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

X-ray diffraction

Source organism: Homo sapiens

Resolution: 2Å

Reported R values:

R R_free R_work

0.22 0.26 0.22

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2

Source organism:

Homo sapiens

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	0 outlier(s) of 3525 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 2612 (%)
Ramachandran outliers in protein molecules	2 outlier(s) of 308 (%)
Sidechain rotamer outliers in protein molecules	22 outlier(s) of 278 (%)

Experimental information

X-ray source:

NSLS BEAMLINE X29A

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 122.256 Å b: 122.256 Å c: 54.707 Å α: 90° β: 90° γ: 120°	Depositor
Number of reflections	32750	Xtriage(Phenix)
Test set size	7.01%	EDS
Data completeness	99.8%	EDS
EDS resolution	1.98Å - 48.6Å	EDS
<I/σ(I)>	3.2	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.36 , <L²> = 0.19	Xtriage(Phenix)
Spacegroup	P 6	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 3.46% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	24 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	31 Å²	EDS
Bulk solvent k	0.35 e^-/Å³	EDS
Fo-Fc correlation	0.955	EDS
R value (DCC)	0.2229	DCC
R_free (DCC)	0.2611	DCC
R value (EDS)	0.1672	EDS

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3bum @ RCSB
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