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Structure of SARS-CoV-2 Main Protease bound to Tofogliflozin.
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 1500, 0.1M MIB, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 1.95 37.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.98 α = 90 b = 53.32 β = 103.07 c = 44.63 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 179 PIXEL DECTRIS PILATUS 6M 2020-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 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 1.3 50 96 0.99 5.36 3.6 61546 26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.74 95 0.9 3.7
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 1.65 48.06 30440 30440 100 0.2345 0.2345 0.2345 0.239 0.2663 0.2347 NONE 33.7
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] 1.644 -0.242 0.244 -1.888
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 50
Software Software Software Name Purpose MAIN refinement XDS data reduction XDS data scaling FFT phasing