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1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex from SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W4H PDB entry 6W4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 9.7 mg/mL 1:1 nsp10/nsp16 in 0.5 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), cryoprotectant: 4 M sodium formate
Crystal Properties Matthews coefficient Solvent content 3.87 68.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.245 α = 90 b = 166.245 β = 90 c = 98.279 γ = 120
Symmetry Space Group P 32 2 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 CCD MARMOSAIC 300 mm CCD Be 2020-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.95 30 100 0.077 0.077 0.083 0.03 25.8 7.6 113483 -3 28.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.742 0.742 0.795 0.285 0.88 3.2 7.6
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 PDB entry 6W4H 1.951 29.925 113455 5610 99.893 0.158 0.1573 0.1642 0.1745 0.1785 33.856
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] 0.578 0.289 0.578 -1.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.895 r_dihedral_angle_3_deg 8.996 r_dihedral_angle_4_deg 7.019 r_lrange_it 6.614 r_lrange_other 6.425 r_dihedral_angle_1_deg 3.157 r_scangle_it 2.853 r_scangle_other 2.853 r_mcangle_it 2.194 r_mcangle_other 2.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.895 r_dihedral_angle_3_deg 8.996 r_dihedral_angle_4_deg 7.019 r_lrange_it 6.614 r_lrange_other 6.425 r_dihedral_angle_1_deg 3.157 r_scangle_it 2.853 r_scangle_other 2.853 r_mcangle_it 2.194 r_mcangle_other 2.194 r_scbond_it 1.971 r_scbond_other 1.914 r_mcbond_it 1.31 r_mcbond_other 1.31 r_angle_refined_deg 1.286 r_angle_other_deg 0.329 r_nbd_other 0.234 r_nbd_refined 0.203 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.149 r_metal_ion_refined 0.147 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_other 0.118 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.058 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6384 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing