8YM1

Structure of SADS-CoV Virus Nucleocapsid Protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate at pH 4.6, and 36% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.417	α = 90
b = 95.897	β = 96.25
c = 103.998	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 EIGER2 S 9M		2022-01-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.9791	SSRF	BL10U2

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	1.9	95.9	98.4	0.997	11.1	6.3		73150

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			0.777	0.787

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	AlphaFold	1.9	51.74	71117	2000	98.28	0.18998	0.18898	0.22563	RANDOM	30.434

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]
0.02		-0.01	-0.03		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	7.589
r_long_range_B_refined	6.856
r_long_range_B_other	6.789
r_scangle_other	5.972
r_dihedral_angle_1_deg	4.749
r_scbond_it	3.957
r_scbond_other	3.956
r_mcangle_it	3.353
r_mcangle_other	3.353
r_mcbond_it	2.588
r_mcbond_other	2.588
r_dihedral_angle_2_deg	1.221
r_angle_refined_deg	0.834
r_angle_other_deg	0.301
r_chiral_restr	0.041
r_gen_planes_refined	0.009
r_bond_refined_d	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6659
Nucleic Acid Atoms
Solvent Atoms	605
Heterogen Atoms

Software

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