better 4
Residues fitting density worse 18
Change in density map fit (RSCC)