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

X-ray diffraction

Source organism: Homo sapiens

Resolution: 2.3Å

Reported R values:

R R_free R_work

0.23 0.26 0.23

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Ligand binding domain of EPHA7

Source organism:

Homo sapiens

Expression system:

Spodoptera frugiperda

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	0 outlier(s) of 21157 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 15598 (%)
Electron density fit in protein, DNA, RNA molecules	195 outlier(s) of 1912 (%)
Ramachandran outliers in protein molecules	2 outlier(s) of 1822 (%)
Sidechain rotamer outliers in protein molecules	16 outlier(s) of 1643 (%)

Experimental information

X-ray source:

RIGAKU FR-E SUPERBRIGHT

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 137.617 Å b: 140.699 Å c: 143.783 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	123625	Xtriage(Phenix)
Test set size	5.04%	EDS
Data completeness	99.8%	EDS
EDS resolution	2.3Å - 19.97Å	EDS
<I/σ(I)>	4.2	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.51 , <L²> = 0.35	Xtriage(Phenix)
Spacegroup	P 2₁ 2₁ 2₁	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 6.30% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	42 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	39 Å²	EDS
Bulk solvent k	0.34 e^-/Å³	EDS
Fo-Fc correlation	0.933	EDS
R value (DCC)	0.2286	DCC
R_free (DCC)	0.2599	DCC
R value (EDS)	0.2302	EDS

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3nru @ RCSB
3nru @ PDBj
3nru @ PDBSum
3nru @ Proteopedia

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Structure Factors
EDS map
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Assembly composition XML
Assembly 1 (mmCIF; gz)
Assembly 10 (mmCIF; gz)
Assembly 11 (mmCIF; gz)
Assembly 12 (mmCIF; gz)
Assembly 2 (mmCIF; gz)
Assembly 3 (mmCIF; gz)
Assembly 4 (mmCIF; gz)
Assembly 5 (mmCIF; gz)
Assembly 6 (mmCIF; gz)
Assembly 7 (mmCIF; gz)
Assembly 8 (mmCIF; gz)
Assembly 9 (mmCIF; gz)
Assembly 1 (atom only; mmCIF)
Assembly 10 (atom only; mmCIF)
Assembly 11 (atom only; mmCIF)
Assembly 12 (atom only; mmCIF)
Assembly 2 (atom only; mmCIF)
Assembly 3 (atom only; mmCIF)
Assembly 4 (atom only; mmCIF)
Assembly 5 (atom only; mmCIF)
Assembly 6 (atom only; mmCIF)
Assembly 7 (atom only; mmCIF)
Assembly 8 (atom only; mmCIF)
Assembly 9 (atom only; mmCIF)
FASTA (Entry)
SIFTS XML file with residue-level mappings
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