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Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain
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 = 43.615 α = 90 b = 119.75 β = 90 c = 128.568 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 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRUS BEAMLINE MANACA 1.3236 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 1.85 43.81 99.95 0.997 9.33 2 58500
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 1.85 1.916 99.98 0.887 2
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 7C22 1.85 43.81 58491 2915 99.976 0.165 0.1628 0.1726 0.207 0.2132 19.406
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] -1.387 0.627 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.638 r_dihedral_angle_4_deg 20.933 r_dihedral_angle_3_deg 13.935 r_dihedral_angle_1_deg 7.13 r_lrange_it 6.326 r_lrange_other 6.325 r_scangle_it 3.89 r_scangle_other 3.889 r_mcangle_it 2.599 r_mcangle_other 2.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.638 r_dihedral_angle_4_deg 20.933 r_dihedral_angle_3_deg 13.935 r_dihedral_angle_1_deg 7.13 r_lrange_it 6.326 r_lrange_other 6.325 r_scangle_it 3.89 r_scangle_other 3.889 r_mcangle_it 2.599 r_mcangle_other 2.598 r_scbond_it 2.476 r_scbond_other 2.476 r_mcbond_it 1.647 r_mcbond_other 1.647 r_angle_refined_deg 1.598 r_angle_other_deg 1.471 r_nbd_refined 0.214 r_nbd_other 0.212 r_symmetry_nbd_other 0.197 r_xyhbond_nbd_refined 0.196 r_symmetry_xyhbond_nbd_other 0.184 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5256 Nucleic Acid Atoms Solvent Atoms 959 Heterogen Atoms 22
Software Software Software Name Purpose MxCuBE data collection XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement