8R6E

SARS-CoV-2 Nucleocapsid dimerization domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YUN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2970.2M sodium chloride, 0.1M sodium/potassium phosphate 6.5 and 25% PEG1000
Crystal Properties
Matthews coefficientSolvent content
2.6253.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.62α = 90
b = 47.372β = 90
c = 134.625γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2M2022-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873128ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5347.3799.60.9975.97.143189
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.550.291

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5344.7340897210499.930.226710.224750.26653RANDOM38.809
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]
-3.945.88-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.196
r_long_range_B_refined8.603
r_long_range_B_other8.602
r_dihedral_angle_2_deg7.817
r_dihedral_angle_1_deg6.972
r_scangle_other6.623
r_mcangle_other4.825
r_mcangle_it4.821
r_scbond_it4.406
r_scbond_other4.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.196
r_long_range_B_refined8.603
r_long_range_B_other8.602
r_dihedral_angle_2_deg7.817
r_dihedral_angle_1_deg6.972
r_scangle_other6.623
r_mcangle_other4.825
r_mcangle_it4.821
r_scbond_it4.406
r_scbond_other4.404
r_mcbond_it3.414
r_mcbond_other3.403
r_angle_refined_deg1.713
r_angle_other_deg0.586
r_chiral_restr0.082
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1856
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing