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Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 10% (v/v) propanol-2, 0.1 M MES/NaOH pH 6.0, 0.2 M Calccium acetate
Crystal Properties Matthews coefficient Solvent content 5.82 78.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.589 α = 90 b = 184.589 β = 90 c = 56.961 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 PILATUS 6M-F 2020-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0711 APS 24-ID-C
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 2.23 92.29 99.9 0.113 0.125 0.054 0.996 8.7 5.3 54383 47.39
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 2.23 2.29 99.7 1.41 1.5 0.675 0.478 1.1 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6WKS 2.5 29.75 1.35 38620 1966 99.87 0.2056 0.2038 0.2405 0.2346 58.58
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 6.9123 f_angle_d 2.3732 f_chiral_restr 0.0992 f_bond_d 0.0335 f_plane_restr 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3131 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing