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SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and beta-chloroethyl theophylline
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 Properties Matthews coefficient Solvent content 4.28 71.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.74 α = 90 b = 167.74 β = 90 c = 51.67 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 2021-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033220 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 2.1 48.42 99.89 0.3913 0.4102 0.1219 0.992 6.77 11.5 48769 40.06
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 2.1 2.175 99.94 3.807 3.986 1.172 0.217 11.6
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 2.1 48.42 2.1 48759 510 99.89 0.184 0.1842 0.1852 0.2038 0.2019 50.15
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 14.8729 f_angle_d 0.8943 f_chiral_restr 0.0506 f_bond_d 0.0069 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3204 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 146
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX refinement Coot model building PHENIX phasing