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Crystal structure of SARS-CoV-2 Mpro with compound 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 PCB: 0.100000 M pH:6.00 ; PEG 1500: 25.000000 %w/v
Crystal Properties Matthews coefficient Solvent content 2.8 56.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.15 α = 90 b = 81.226 β = 114.78 c = 51.732 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 EIGER2 X 16M 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9995 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.47 47.01 96.1 0.056 10.1 4.5 261893
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 1.47 1.5 0.824
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.476 47.01 54783 4593 96.09 0.1386 0.1354 0.1769 0.219 RANDOM 33.05
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] 1.8 -0.12 0.97 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.883 r_dihedral_angle_3_deg 12.314 r_dihedral_angle_4_deg 11.05 r_dihedral_angle_1_deg 6.873 r_mcangle_it 3.447 r_mcbond_other 2.695 r_mcbond_it 2.694 r_rigid_bond_restr 1.498 r_angle_refined_deg 1.388 r_angle_other_deg 1.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.883 r_dihedral_angle_3_deg 12.314 r_dihedral_angle_4_deg 11.05 r_dihedral_angle_1_deg 6.873 r_mcangle_it 3.447 r_mcbond_other 2.695 r_mcbond_it 2.694 r_rigid_bond_restr 1.498 r_angle_refined_deg 1.388 r_angle_other_deg 1.304 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing