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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)