PDB 6hvu experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organisms:

Resolution: 2.9Å

Reported R values:

R R_free R_work

0.19 0.22 0.18

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Yeast 20S proteasome with human beta2i (1-53) in complex with 29

Source organisms:

Expression system:

Saccharomyces cerevisiae S288C

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	19 outlier(s) of 67910 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 50228 (%)
Electron density fit in protein, DNA, RNA molecules	132 outlier(s) of 6341 (%)
Ramachandran outliers in protein molecules	5 outlier(s) of 6281 (%)
Sidechain rotamer outliers in protein molecules	214 outlier(s) of 5315 (%)

Experimental information

X-ray source:

SLS BEAMLINE X06SA

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 135.31 Å b: 299.46 Å c: 143.92 Å α: 90° β: 112.44° γ: 90°	Depositor
Number of reflections	226102	Xtriage(Phenix)
Test set size	5%	EDS
Data completeness	97.7%	EDS
EDS resolution	2.9Å - 15Å	EDS
<I/σ(I)>	2.7	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.48 , <L²> = 0.31	Xtriage(Phenix)
Spacegroup	P 1 2₁ 1	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 2.27% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	63 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	39 Å²	EDS
Bulk solvent k	0.3 e^-/Å³	EDS
Fo-Fc correlation	0.944	EDS
R value (DCC)	0.196	DCC
R_free (DCC)	0.2242	DCC
R value (EDS)	0.1971	EDS

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6hvu @ RCSB
6hvu @ PDBj
6hvu @ PDBSum
6hvu @ Proteopedia

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