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5xc2 redone

Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose

This information was created with PDB-REDO version 7.32. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup	P 1 21 1	a: 108.700 Å	b: 99.020 Å	c: 138.430 Å	α: 90.00°	β: 111.35°	γ: 90.00°
Resolution	2.70 Å	Reflections	74950	Test set	2005 (2.7%)
R	0.1760	R-free	0.2320
According to PDB-REDO
Resolution	2.70 Å	Reflections	74950	Test set	2005 (2.7%)	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	0.2008	0.2246
R-free	0.2436	0.2489
Bond length RMS Z-score	0.435	0.420
Bond angle RMS Z-score	0.676	0.671
Model quality (raw scores \| percentiles)
Ramachandran plot appearance	-2.782 18	-2.890 17
Rotamer normality	-3.018 39	-3.387 34
Coarse packing	-1.085 14	-0.878 20
Fine packing	-1.800 20	-1.442 34
Bump severity	0.026 33	0.035 26
Hydrogen bond satisfaction	0.875 25	0.867 20
WHAT_CHECK	Report	Report

Kleywegt-like plot

Model quality compared to resolution neighbours

Significant model changes
Description	Count
Rotamers changed	37
Side chains flipped	69
Waters removed	295
Peptides flipped	7
Chiralities fixed	0
Residues fitting density better	4
Residues fitting density worse	18

Change in density map fit (RSCC)