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Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.1 M MMT (DL-malic acid, MES, and Tris base in molar ratio 1:2:2), pH 7.0, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.754 α = 90 b = 99.036 β = 90 c = 101.986 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2022-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 49.52 99.5 0.077 0.077 0.081 0.025 0.998 16.1 10.4 64002 32.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 1.461 1.726 0.603 0.485 1
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.8 44.54 1.34 63916 3172 99.44 0.1848 0.1832 0.1833 0.2146 0.2146 40.38
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 13.2872 f_angle_d 1.2946 f_chiral_restr 0.0797 f_bond_d 0.0134 f_plane_restr 0.0099
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4689 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing