7BM0

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

X-RAY DIFFRACTION

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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, 0.02 M sodium potassium phosphate pH. 7.5, 20% w/v PEG 3350, 10% v/v ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.952	α = 90
b = 72.952	β = 90
c = 196.45	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	1.9	45.71	99.9	0.083	0.999	19.1	14.25		43006

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	1.9	2	99.7		0.795	2.03	14.64

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	1.9	45.71	43006	959	99.916	0.217	0.2162	0.2294	42.597

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]
0.679			0.679		-1.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.289
r_dihedral_angle_4_deg	20.263
r_dihedral_angle_3_deg	15.435
r_rigid_bond_restr	7.214
r_dihedral_angle_1_deg	7.162
r_angle_refined_deg	1.765
r_nbtor_refined	0.299
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.183
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.111
r_chiral_restr	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it
r_lrange_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3369
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	33

Software

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