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

X-ray diffraction

Source organism: Homo sapiens

Resolution: 2.6Å

Reported R values:

R R_free R_work

0.25 0.29 0.25

Entry percentile scores

X-ray diffraction

Sample information

Author description:

STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE DEPENDENT HEMEPROTEIN

Source organism:

Homo sapiens

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	2 outlier(s) of 22055 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 16308 (%)
Electron density fit in protein, DNA, RNA molecules	136 outlier(s) of 2090 (%)
Ramachandran outliers in protein molecules	29 outlier(s) of 2066 (%)
Sidechain rotamer outliers in protein molecules	97 outlier(s) of 1730 (%)

Experimental information

X-ray source:

ESRF BEAMLINE BM1A, EMBL/DESY, HAMBURG BEAMLINE BW7A

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 144.52 Å b: 144.52 Å c: 108.16 Å α: 90° β: 90° γ: 120°	Depositor
Number of reflections	66710	Xtriage(Phenix)
Test set size	4.83%	EDS
Data completeness	82.3%	EDS
EDS resolution	2.6Å - 43.34Å	EDS
<I/σ(I)>	4.5	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.47 , <L²> = 0.3	Xtriage(Phenix)
Spacegroup	P 3₁	Depositor
Possible (pseudo-) translation	The analyses of the Patterson function reveals a significant off-origin peak that is 43.39 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 1.7767e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.	Xtriage(Phenix)
Wilson B	36 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	48 Å²	EDS
Bulk solvent k	0.34 e^-/Å³	EDS
Fo-Fc correlation	0.901	EDS
R value (DCC)	0.2497	DCC
R_free (DCC)	0.2885	DCC
R value (EDS)	0.2532	EDS

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1jbq @ RCSB
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Assembly 1 (mmCIF; gz)
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