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SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5
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), 11% PEG 3350, 0.24 M magnesium chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.131 α = 90 b = 168.131 β = 90 c = 52.131 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 PILATUS3 S 6M 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.7 49.08 100 0.094 0.097 0.021 1 21.2 20.5 92755 26.98
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 1.7 1.73 100 2.739 2.891 0.628 0.509 1.3 21
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 1.7 42.39 1.34 92724 4607 99.99 0.1871 0.1866 0.1901 0.1958 0.1995 34.55
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 18.2385 f_angle_d 0.9364 f_chiral_restr 0.0552 f_bond_d 0.0074 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3187 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing