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SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 1118
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, 0.16 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 4.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.41 α = 90 b = 169.41 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 293 PIXEL DECTRIS EIGER2 XE 16M 2024-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 2.2 48.9 100 0.132 0.139 0.043 0.999 14.9 20.5 43499 49.98
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 2.2 2.27 100 2.748 2.902 0.929 0.585 1.2
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 2.2 44.21 1.34 43472 2194 99.98 0.1968 0.1957 0.2046 0.2166 0.2251 56.33
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 17.5208 f_angle_d 1.0305 f_chiral_restr 0.0569 f_bond_d 0.0083 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3181 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction Aimless data scaling MOLREP phasing