7NXU

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BM0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M Bis Tris Propane, 0.02 M Sodium potassium phosphate pH 7.5, 20% w/v, PEG 3350 10% v/v, Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.98	α = 90
b = 72.98	β = 90
c = 196.586	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 PILATUS 6M		2021-03-10	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)	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	2.097	48.81	99.5	0.99	23.02	13.67		31603

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22	99.5		0.904	3.21

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	7BM0	2.1	48.806	31594	1547	98.396	0.216	0.2138	0.2507	39.018

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]
1.072			1.072		-2.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.914
r_dihedral_angle_4_deg	16.913
r_dihedral_angle_3_deg	14.714
r_lrange_other	7.95
r_lrange_it	7.873
r_dihedral_angle_1_deg	7.53
r_scangle_it	6.762
r_scangle_other	6.761
r_mcangle_it	5.111
r_mcangle_other	5.11
r_scbond_it	4.36
r_scbond_other	4.356
r_mcbond_it	3.565
r_mcbond_other	3.56
r_angle_other_deg	2.363
r_angle_refined_deg	1.54
r_nbd_other	0.323
r_symmetry_nbd_other	0.219
r_nbd_refined	0.204
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.1
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.071
r_bond_other_d	0.035
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3390
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	1

Software

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