PDB 8pnm experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Homo sapiens

Resolution: 1.94Å

Reported R values:

R R_free R_work

0.23 0.27 0.23

wwPDB Validation report is not available for this entry.

X-ray diffraction

Sample information

Author description:

Structure of human KCTD15 BTB domain mutant G88D crystal form 2

Source organism:

Homo sapiens

Expression system:

Escherichia coli BL21(DE3)

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	11 outlier(s) of 13126 (%)
Bond lengths in protein, DNA, RNA molecules	2 outlier(s) of 9618 (%)
Electron density fit in protein, DNA, RNA molecules	40 outlier(s) of 1214 (%)
Ramachandran outliers in protein molecules	4 outlier(s) of 1168 (%)
Sidechain rotamer outliers in protein molecules	11 outlier(s) of 920 (%)

Experimental information

X-ray source:

DIAMOND BEAMLINE I03

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 71.262 Å b: 72.091 Å c: 94.413 Å α: 89.63° β: 77.08° γ: 60.5°	Depositor
Number of reflections	75764	Xtriage(Phenix)
Test set size	4.99%	EDS
Data completeness	65.2%	EDS
EDS resolution	1.94Å - 61.31Å	EDS
<I/σ(I)>	1	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.51 , <L²> = 0.35	Xtriage(Phenix)
Spacegroup	P 1	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 5.25% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	44 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	39 Å²	EDS
Bulk solvent k	0.3 e^-/Å³	EDS
Fo-Fc correlation	0.933	EDS
R value (DCC)	0.2352	DCC
R_free (DCC)	0.27	DCC
R value (EDS)	0.2468	EDS

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8pnm @ RCSB
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