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SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor GSA948
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), 12% PEG 3350, 40 mM magnesium chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.951 α = 90 b = 167.951 β = 90 c = 51.731 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 2025-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 1.7 145.45 99.9 0.108 0.113 0.034 0.995 15.1 20.8 91809 28.65
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 99.6 2.399 2.518 0.762 0.551 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 72.72 1.34 91766 4569 99.9 0.1902 0.1896 0.1936 0.202 0.2071 34.56
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 18.2372 f_angle_d 0.9761 f_chiral_restr 0.0553 f_bond_d 0.0067 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3160 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction Aimless data scaling MOLREP phasing