9F7A | pdb_00009f7a

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R

X-RAY DIFFRACTION

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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, SITTING DROP	9	285	22% PEG 3350 200mM Zinc Acetate dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.753	α = 90
b = 66.753	β = 90
c = 121.214	γ = 120

Symmetry
Space Group	P 65 2 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		2024-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97626	PETRA III, EMBL c/o DESY	P13 (MX1)

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	121.21	99.9	1	20.2	36.4		13269

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	1.9	1.94	99.9		0.38	0.3

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	57.81	13209	692	99.909	0.281	0.277	0.2758	0.3477	0.3484	RANDOM	77.817

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]
1.782	0.891		1.782		-5.782

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.192
r_dihedral_angle_2_deg	14.176
r_dihedral_angle_3_deg	13.539
r_lrange_other	13.273
r_lrange_it	13.172
r_mcangle_it	10.168
r_mcangle_other	10.162
r_scangle_it	10.108
r_scangle_other	10.101
r_dihedral_angle_1_deg	8.529
r_scbond_it	7.361
r_mcbond_it	7.327
r_mcbond_other	7.325
r_scbond_other	7.276
r_angle_refined_deg	1.782
r_angle_other_deg	0.721
r_symmetry_nbd_refined	0.321
r_nbd_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.167
r_symmetry_nbd_other	0.156
r_xyhbond_nbd_refined	0.15
r_nbd_other	0.126
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	921
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	1

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
PHASER	phasing