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Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-adenosyl-L-homocysteine.
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 6.5 292 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 (A10), 0.1M MES pH 6.5, 0.6M tri-Sodium citrate;
Soak and Cryo: 1mM SAH, 0.5mM GpppA, 2M Lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 4.34 71.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.648 α = 90 b = 169.648 β = 90 c = 52.055 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 2020-04-23 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 2.1 30 98.8 0.075 0.075 0.081 0.028 0.995 21.1 7.7 50035 -3 45.4
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 2.1 2.14 98.9 0.811 0.811 0.868 0.3 0.755 2.3 7.8
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 2.1 28.31 47173 2511 98.81 0.1671 0.1661 0.1729 0.1859 0.1949 RANDOM 53.778
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] 0.43 0.21 0.43 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.879 r_dihedral_angle_4_deg 11.27 r_dihedral_angle_3_deg 9.172 r_dihedral_angle_1_deg 3.036 r_angle_refined_deg 1.266 r_angle_other_deg 0.533 r_chiral_restr 0.054 r_gen_planes_refined 0.048 r_gen_planes_other 0.045 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.879 r_dihedral_angle_4_deg 11.27 r_dihedral_angle_3_deg 9.172 r_dihedral_angle_1_deg 3.036 r_angle_refined_deg 1.266 r_angle_other_deg 0.533 r_chiral_restr 0.054 r_gen_planes_refined 0.048 r_gen_planes_other 0.045 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3223 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing