Experiment: 8DK6

Structure of hepatitis C virus envelope N-terminal truncated glycoprotein 2 (E2) (residues 456-713) from J6 genotype

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WEB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	293.15	0.2M sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 8.3, Cryoprotectant used 30% Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.97	α = 90
b = 125.54	β = 90
c = 157.32	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2020-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.979	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.45	48.97	97.8	0.109	0.062	0.991	8.8	4		35577			39.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.58	99.1		0.582	0.334	0.571	3.1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4WEB	2.45	48.39	35524	3268	94.29	0.2046	0.2031	0.2052	0.2318	0.2312	54

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.2525
f_angle_d	0.6822
f_chiral_restr	0.0446
f_plane_restr	0.0051
f_bond_d	0.0028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4396
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	28

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing