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Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 4.0 mg/ml (Nsp10/Nsp16 1:1), 0.15 M NaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1 M MES pH 6.5, 0.9 M NaF. Sitting drops made using 0.4 ul of protein mixed with 0.4 ul of precipitation buffer.
Crystal Properties Matthews coefficient Solvent content 4.49 72.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.83 α = 90 b = 170.83 β = 90 c = 52.738 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 295 PIXEL DECTRIS PILATUS3 X 6M 2020-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.65 50 99.6 0.148 0.071 0.981 15 5.2 25799 -3 49.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 99.8 1.037 0.507 0.537 1.87 4.9
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 6WQ3 2.65 29.59 24366 1260 98.96 0.1562 0.1549 0.1809 0.1758 RANDOM 55.906
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] -0.31 -0.15 -0.31 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.658 r_dihedral_angle_3_deg 8.603 r_dihedral_angle_4_deg 8.08 r_dihedral_angle_1_deg 2.042 r_angle_refined_deg 1.291 r_angle_other_deg 0.326 r_gen_planes_refined 0.053 r_chiral_restr 0.052 r_gen_planes_other 0.05 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.658 r_dihedral_angle_3_deg 8.603 r_dihedral_angle_4_deg 8.08 r_dihedral_angle_1_deg 2.042 r_angle_refined_deg 1.291 r_angle_other_deg 0.326 r_gen_planes_refined 0.053 r_chiral_restr 0.052 r_gen_planes_other 0.05 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing