7UXX

Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C22

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	291	100 mM Tris-HCl (pH 8.3), 30% PEG 4000, 0.2 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.615	α = 90
b = 119.75	β = 90
c = 128.568	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 2M		2020-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRUS BEAMLINE MANACA	1.3236	LNLS SIRUS	MANACA

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	1.85	43.81	99.95	0.997	9.33	2		58500

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	1.85	1.916	99.98		0.887		2

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	7C22	1.85	43.81	58491	2915	99.976	0.165	0.1628	0.207	19.406

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]
-1.387			0.627		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.638
r_dihedral_angle_4_deg	20.933
r_dihedral_angle_3_deg	13.935
r_dihedral_angle_1_deg	7.13
r_lrange_it	6.326
r_lrange_other	6.325
r_scangle_it	3.89
r_scangle_other	3.889
r_mcangle_it	2.599
r_mcangle_other	2.598
r_scbond_it	2.476
r_scbond_other	2.476
r_mcbond_it	1.647
r_mcbond_other	1.647
r_angle_refined_deg	1.598
r_angle_other_deg	1.471
r_nbd_refined	0.214
r_nbd_other	0.212
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.196
r_symmetry_xyhbond_nbd_other	0.184
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5256
Nucleic Acid Atoms
Solvent Atoms	959
Heterogen Atoms	22

Software

Software
Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement