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

X-ray diffraction

Source organism: Agarophyton chilense

Resolution: 2.3Å

Reported R values:

R R_free R_work

0.25 0.28 0.25

Entry percentile scores

X-ray diffraction

Sample information

Author description:

The crystal structure of Allophycocyanin from the red algae Gracilaria chilensis

Source organism:

Agarophyton chilense

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	4 outlier(s) of 3296 (%)
Bond lengths in protein, DNA, RNA molecules	6 outlier(s) of 2442 (%)
Electron density fit in protein, DNA, RNA molecules	57 outlier(s) of 320 (%)
Ramachandran outliers in protein molecules	1 outlier(s) of 313 (%)
Sidechain rotamer outliers in protein molecules	13 outlier(s) of 250 (%)

Experimental information

X-ray source:

SOLEIL BEAMLINE PROXIMA 1

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 97.41 Å b: 97.41 Å c: 63.83 Å α: 90° β: 90° γ: 120°	Depositor
Outlier reflections	Acentric: 1 , Centric: 1	Xtriage(Phenix)
Number of reflections	22735	Xtriage(Phenix)
Test set size	5%	EDS
Data completeness	97.2%	EDS
EDS resolution	2.02Å - 42.18Å	EDS
<I/σ(I)>	1.1	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.49 , <L²> = 0.32	Xtriage(Phenix)
Spacegroup	P 3 2 1	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 5.24% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	23 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	PHENIX	DCC
Bulk solvent B	71 Å²	EDS
Bulk solvent k	0.39 e^-/Å³	EDS
Fo-Fc correlation	0.894	EDS
R value (DCC)	0.26	DCC
R_free (DCC)	0.29	DCC
R value (EDS)	0.31	EDS

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5tjf @ RCSB
5tjf @ PDBj
5tjf @ PDBSum
5tjf @ Proteopedia

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