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6c01 redone
Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c)

This information was created with PDB-REDO version 7.31. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 96.184 Å b: 133.640 Å c: 167.430 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.30 Å Reflections 87320 Test set 1918 (2.2%)
R 0.1740 R-free 0.2140
According to PDB-REDO
Resolution 2.30 Å Reflections 87320 Test set 1918 (2.2%) 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 0.1850 0.2024
R-free 0.2230 0.2439
Bond length RMS Z-score 0.259 0.458
Bond angle RMS Z-score 0.595 0.716
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.498 40 -1.979 30
Rotamer normality -1.203 74 -2.100 56
Coarse packing -1.287 9 -1.288 9
Fine packing -2.539 5 -2.487 5
Bump severity 0.810 0 0.063 15
Hydrogen bond satisfaction 0.856 15 0.864 19
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 35
Side chains flipped 1
Waters removed 89
Peptides flipped 2
Chiralities fixed 0
Residues fitting density better 2
Residues fitting density worse 19
Change in density map fit (RSCC)