PDB 6gne experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Arabidopsis thaliana

Resolution: 2.55Å

Reported R values:

R R_free R_work

0.18 0.22 0.18

wwPDB Validation report is not available for this entry.

X-ray diffraction

Sample information

Author description:

Catalytic domain of Starch Synthase IV from Arabidopsis thaliana bound to ADP and acarbose

Source organism:

Arabidopsis thaliana

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	13 outlier(s) of 10903 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 8057 (%)
Electron density fit in protein, DNA, RNA molecules	14 outlier(s) of 987 (%)
Ramachandran outliers in protein molecules	4 outlier(s) of 983 (%)
Sidechain rotamer outliers in protein molecules	36 outlier(s) of 840 (%)

Experimental information

X-ray source:

MAX II BEAMLINE I911-3

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 129.76 Å b: 166.94 Å c: 47.94 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	32689	Xtriage(Phenix)
Test set size	3%	EDS
Data completeness	93.6%	EDS
EDS resolution	2.55Å - 41.87Å	EDS
<I/σ(I)>	1.2	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.49 , <L²> = 0.32	Xtriage(Phenix)
Spacegroup	P 2₁ 2₁ 2	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 4.25% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	45 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	30 Å²	EDS
Bulk solvent k	0.31 e^-/Å³	EDS
Fo-Fc correlation	0.951	EDS
R value (DCC)	0.188	DCC
R_free (DCC)	0.2272	DCC
R value (EDS)	0.1879	EDS

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