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PDB-REDO Databank

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5egh redone
Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine

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 a: 63.620 Å b: 68.849 Å c: 69.761 Å α: 60.59° β: 86.99° γ: 68.10°
Resolution 1.80 Å Reflections 81806 Test set 4091 (5.0%)
R 0.1750 R-free 0.2110
According to PDB-REDO
Resolution 1.80 Å Reflections 81806 Test set 4091 (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 0.1794 0.1667
R-free 0.2099 0.1889
Bond length RMS Z-score 0.319 0.537
Bond angle RMS Z-score 0.647 0.755
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.248 74 0.194 84
Rotamer normality -1.135 75 -0.482 86
Coarse packing -0.125 55 -0.157 54
Fine packing -2.119 11 -1.753 22
Bump severity 0.464 2 0.074 13
Hydrogen bond satisfaction 0.887 35 0.898 48
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 8
Side chains flipped 5
Waters removed 50
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 9
Residues fitting density worse 1
Change in density map fit (RSCC)