PDB 2y5i experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Danio rerio

Resolution: 2.03Å

Reported R values:

R R_free R_work

0.17 0.22 0.17

Entry percentile scores

X-ray diffraction

Sample information

Author description:

S100Z from zebrafish in complex with calcium

Source organism:

Danio rerio

Expression system:

Escherichia coli BL21(DE3)

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	8 outlier(s) of 6395 (%)
Bond lengths in protein, DNA, RNA molecules	3 outlier(s) of 4763 (%)
Electron density fit in protein, DNA, RNA molecules	14 outlier(s) of 605 (%)
Ramachandran outliers in protein molecules	1 outlier(s) of 593 (%)
Sidechain rotamer outliers in protein molecules	15 outlier(s) of 517 (%)

Experimental information

X-ray source:

ESRF BEAMLINE ID14-1

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 75.611 Å b: 132.25 Å c: 58.209 Å α: 90° β: 90° γ: 90°	Depositor
Outlier reflections	Acentric: 7 , Centric: 7	Xtriage(Phenix)
Number of reflections	38197	Xtriage(Phenix)
Test set size	4.98%	EDS
Data completeness	98.9%	EDS
EDS resolution	2.03Å - 46.12Å	EDS
<I/σ(I)>	5.9	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.5 , <L²> = 0.33	Xtriage(Phenix)
Spacegroup	P 2₁ 2₁ 2	Depositor
Possible (pseudo-) translation	The analyses of the Patterson function reveals a significant off-origin peak that is 77.87 % 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 7.7877e-07. 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	16 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	54 Å²	EDS
Bulk solvent k	0.36 e^-/Å³	EDS
Fo-Fc correlation	0.956	EDS
R value (DCC)	0.1791	DCC
R_free (DCC)	0.2062	DCC
R value (EDS)	0.1793	EDS

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2y5i @ RCSB
2y5i @ PDBj
2y5i @ PDBSum
2y5i @ Proteopedia

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Assembly 1 (mmCIF; gz)
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