PDB 3m4y experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Pyrococcus horikoshii OT3

Resolution: 2.38Å

Reported R values:

R R_free R_work

0.2 0.25 0.19

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Structural characterization of the subunit A mutant P235A of the A-ATP synthase

Source organism:

Pyrococcus horikoshii OT3

Expression system:

Pyrococcus horikoshii

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	2 outlier(s) of 6109 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 4512 (%)
Electron density fit in protein, DNA, RNA molecules	83 outlier(s) of 561 (%)
Ramachandran outliers in protein molecules	23 outlier(s) of 557 (%)
Sidechain rotamer outliers in protein molecules	44 outlier(s) of 471 (%)

Experimental information

X-ray source:

NSRRC BEAMLINE BL13B1

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 127.564 Å b: 127.564 Å c: 105.403 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	35342	Xtriage(Phenix)
Test set size	5.01%	EDS
Data completeness	99.8%	EDS
EDS resolution	2.38Å - 24.93Å	EDS
<I/σ(I)>	5.3	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.49 , <L²> = 0.33	Xtriage(Phenix)
Spacegroup	P 4₃ 2₁ 2	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 4.08% 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	68 Å²	EDS
Bulk solvent k	0.32 e^-/Å³	EDS
Fo-Fc correlation	0.943	EDS
R value (DCC)	0.1976	DCC
R_free (DCC)	0.2548	DCC
R value (EDS)	0.2005	EDS

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3m4y @ RCSB
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