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Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence (form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JOY PDB entry 7JOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293 20% PEG3350, 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 1.85 33.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.856 α = 90 b = 105.078 β = 104.46 c = 52.29 γ = 90
Symmetry Space Group P 1 21 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 S 6M 2021-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 1.26 105.08 68 0.046 0.052 0.023 0.998 16.8 4.9 79812 16.07
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 1.5 45.61 94.74 0.052 0.026 0.995 21.52 5.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 7JOY 1.5 50.63 1.39 75616 3798 94.75 0.156 0.1546 0.1827 0.1962 23.1
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 13.1116 f_angle_d 0.9452 f_chiral_restr 0.0611 f_bond_d 0.0065 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4721 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing