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Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the SS148 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10% w/v PEG 20,000, 20% v/v PEG MME 550;
0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate;
0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.51 72.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.216 α = 90 b = 168.216 β = 90 c = 51.505 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 2022-01-20 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) 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 2.7 48.56 100 0.4601 0.4718 0.991 8.07 20.4 23182 59.7664577488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.797 100 4.19 4.292 0.27 0.56 21.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6YZ1 2.7 48.56 1.33624063448 23142 1157 99.8274523337 0.207260985597 0.205182963111 0.2046 0.247353210629 0.2472 random selection 57.6178698225
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 15.7846290342 f_angle_d 1.04126864226 f_chiral_restr 0.0434000016927 f_bond_d 0.0285182508588 f_plane_restr 0.0036438018931
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3133 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 52
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing Coot model building PHENIX refinement