7BLV

Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with ADP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M Bis Tris Propane pH 6.5, 0.2 M sodium acetate truhydrate, 20% w/v PEG 3350, 10% v/v ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.12	α = 90
b = 73.12	β = 90
c = 196.124	γ = 90

Symmetry
Space Group	P 41 21 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 PILATUS3 S 6M		2020-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.099	50	99.9	0.067	0.999	24.38	14.3		32056

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.099	2.23	99.7		0.99	0.839	2.53

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AY4	2.099	45.778	32056	1565	99.888	0.234	0.2329	0.259	57.908

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]
1.42			1.42		-2.839

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.025
r_dihedral_angle_4_deg	18.024
r_dihedral_angle_3_deg	14.533
r_lrange_it	9.815
r_scangle_it	7.951
r_dihedral_angle_1_deg	7.27
r_mcangle_it	6.769
r_scbond_it	5.637
r_mcbond_it	5.049
r_angle_refined_deg	1.619

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.025
r_dihedral_angle_4_deg	18.024
r_dihedral_angle_3_deg	14.533
r_lrange_it	9.815
r_scangle_it	7.951
r_dihedral_angle_1_deg	7.27
r_mcangle_it	6.769
r_scbond_it	5.637
r_mcbond_it	5.049
r_angle_refined_deg	1.619
r_nbtor_refined	0.305
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.213
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.111
r_symmetry_xyhbond_nbd_refined	0.105
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3414
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	1

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.