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Structure of SARS-CoV-2 Main Protease bound to Tretazicar.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 282 25% PEG 1.500, 0.1 M MIB pH 7.5, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 1.93 36.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.92 α = 90 b = 52.97 β = 102.94 c = 44.76 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 170 PIXEL DECTRIS PILATUS 6M 2020-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03322 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.359 48.112 98.5 0.99 6.79 3.6 62865 31.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.75 99.6 1.22 0.5 1.02 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS NONE 6YNQ 1.63 38.79 32753 32753 100 0.1933 0.1933 0.1933 0.2018 0.2205 0.2122 NONE 0.63
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] 1.363 -0.391 -0.001 -1.363
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 40
Software Software Software Name Purpose MAIN refinement XDS data reduction XDS data scaling MolProbity phasing