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Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.
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: 3.8 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol;Screen: Classics II (B3), 0.5M Magnesium formate, 0.1M HEPES pH 7.5;Soak: 6hours, 0.2mM m7GpppAUUAAA, 5mM SAM, in screen solution;Cryo: 25% Sucrose in screen solution.
Crystal Properties Matthews coefficient Solvent content 4.39 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.351 α = 90 b = 169.351 β = 90 c = 52.629 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 PIXEL DECTRIS EIGER X 9M Be 2020-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12708 APS 21-ID-D
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 1.78 30 96.6 0.09 0.09 0.097 0.036 0.996 20.8 6.8 81048 -3 24.4
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 1.78 1.81 84.2 1.156 1.156 1.269 0.513 0.56 2.1 5.8
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 1.78 29.33 76229 3950 96.81 0.1418 0.1408 0.15 0.1615 0.1683 RANDOM 33.036
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] 0.75 0.38 0.75 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.239 r_dihedral_angle_3_deg 8.898 r_dihedral_angle_4_deg 7.69 r_dihedral_angle_1_deg 3.421 r_angle_refined_deg 1.33 r_angle_other_deg 0.379 r_chiral_restr 0.064 r_gen_planes_refined 0.054 r_gen_planes_other 0.048 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.239 r_dihedral_angle_3_deg 8.898 r_dihedral_angle_4_deg 7.69 r_dihedral_angle_1_deg 3.421 r_angle_refined_deg 1.33 r_angle_other_deg 0.379 r_chiral_restr 0.064 r_gen_planes_refined 0.054 r_gen_planes_other 0.048 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3191 Nucleic Acid Atoms 96 Solvent Atoms 531 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing