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Structure of SADS-CoV Virus Nucleocapsid Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate at pH 4.6, and 36% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.417 α = 90 b = 95.897 β = 96.25 c = 103.998 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 S 9M 2022-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9791 SSRF BL10U2
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 1.9 95.9 98.4 0.997 11.1 6.3 73150
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.777 0.787
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AlphaFold 1.9 51.74 71117 2000 98.28 0.18998 0.18898 0.1962 0.22563 0.2295 RANDOM 30.434
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] 0.02 -0.01 -0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 7.589 r_long_range_B_refined 6.856 r_long_range_B_other 6.789 r_scangle_other 5.972 r_dihedral_angle_1_deg 4.749 r_scbond_it 3.957 r_scbond_other 3.956 r_mcangle_it 3.353 r_mcangle_other 3.353 r_mcbond_it 2.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 7.589 r_long_range_B_refined 6.856 r_long_range_B_other 6.789 r_scangle_other 5.972 r_dihedral_angle_1_deg 4.749 r_scbond_it 3.957 r_scbond_other 3.956 r_mcangle_it 3.353 r_mcangle_other 3.353 r_mcbond_it 2.588 r_mcbond_other 2.588 r_dihedral_angle_2_deg 1.221 r_angle_refined_deg 0.834 r_angle_other_deg 0.301 r_chiral_restr 0.041 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.003 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 Atoms Number Protein Atoms 6659 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing