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Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 with 7-methyl-GpppA and S-adenosyl-L-homocysteine in the Active Site and Sulfates in the mRNA Binding Groove.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol;
Screen: Anions (F3), 0.1M HEPES pH 7.5, 0.9M Sodium phosphate, 0.9M Potassium phosphate;
Soak and Cryo: 1mM SAH, 0.5mM GpppA, 2M Lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 4.3 71.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.147 α = 90 b = 169.147 β = 90 c = 51.834 γ = 120
Symmetry Space Group P 31 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 2020-04-17 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) 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 2.25 30 99 0.077 0.077 0.083 0.029 0.992 23.4 7.7 40141 -3 45.1
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 2.25 2.29 99.6 0.857 0.857 0.921 0.332 0.79 2.8 7.3
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 6w4h 2.25 29.91 38166 1960 98.98 0.1634 0.162 0.1669 0.1902 0.1905 RANDOM 53.482
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] 0.53 0.26 0.53 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.543 r_dihedral_angle_3_deg 9.393 r_dihedral_angle_4_deg 9.345 r_dihedral_angle_1_deg 3.035 r_angle_refined_deg 1.246 r_angle_other_deg 0.327 r_gen_planes_refined 0.054 r_chiral_restr 0.052 r_gen_planes_other 0.05 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.543 r_dihedral_angle_3_deg 9.393 r_dihedral_angle_4_deg 9.345 r_dihedral_angle_1_deg 3.035 r_angle_refined_deg 1.246 r_angle_other_deg 0.327 r_gen_planes_refined 0.054 r_chiral_restr 0.052 r_gen_planes_other 0.05 r_bond_refined_d 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3214 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing