☰ Navigation Tabs
SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA-RNA (Cap0-RNA)
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 4.26 71.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.14 α = 90 b = 167.14 β = 90 c = 51.83 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 2023-12-07 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 2.099 48.8 99.78 0.2527 0.264 0.07598 0.996 6.88 11.9 94499 45.5
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 2.19 99.75 3.55 3.708 1.064 0.227 0.45 11.9
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 48.8 1.35 48570 1080 99.78 0.1878 0.187 0.1875 0.2237 0.224 53.41
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 17.9127 f_angle_d 1.2131 f_chiral_restr 0.0577 f_bond_d 0.0112 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3189 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 171
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building