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SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1 M MES (pH 5.6), 7% PEG 3350, 0.12 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 4.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.816 α = 90 b = 167.816 β = 90 c = 51.857 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 90 PIXEL DECTRIS EIGER2 XE 16M 2023-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
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 1.8 83.91 99.7 0.174 0.178 0.038 0.999 13 21.9 77282 25.62
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 1.8 1.84 99.9 2.625 2.684 0.56 0.597 1.4 22.4
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 1.8 72.67 1.34 77218 3769 99.54 0.1966 0.1961 0.2012 0.2045 0.2094 31.54
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 18.1771 f_angle_d 0.9271 f_chiral_restr 0.0575 f_bond_d 0.0069 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3187 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling MOLREP phasing