7UXZ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7C22 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3291100 mM Tris -HCl (pH 8.3), 30% PEG 4000, 0.2 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.669α = 90
b = 120.655β = 90
c = 128.503γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2021-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRUS BEAMLINE MANACA0.9772LNLS SIRUSMANACA

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
11.7343.9899.860.9959.4610.671415
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)
11.731.790.509

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7C221.73343.9871414357199.870.1760.1740.214920.275
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]
-0.8330.8050.028
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.787
r_dihedral_angle_4_deg15.566
r_dihedral_angle_3_deg14.749
r_dihedral_angle_1_deg7.027
r_lrange_it6.135
r_lrange_other5.962
r_scangle_it4.305
r_scangle_other4.304
r_mcangle_it2.811
r_mcangle_other2.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.787
r_dihedral_angle_4_deg15.566
r_dihedral_angle_3_deg14.749
r_dihedral_angle_1_deg7.027
r_lrange_it6.135
r_lrange_other5.962
r_scangle_it4.305
r_scangle_other4.304
r_mcangle_it2.811
r_mcangle_other2.811
r_scbond_it2.733
r_scbond_other2.732
r_mcbond_it1.781
r_mcbond_other1.781
r_angle_refined_deg1.628
r_angle_other_deg1.484
r_nbd_other0.224
r_nbd_refined0.218
r_symmetry_nbd_other0.194
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.179
r_symmetry_xyhbond_nbd_refined0.167
r_symmetry_nbd_refined0.152
r_metal_ion_refined0.094
r_symmetry_nbtor_other0.084
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5250
Nucleic Acid Atoms
Solvent Atoms774
Heterogen Atoms68

Software

Software
Software NamePurpose
MxCuBEdata collection
autoPROCdata reduction
PHASERphasing
REFMACrefinement
autoPROCdata processing