6WJI | pdb_00006wji

2.05 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CJR	PDB entry 2CJR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	20.0 mg/mL protein in 0.1 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II screen D8 (0.1 M HEPES, pH 7.5, 25% w/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.612	α = 90
b = 122.317	β = 90
c = 130.633	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	CCD	MARMOSAIC 300 mm CCD	Be	2020-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	30	97	0.171	0.171	0.187	0.073	0.976	9.7	6.2		43336		-3	17.1

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)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	80.6		0.63	0.63	0.697	0.288	0.698	2.6	5.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 2CJR	2.052	29.881	43303	2192	96.857	0.189	0.1869	0.19	0.2275	0.23	18.645

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]
1.169			-0.386		-0.784

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.429
r_dihedral_angle_4_deg	9.126
r_dihedral_angle_3_deg	7.608
r_lrange_it	4.641
r_lrange_other	4.398
r_dihedral_angle_1_deg	2.439
r_scangle_it	1.621
r_scangle_other	1.621
r_angle_refined_deg	1.493
r_mcangle_it	1.322
r_mcangle_other	1.322
r_scbond_it	0.96
r_scbond_other	0.96
r_mcbond_it	0.769
r_mcbond_other	0.769
r_angle_other_deg	0.394
r_nbd_refined	0.208
r_nbd_other	0.191
r_symmetry_nbd_refined	0.187
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.072
r_gen_planes_refined	0.053
r_gen_planes_other	0.048
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5196
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing