7XWZ

Crystal structure of SARS-CoV-2 N-NTD and dsRNA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OFZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	Malonic Acid, Imidazole, Boric Acid, PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.848	α = 90
b = 39.119	β = 97.605
c = 84.157	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 PILATUS3 6M		2020-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.18057	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.25	47.977	99.6	0.049	17.7	4.1		16782

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.32			0.432

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	2OFZ	2.25	47.977	16773	814	99.567	0.228	0.2264	0.2685	44.328

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]
-0.884		-0.434	-2.337		3.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.569
r_dihedral_angle_4_deg	17.179
r_dihedral_angle_3_deg	12.965
r_lrange_it	7.525
r_lrange_other	7.524
r_dihedral_angle_1_deg	6.632
r_paralell_plane_angle_deg	3.194
r_scangle_it	2.833
r_scangle_other	2.833
r_mcangle_it	2.832
r_mcangle_other	2.831
r_scbond_it	1.731
r_scbond_other	1.731
r_mcbond_it	1.665
r_mcbond_other	1.665
r_angle_refined_deg	1.287
r_angle_other_deg	1.01
r_nbd_other	0.206
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.168
r_nbd_refined	0.159
r_symmetry_nbd_refined	0.157
r_chiral_restr	0.14
r_xyhbond_nbd_refined	0.127
r_symmetry_xyhbond_nbd_refined	0.083
r_symmetry_nbtor_other	0.076
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1815
Nucleic Acid Atoms	590
Solvent Atoms	86
Heterogen Atoms	18

Software

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