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Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
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: 0.5 hours, 0.2mM m7GpppAUU, 5mM SAH, in 2M Lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.471 α = 90 b = 168.471 β = 90 c = 99.945 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 PIXEL DECTRIS PILATUS 6M 2021-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97913 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.95 30 100 0.167 0.167 0.064 0.992 15.3 7.9 117967 -3 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.43 1.6 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.95 29.46 112081 5861 99.84 0.1693 0.168 0.1741 0.1925 0.1978 RANDOM 45.607
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] 0.48 0.24 0.48 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.237 r_dihedral_angle_4_deg 10.765 r_dihedral_angle_3_deg 9.645 r_dihedral_angle_1_deg 3.278 r_angle_refined_deg 1.223 r_angle_other_deg 0.32 r_chiral_restr 0.059 r_gen_planes_refined 0.054 r_gen_planes_other 0.048 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.237 r_dihedral_angle_4_deg 10.765 r_dihedral_angle_3_deg 9.645 r_dihedral_angle_1_deg 3.278 r_angle_refined_deg 1.223 r_angle_other_deg 0.32 r_chiral_restr 0.059 r_gen_planes_refined 0.054 r_gen_planes_other 0.048 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6482 Nucleic Acid Atoms 182 Solvent Atoms 538 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing