PDB 1jr9 experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Virgibacillus halodenitrificans

Resolution: 2.8Å

Reported R values:

R R_free R_work

0.22 0.28 0.22

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Crystal Structure of manganese superoxide dismutases from Bacillus halodenitrificans

Source organism:

Virgibacillus halodenitrificans

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	1 outlier(s) of 2211 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 1627 (%)
Electron density fit in protein, DNA, RNA molecules	2 outlier(s) of 201 (%)
Ramachandran outliers in protein molecules	8 outlier(s) of 199 (%)
Sidechain rotamer outliers in protein molecules	10 outlier(s) of 162 (%)

Experimental information

X-ray source:

OTHER

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 93.12 Å b: 93.12 Å c: 63.527 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	6739	Xtriage(Phenix)
Data completeness	74.9%	EDS
EDS resolution	2.6Å - 19.79Å	EDS
<I/σ(I)>	5.6	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.46 , <L²> = 0.29	Xtriage(Phenix)
Spacegroup	P 4₃ 2₁ 2	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 4.67% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	39 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	CNS	DCC
Bulk solvent B	52 Å²	EDS
Bulk solvent k	0.24 e^-/Å³	EDS
Fo-Fc correlation	0.918	EDS
R value (DCC)	0.2192	DCC
R value (EDS)	0.2182	EDS

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1jr9 @ RCSB
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