7JNO

X-ray crystallographic structure of the NS3 helicase domain from Tick-borne encephalitis virus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GJC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals were initially identified in the Morpheus II screen condition G5 (15% PEG 3K, 20% 1,2,4 butanetriol, 1% NDSB-256, 20 mM arginine, 20 mM threonine, 20 mM histidine, 20 mM hydroxylysine, 20 mM trans-4-hydroxy-L-proline, and buffered by 50 mM BES and 50 mM triethanolamine at pH 7.5). Seeds were generated from this condition and used for random microseed matrix screening (rMMS) using a protein concentration of 10-12 mg/ml. Final crystals were identified in the Index HT screen condition H2 (0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350). Crystals were cryoprotected by transfer to a drop containing a 4:1 ratio of precipitant ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.787	α = 90
b = 55.442	β = 93.75
c = 91.267	γ = 90

Symmetry
Space Group	P 1 21 1

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 9M		2019-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.920089	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	45.55	99.5	0.123	0.135	0.053	0.986	7.7	6.1		31169

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	93.7		0.28	0.327	0.162	0.453		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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GJC	1.95	45.55	29614	1523	99.45	0.1841	0.1821	0.2237	RANDOM	26.02

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]
1.16		1.36	-2.97		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.36
r_dihedral_angle_4_deg	17.739
r_dihedral_angle_3_deg	13.281
r_dihedral_angle_1_deg	6.751
r_angle_refined_deg	1.632
r_angle_other_deg	1.371
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.36
r_dihedral_angle_4_deg	17.739
r_dihedral_angle_3_deg	13.281
r_dihedral_angle_1_deg	6.751
r_angle_refined_deg	1.632
r_angle_other_deg	1.371
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3346
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

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.