PDB 5i2h experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Planctopirus limnophila DSM 3776

Resolution: 1.551Å

Reported R values:

R R_free R_work

0.15 0.19 0.15

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Crystal structure of O-methyltransferase family 2 protein Plim_1147 from Planctomyces limnophilus DSM 3776 complex with Apigenin

Source organism:

Planctopirus limnophila DSM 3776

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	2 outlier(s) of 7361 (%)
Bond lengths in protein, DNA, RNA molecules	1 outlier(s) of 5422 (%)
Electron density fit in protein, DNA, RNA molecules	45 outlier(s) of 688 (%)
Ramachandran outliers in protein molecules	4 outlier(s) of 683 (%)
Sidechain rotamer outliers in protein molecules	5 outlier(s) of 563 (%)

Experimental information

X-ray source:

APS BEAMLINE 19-ID

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 66.516 Å b: 83.192 Å c: 119.099 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	90371	Xtriage(Phenix)
Test set size	2.21%	EDS
Data completeness	91.6%	EDS
EDS resolution	1.55Å - 29.89Å	EDS
<I/σ(I)>	3.8	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.49 , <L²> = 0.32	Xtriage(Phenix)
Spacegroup	P 2₁ 2₁ 2₁	Depositor
Possible (pseudo-) translation	The analyses of the Patterson function reveals a significant off-origin peak that is 51.06 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 5.9241e-05. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.	Xtriage(Phenix)
Wilson B	13 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	54 Å²	EDS
Bulk solvent k	0.4 e^-/Å³	EDS
Fo-Fc correlation	0.969	EDS
R value (DCC)	0.1571	DCC
R_free (DCC)	0.1995	DCC
R value (EDS)	0.1591	EDS

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5i2h @ RCSB
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