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6a57 redone
STRUCTURE OF HISTONE DEMETHYLASE REF6 COMPLEXED WITH DNA

This information was created with PDB-REDO version 7.37. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 32 2 1 a: 96.087 Å b: 96.087 Å c: 73.905 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.70 Å Reflections 11112 Test set 596 (5.4%)
R 0.2210 R-free 0.2570
According to PDB-REDO
Resolution 2.70 Å Reflections 11112 Test set 596 (5.4%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.2219 0.1912
R-free 0.2573 0.2347
Bond length RMS Z-score 0.358 0.501
Bond angle RMS Z-score 0.693 0.816
Model quality (raw scores | percentiles)
Ramachandran plot appearance -3.673 11 -3.313 14
Rotamer normality -4.244 23 -5.064 15
Coarse packing N/A N/A -3.612 0
Fine packing N/A N/A -4.112 0
Dinucleotide conformation (CONFAL) 68.8 91 59.4 78
Base pair conformation 1.2 81 1.0 91
Bump severity 0.036 25 0.064 15
Hydrogen bond satisfaction 0.689 1 0.700 1
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 1
Side chains flipped 25
Waters removed 3
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 3
Residues fitting density worse 2
Change in density map fit (RSCC)