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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalent inhibitor GUE-3899 (compound 58 in publication)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 20% PEG 3350, 0.2 M potassium sodium tartrate
Crystal Properties Matthews coefficient Solvent content 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.705 α = 90 b = 54.097 β = 100.69 c = 46.463 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 PILATUS3 6M 2022-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.96 48.61 56.9 0.149 0.064 0.994 7.4 6.3 11295 34.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.24 1.121 0.562 0.409 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.97 48.61 1.34 11289 595 57.69 0.2255 0.2222 0.2222 0.2875 0.288
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 13.979 f_angle_d 0.671 f_chiral_restr 0.044 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling PHENIX phasing