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SARS-CoV-2 methyltransferase nsp10-16 in complex with Toyocamycin and m7GpppA (Cap0-analog)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 400 mM sodium fluoride, 100 mM 2-(N-morpholino)ethanesulfonic acid
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.7 α = 90 b = 168.7 β = 90 c = 52.25 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 EIGER2 X 16M 2023-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033210 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.79 44.42 99.2 0.1703 0.178 0.05143 0.998 9.22 11.8 79674 31.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.854 98.38 2.292 2.391 0.6777 0.427 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.79 44.42 1.33 79603 1034 99.21 0.1813 0.181 0.181 0.2068 0.2039 36.55
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.0273 f_angle_d 1.1867 f_chiral_restr 0.0633 f_bond_d 0.0106 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3212 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 107
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX refinement Coot model building PHENIX phasing