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6p4q redone

Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

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

Crystallographic data
From PDB header
Spacegroup	P 21 21 21	a: 61.053 Å	b: 96.894 Å	c: 119.006 Å	α: 90.00°	β: 90.00°	γ: 90.00°
Resolution	1.77 Å	Reflections	69142	Test set	2000 (2.9%)
R	0.1800	R-free	0.2030
According to PDB-REDO
Resolution	1.77 Å	Reflections	69142	Test set	2000 (2.9%)	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	0.1818	0.1778
R-free	0.2023	0.1935
Bond length RMS Z-score	0.349	0.703
Bond angle RMS Z-score	0.647	0.833
Model quality (raw scores \| percentiles)
Ramachandran plot appearance	-0.333 72	-0.080 78
Rotamer normality	-0.382 87	-0.045 92
Coarse packing	1.061 95	0.974 94
Fine packing	-1.324 39	-1.353 38
Bump severity	0.008 64	0.006 70
Hydrogen bond satisfaction	0.901 52	0.902 53
WHAT_CHECK	Report	Report

Kleywegt-like plot

Model quality compared to resolution neighbours

Significant model changes
Description	Count
Rotamers changed	3
Side chains flipped	0
Waters removed	0
Peptides flipped	1
Chiralities fixed	0
Residues fitting density better	1
Residues fitting density worse	0

Change in density map fit (RSCC)