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PDB-REDO Databank

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6weu redone
Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate

This information was created with PDB-REDO version 7.33. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 83.010 Å b: 160.143 Å c: 209.632 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.65 Å Reflections 81930 Test set 4208 (5.1%)
R 0.2070 R-free 0.2390
According to PDB-REDO
Resolution 2.65 Å Reflections 81930 Test set 4208 (5.1%) 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 0.2083 0.2034
R-free 0.2403 0.2308
Bond length RMS Z-score 0.661 0.386
Bond angle RMS Z-score 0.982 0.695
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.273 25 -1.873 32
Rotamer normality -2.951 41 -2.850 42
Coarse packing -1.968 3 -1.688 5
Fine packing -3.176 1 -2.609 4
Bump severity 0.312 3 0.156 7
Hydrogen bond satisfaction 0.831 9 0.831 9
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 17
Side chains flipped 95
Waters removed 5
Peptides flipped 16
Chiralities fixed 0
Residues fitting density better 47
Residues fitting density worse 3
Change in density map fit (RSCC)