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SARS-CoV-2 main protease (Mpro) complex with AC1115
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 0.1 M imidazole pH 8, 0.1 M LiSO4, 1 mM DTT, 12% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.01 38.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.867 α = 90 b = 53.4 β = 101.111 c = 113.373 γ = 90
Symmetry Space Group I 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 2022-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.78 48.19 97.6 0.088 0.096 0.036 0.999 10.9 6.8 25214
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 1.78 1.82 97.2 2.259 2.44 0.912 0.429 0.8 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.781 48.187 25178 1996 97.186 0.196 0.1926 0.2284 0.2154 40.617
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] -0.94 0.662 0.037 0.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 16.675 r_dihedral_angle_3_deg 15.915 r_dihedral_angle_6_deg 13.673 r_dihedral_angle_2_deg 10.467 r_dihedral_angle_1_deg 7.257 r_dihedral_angle_other_2_deg 7.07 r_lrange_it 6.454 r_lrange_other 6.384 r_scangle_it 3.904 r_scangle_other 3.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 16.675 r_dihedral_angle_3_deg 15.915 r_dihedral_angle_6_deg 13.673 r_dihedral_angle_2_deg 10.467 r_dihedral_angle_1_deg 7.257 r_dihedral_angle_other_2_deg 7.07 r_lrange_it 6.454 r_lrange_other 6.384 r_scangle_it 3.904 r_scangle_other 3.903 r_mcangle_it 2.812 r_mcangle_other 2.811 r_scbond_it 2.454 r_scbond_other 2.454 r_mcbond_it 1.83 r_mcbond_other 1.83 r_angle_other_deg 1.599 r_angle_refined_deg 1.422 r_symmetry_xyhbond_nbd_other 0.421 r_nbd_refined 0.247 r_nbd_other 0.232 r_symmetry_nbd_other 0.223 r_symmetry_nbd_refined 0.19 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.068 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing