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PDB-REDO Databank

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5veo redone
Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5), inactive (T72A), in complex with AMP

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

Crystallographic data
From PDB header
Spacegroup P 65 2 2 a: 84.239 Å b: 84.239 Å c: 295.796 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 1.53 Å Reflections 81417 Test set 2000 (2.5%)
R 0.1150 R-free 0.1450
According to PDB-REDO
Resolution 1.53 Å Reflections 81417 Test set 2000 (2.5%) 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 0.1226 0.1155
R-free 0.1522 0.1510
Bond length RMS Z-score 0.392 0.725
Bond angle RMS Z-score 0.757 0.895
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.022 80 -0.084 78
Rotamer normality -0.093 91 -0.228 89
Coarse packing -0.079 58 -0.065 58
Fine packing -2.855 3 -2.761 3
Bump severity 0.790 1 0.805 0
Hydrogen bond satisfaction 0.875 25 0.880 28
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 6
Side chains flipped 0
Waters removed 90
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 11
Residues fitting density worse 0
Change in density map fit (RSCC)