PDB 5m6g experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Saccharopolyspora erythraea D

Resolution: 1.829Å

Reported R values:

R R_free R_work

0.17 0.2 0.17

wwPDB Validation report is not available for this entry.

X-ray diffraction

Sample information

Author description:

Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea

Source organism:

Saccharopolyspora erythraea D

Expression system:

Komagataella phaffii GS115

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	0 outlier(s) of 6074 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 4472 (%)
Electron density fit in protein, DNA, RNA molecules	2 outlier(s) of 583 (%)
Ramachandran outliers in protein molecules	1 outlier(s) of 581 (%)
Sidechain rotamer outliers in protein molecules	4 outlier(s) of 453 (%)

Experimental information

X-ray source:

PETRA III, DESY BEAMLINE P11

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 64.292 Å b: 75.717 Å c: 113.893 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	47444	Xtriage(Phenix)
Test set size	4.43%	EDS
Data completeness	95.1%	EDS
EDS resolution	1.83Å - 45.51Å	EDS
<I/σ(I)>	2	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.47 , <L²> = 0.31	Xtriage(Phenix)
Spacegroup	P 2₁ 2₁ 2₁	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 4.85% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	16 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	47 Å²	EDS
Bulk solvent k	0.41 e^-/Å³	EDS
Fo-Fc correlation	0.96	EDS
R value (DCC)	0.173	DCC
R_free (DCC)	0.2038	DCC
R value (EDS)	0.1747	EDS

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5m6g @ RCSB
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