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SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin
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 = 168.05 α = 90 b = 168.05 β = 90 c = 51.71 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 2023-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033200 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 1.93 48.73 99.9 0.1371 0.1465 0.05097 0.997 9.1 8.1 62937 38.46
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 1.93 1.999 100 1.973 2.104 0.7243 0.398 0.8 8.3
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 1.93 48.73 1.35 62934 651 99.91 0.1793 0.179 0.1795 0.2075 0.2076 47.81
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 10.3504 f_angle_d 1.2177 f_chiral_restr 0.0638 f_bond_d 0.0116 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3220 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 123
Software Software Software Name Purpose XDS data reduction XDS data scaling Coot model building PHENIX phasing PHENIX refinement