6ZCO

Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2, crystal form II

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YUN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		277	tba

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.203	α = 90
b = 88.203	β = 90
c = 42.763	γ = 90

Symmetry
Space Group	I 41

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 6M		2020-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.36	44.096	97.8	0.041	0.047	0.016	20.2	7.6		34588

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.361	1.43	86.6		1.093	1.093	1.446	0.698	0.7	3.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6yun	1.361	30	32473	1709	96.81	0.1517	0.1495	0.1962	RANDOM	28.894

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]
-1.14			-1.14		2.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.809
r_sphericity_free	26.737
r_dihedral_angle_4_deg	17.93
r_dihedral_angle_3_deg	13.639
r_sphericity_bonded	12.693
r_dihedral_angle_1_deg	6.069
r_rigid_bond_restr	3.06
r_angle_refined_deg	1.645
r_angle_other_deg	1.023
r_chiral_restr	0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.809
r_sphericity_free	26.737
r_dihedral_angle_4_deg	17.93
r_dihedral_angle_3_deg	13.639
r_sphericity_bonded	12.693
r_dihedral_angle_1_deg	6.069
r_rigid_bond_restr	3.06
r_angle_refined_deg	1.645
r_angle_other_deg	1.023
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	936
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.