PDB 1yar experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organisms:

Resolution: 1.9Å

Reported R values:

R R_free R_work

0.18 0.21 0.18

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex

Source organisms:

Expression system:

Escherichia coli BL21(DE3)

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	58 outlier(s) of 49161 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 36438 (%)
Electron density fit in protein, DNA, RNA molecules	241 outlier(s) of 4657 (%)
Ramachandran outliers in protein molecules	18 outlier(s) of 4601 (%)
Sidechain rotamer outliers in protein molecules	98 outlier(s) of 3894 (%)

Experimental information

X-ray source:

NSLS BEAMLINE X25

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 254.874 Å b: 127.512 Å c: 181.182 Å α: 90° β: 92.45° γ: 90°	Depositor
Outlier reflections	Acentric: 2 , Centric: 1	Xtriage(Phenix)
Number of reflections	442001	Xtriage(Phenix)
Test set size	0.3%	EDS
Data completeness	97.2%	EDS
EDS resolution	1.9Å - 47.3Å	EDS
<I/σ(I)>	2.7	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.51 , <L²> = 0.35	Xtriage(Phenix)
Spacegroup	C 1 2 1	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 2.93% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	28 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	55 Å²	EDS
Bulk solvent k	0.38 e^-/Å³	EDS
Fo-Fc correlation	0.961	EDS
R value (DCC)	0.1818	DCC
R_free (DCC)	0.2135	DCC
R value (EDS)	0.1818	EDS

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1yar @ RCSB
1yar @ PDBj
1yar @ PDBSum
1yar @ Proteopedia

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