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SARS-CoV-2 nsp10-16 methyltransferase in complex with SAM analog BDH 33959089
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JIB same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 900 mM sodium fluoride, 100 mM 2-(N-morpholino)ethanesulfonic acid
Crystal Properties Matthews coefficient Solvent content 4.26 71.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.6 α = 90 b = 167.6 β = 90 c = 51.48 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 S 16M 2021-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033150 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 1.77 41.99 99.79 0.05613 0.07937 0.05613 0.998 8.41 2 80684 35.9
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 1.77 1.833 98.26 2.541 3.594 2.541 0.158 0.27 2
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 1.77 41.99 1.33 80533 825 99.8 0.1882 0.188 0.1882 0.2095 0.2093 41.66
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 10.8432 f_angle_d 0.9608 f_chiral_restr 0.0606 f_bond_d 0.0073 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3222 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 181
Software Software Software Name Purpose XDS data reduction XDS data scaling Coot model building PHENIX refinement PHENIX phasing