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Crystal Structure of Nsp16-Nsp10 from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-Adenosylmethionine.
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: 5mM SAM, 0.5mM GpppA, 2M Lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 4.33 71.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.372 α = 90 b = 169.372 β = 90 c = 52.083 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 30 99.8 0.07 0.07 0.078 0.034 0.998 20.3 5.1 58029 -3 37.4
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 2 2.03 100 0.867 0.867 0.966 0.421 0.712 2.05 5.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6w4h 2 29.35 54988 2866 99.81 0.1631 0.1623 0.178 0.195 RANDOM 46.88
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] 0.34 0.17 0.34 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.392 r_dihedral_angle_4_deg 9.617 r_dihedral_angle_3_deg 8.564 r_dihedral_angle_1_deg 2.684 r_angle_refined_deg 1.194 r_angle_other_deg 0.31 r_gen_planes_refined 0.054 r_chiral_restr 0.052 r_gen_planes_other 0.051 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.392 r_dihedral_angle_4_deg 9.617 r_dihedral_angle_3_deg 8.564 r_dihedral_angle_1_deg 2.684 r_angle_refined_deg 1.194 r_angle_other_deg 0.31 r_gen_planes_refined 0.054 r_chiral_restr 0.052 r_gen_planes_other 0.051 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3252 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing