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7kdm redone

Ricin bound to VHH antibody V5G6

This information was created with PDB-REDO version 7.35. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup	P 1	a: 44.345 Å	b: 77.438 Å	c: 101.577 Å	α: 89.97°	β: 90.18°	γ: 89.98°
Resolution	2.30 Å	Reflections	57474	Test set	2742 (4.8%)
R	0.1870	R-free	0.2380
According to PDB-REDO
Resolution	2.30 Å	Reflections	57474	Test set	2742 (4.8%)	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	0.2066	0.1923
R-free	0.2567	0.2343
Bond length RMS Z-score	0.267	0.411
Bond angle RMS Z-score	0.581	0.651
Model quality (raw scores \| percentiles)
Ramachandran plot appearance	-1.388 43	-1.112 50
Rotamer normality	-3.445 33	-1.071 76
Coarse packing	-0.259 48	-0.255 49
Fine packing	-0.744 63	-0.339 75
Bump severity	0.371 2	0.328 3
Hydrogen bond satisfaction	0.847 13	0.600 0
WHAT_CHECK	Report	Report

Kleywegt-like plot

Model quality compared to resolution neighbours

Significant model changes
Description	Count
Rotamers changed	21
Side chains flipped	1
Waters removed	25
Peptides flipped	7
Chiralities fixed	0
Residues fitting density better	1
Residues fitting density worse	0

Change in density map fit (RSCC)