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SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.48 A Resolution (Cryo-protected)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 22% PEG 4000, 100 mM HEPES pH 7.0, 3% DMSO, 1 mM telaprevir
Crystal Properties Matthews coefficient Solvent content 2.1 41.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.76 α = 90 b = 54.82 β = 101.233 c = 48.24 γ = 90
Symmetry Space Group C 1 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 EIGER X 9M 2020-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 NSLS-II 17-ID-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 1.48 53.83 100 0.135 0.142 0.045 0.997 7.7 10 46900
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 1.48 1.51 100 3.003 3.229 0.352 1.2 7.2
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 7JYC 1.48 53.83 1.33 46890 2000 99.97 0.1861 0.1847 0.1847 0.2153 0.2111 RANDOM 38.45
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 18.3712 f_angle_d 1.0863 f_chiral_restr 0.0828 f_bond_d 0.0079 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing AutoProcess data reduction Aimless data reduction pointless data processing