9F7C | pdb_00009f7c

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	22% PEG 3350 200mM Zinc Acetate dihydrate

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.616	α = 90
b = 58.616	β = 90
c = 111.588	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 EIGER X 16M		2023-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2	41.45	99.3	0.999	15.8	12.4		13840

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	2	2.05			0.938	1.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2	41.45	13760	685	99.761	0.243	0.2411	0.2414	0.2733	0.2753	RANDOM	81.96

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]
2.817			2.817		-5.633

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.137
r_dihedral_angle_3_deg	14.337
r_lrange_it	10.054
r_lrange_other	10.054
r_scangle_it	7.983
r_scangle_other	7.978
r_dihedral_angle_2_deg	7.173
r_mcangle_it	6.427
r_mcangle_other	6.423
r_scbond_it	6.049
r_scbond_other	6.047
r_mcbond_it	4.78
r_mcbond_other	4.779
r_dihedral_angle_1_deg	4.716
r_angle_refined_deg	2.561
r_angle_other_deg	0.88
r_symmetry_nbd_refined	0.337
r_nbd_refined	0.199
r_nbd_other	0.178
r_nbtor_refined	0.174
r_symmetry_nbd_other	0.169
r_xyhbond_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.105
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.078
r_symmetry_metal_ion_refined	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1046
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Coot	model building
BUCCANEER	model building
Aimless	data scaling
pointless	data scaling
STARANISO	data scaling
autoPROC	data reduction
XDS	data reduction
CRANK2	phasing