Experiment: 9EWH

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Y109A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.836	α = 90
b = 55.139	β = 95.24
c = 84.088	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 16M		2024-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.96862	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.92	83.74	98.9	0.1	0.114	0.054	0.998	12.5	8.2		40470

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)
	1.92	1.97	99.2		0.605	0.687	0.32	0.889	3.1	8.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.93	83.74	40129	1997	98.8	0.2137	0.2116	0.2093	0.2551	0.2524	RANDOM	30.25

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]
1.5017		-0.8659	-0.5672		-0.9345

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	12.64
t_omega_torsion	3.86
t_angle_deg	1
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3932
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
Coot	model building
BUCCANEER	model building
Aimless	data scaling
pointless	data scaling
STARANISO	data scaling
autoPROC	data reduction
XDS	data reduction
PHASER	phasing