8R2L

Crystal structure of the ectodomain of TBEV E protein (Sofjin strain)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6J5C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	Ammonium sulfate, MPD, citric acid

Crystal Properties
Matthews coefficient	Solvent content
4.32	71.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.061	α = 90
b = 165.061	β = 90
c = 165.061	γ = 90

Symmetry
Space Group	P 41 3 2

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 EIGER X 16M		2021-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.899990	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.2	116.4	100	0.94	32.5	7.5		50365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.42			0.221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.2	15	13060	650	98.7	0.206	0.202	0.2054	0.2865	0.2788	110.944

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
r_dihedral_angle_2_deg	36.677
r_lrange_it	27.528
r_lrange_other	27.524
r_dihedral_angle_3_deg	24.45
r_scangle_it	22.884
r_scangle_other	22.879
r_mcangle_it	21.409
r_mcangle_other	21.406
r_dihedral_angle_4_deg	19.973
r_scbond_it	16.408
r_scbond_other	16.403
r_mcbond_other	15.144
r_mcbond_it	15.143
r_dihedral_angle_1_deg	13.433
r_angle_refined_deg	2.461
r_angle_other_deg	1.379
r_nbd_refined	0.258
r_symmetry_nbd_other	0.232
r_symmetry_nbd_refined	0.232
r_nbd_other	0.23
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.17
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.094
r_symmetry_xyhbond_nbd_other	0.045
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3028
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing