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

X-ray diffraction

Source organism: Schizosaccharomyces pombe 972h-

Resolution: 3.501Å

Reported R values:

R R_free R_work

0.26 0.27 0.26

wwPDB Validation report is not available for this entry.

X-ray diffraction

Sample information

Author description:

Crystal structure of the binding domain of SREBP from fission yeast

Source organism:

Schizosaccharomyces pombe 972h-

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	5 outlier(s) of 4046 (%)
Bond lengths in protein, DNA, RNA molecules	7 outlier(s) of 2978 (%)
Electron density fit in protein, DNA, RNA molecules	4 outlier(s) of 384 (%)
Ramachandran outliers in protein molecules	10 outlier(s) of 370 (%)
Sidechain rotamer outliers in protein molecules	24 outlier(s) of 335 (%)

Experimental information

X-ray source:

SSRF BEAMLINE BL17U

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 96.903 Å b: 96.903 Å c: 151.595 Å α: 90° β: 90° γ: 120°	Depositor
Number of reflections	10637	Xtriage(Phenix)
Test set size	4.8%	EDS
Data completeness	92%	EDS
EDS resolution	3.5Å - 34.97Å	EDS
<I/σ(I)>	2.9	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.49 , <L²> = 0.32	Xtriage(Phenix)
Spacegroup	P 3₁ 2 1	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 5.73% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	137 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	118 Å²	EDS
Bulk solvent k	0.3 e^-/Å³	EDS
Fo-Fc correlation	0.916	EDS
R value (DCC)	0.27	DCC
R_free (DCC)	0.28	DCC
R value (EDS)	0.28	EDS

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5gpd @ RCSB
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