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PDB-REDO Databank

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4lqy redone
Crystal Structure of Human ENPP4 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 C 1 2 1 a: 181.533 Å b: 51.143 Å c: 52.741 Å α: 90.00° β: 102.38° γ: 90.00°
Resolution 1.54 Å Reflections 69525 Test set 3515 (5.1%)
R 0.1400 R-free 0.1840
According to PDB-REDO
Resolution 1.54 Å Reflections 69525 Test set 3515 (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 0.1452 0.1277
R-free 0.1829 0.1653
Bond length RMS Z-score 0.412 0.542
Bond angle RMS Z-score 0.668 0.787
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.713 61 -0.623 64
Rotamer normality -0.573 84 -0.533 85
Coarse packing -0.148 54 -0.215 51
Fine packing -2.075 12 -2.171 10
Bump severity 0.419 2 0.396 2
Hydrogen bond satisfaction 0.882 30 0.879 28
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 7
Side chains flipped 1
Waters removed 96
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 31
Residues fitting density worse 0
Change in density map fit (RSCC)