7UXZ

Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid

X-RAY DIFFRACTION

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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 = 43.669	α = 90
b = 120.655	β = 90
c = 128.503	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		2021-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRUS BEAMLINE MANACA	0.9772	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	1.73	43.98	99.86	0.995	9.46	10.6		71415

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	1.73	1.79			0.509

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	1.733	43.98	71414	3571	99.87	0.176	0.174	0.2149	20.275

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]
-0.833			0.805		0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.787
r_dihedral_angle_4_deg	15.566
r_dihedral_angle_3_deg	14.749
r_dihedral_angle_1_deg	7.027
r_lrange_it	6.135
r_lrange_other	5.962
r_scangle_it	4.305
r_scangle_other	4.304
r_mcangle_it	2.811
r_mcangle_other	2.811
r_scbond_it	2.733
r_scbond_other	2.732
r_mcbond_it	1.781
r_mcbond_other	1.781
r_angle_refined_deg	1.628
r_angle_other_deg	1.484
r_nbd_other	0.224
r_nbd_refined	0.218
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.152
r_metal_ion_refined	0.094
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5250
Nucleic Acid Atoms
Solvent Atoms	774
Heterogen Atoms	68

Software

Software
Software Name	Purpose
MxCuBE	data collection
autoPROC	data reduction
PHASER	phasing
REFMAC	refinement
autoPROC	data processing