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Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid
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 (Depositor) R-Free (Depositor) R-Free (DCC) 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 0.1974 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
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