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5mhp redone
Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity

This information was created with PDB-REDO version 7.36. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 77.230 Å b: 79.530 Å c: 79.740 Å α: 90.00° β: 100.78° γ: 90.00°
Resolution 2.43 Å Reflections 35484 Test set 1778 (5.0%)
R 0.2070 R-free 0.2450
According to PDB-REDO
Resolution 2.43 Å Reflections 35484 Test set 1778 (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 0.2070 0.2073
R-free 0.2453 0.2516
Bond length RMS Z-score 0.392 0.420
Bond angle RMS Z-score 0.636 0.700
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.860 57 -1.967 30
Rotamer normality -1.751 63 -2.420 50
Coarse packing -2.077 2 -1.888 3
Fine packing -2.962 2 -2.486 5
Bump severity 0.151 7 0.067 15
Hydrogen bond satisfaction 0.840 11 0.849 13
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 12
Side chains flipped 41
Waters removed 8
Peptides flipped 2
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 1
Change in density map fit (RSCC)