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Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W4H 6w4h
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 4 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 5% Glycerol;
Screen: Anions (B2), 0.1M HEPES pH 7.5, 1.25M Sodium acetate;
Soaks: Compound 5a, 24 hours;
Cryo: 4M Sodium formate
Crystal Properties Matthews coefficient Solvent content 4.4 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.847 α = 90 b = 170.847 β = 90 c = 51.881 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 2021-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12705 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 2.15 30 99.9 0.178 0.178 0.183 0.04 0.996 24.4 20.6 47404 -3 48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 100 0.756 0.575 1.7 21.2
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 2.15 29.59 44897 2416 99.87 0.1669 0.1656 0.1706 0.1909 0.1932 RANDOM 60.406
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] 0.29 0.15 0.29 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 7.761 r_dihedral_angle_2_deg 4.185 r_dihedral_angle_1_deg 3.088 r_angle_refined_deg 1.214 r_angle_other_deg 0.43 r_chiral_restr 0.057 r_gen_planes_refined 0.019 r_gen_planes_other 0.017 r_bond_other_d 0.006 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3143 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing