PDB 3vrf experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Mammuthus primigenius

Resolution: 1.55Å

Reported R values:

R R_free R_work

0.17 0.19 0.17

Entry percentile scores

X-ray diffraction

Sample information

Author description:

The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms

Source organism:

Mammuthus primigenius

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	15 outlier(s) of 3126 (%)
Bond lengths in protein, DNA, RNA molecules	2 outlier(s) of 2307 (%)
Electron density fit in protein, DNA, RNA molecules	17 outlier(s) of 288 (%)
Sidechain rotamer outliers in protein molecules	7 outlier(s) of 245 (%)

Experimental information

X-ray source:

PHOTON FACTORY BEAMLINE BL-17A

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 109.486 Å b: 61.79 Å c: 53.57 Å α: 90° β: 110.35° γ: 90°	Depositor
Number of reflections	47291	Xtriage(Phenix)
Test set size	5.05%	EDS
Data completeness	97.3%	EDS
EDS resolution	1.55Å - 19.98Å	EDS
<I/σ(I)>	8.9	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.49 , <L²> = 0.32	Xtriage(Phenix)
Spacegroup	C 1 2 1	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 6.59% 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	REFMAC	DCC
Bulk solvent B	51 Å²	EDS
Bulk solvent k	0.47 e^-/Å³	EDS
Fo-Fc correlation	0.96	EDS
R value (DCC)	0.18	DCC
R_free (DCC)	0.2	DCC
R value (EDS)	0.17	EDS

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3vrf @ RCSB
3vrf @ PDBj
3vrf @ PDBSum
3vrf @ Proteopedia

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