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

X-ray diffraction

Entry percentile scores

Source organism: Mytilus galloprovincialis

Resolution: 1.05Å

Reported R values:

R R_work R_free

0.137 0.136 0.155

Sample information

Author description:

The structure of an anti-cancer lectin mytilec with ligand from the mussel Mytilus galloprovincialis

Source organism: Mytilus galloprovincialis
Expression system: Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	20 outliers of 3350 (0.60%)
Bond lengths in protein, DNA, RNA molecules	11 outliers of 2485 (0.44%)
Electron density fit in protein, DNA, RNA molecules	5 outliers of 304 (1.64%)
Ramachandran outliers in protein molecules	0 outliers of 300 (0%)
Sidechain rotamer outliers in protein molecules	5 outliers of 260 (1.92%)

Experimental information

X-ray source:

PHOTON FACTORY BEAMLINE BL-17A

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 80.276Å b: 64.215Å c: 74.282Å α: 90° β: 121.51° γ: 90°	Depositor
Outlier reflections	Acentric: 0 , Centric: 0	Xtriage (Phenix)
Number of reflections	147427	Xtriage (Phenix)
Test set size	5.27%	DCC
Data completeness	98.4%	EDS
EDS resolution range	1.05Å - 28.64Å	EDS
<I/σ(I)>	4.9	Xtriage (Phenix)
Twinning statistics	<\|L\|> = 0.50 , <L²> = 0.34	Xtriage (Phenix)
Spacegroup	C2	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 6.66% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage (Phenix)
Wilson B	8 Å²	Xtriage (Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	54 Å²	EDS
Bulk solvent k	0.47 e^-/Å³	EDS
Fo-Fc correlation	0.968	EDS
R value (DCC)	0.14	DCC
R_free (DCC)	0.16	DCC
R value (EDS)	0.14	EDS

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3wmv @ RCSB
3wmv @ PDBj
3wmv @ PDBSum

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