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Mpro of SARS-CoV-2 in complex with the RK-68 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E 6y2e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.002 M zinc chloride, 0.1 M Tris 8.0, 20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.8 α = 90 b = 52.8 β = 103.08 c = 45.35 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 EIGER X 16M 2021-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.99 47.67 98.9 0.998 13.1 6.8 17855
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 1.99 2.06 0.916
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6y2e 1.992 47.668 17855 893 98.75 0.181 0.1784 0.1857 0.2239 0.2258 36.591
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] -0.094 0.042 0.033 0.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.951 r_dihedral_angle_4_deg 16.182 r_dihedral_angle_3_deg 16.147 r_dihedral_angle_1_deg 7.605 r_lrange_other 6.761 r_lrange_it 6.758 r_scangle_it 5.37 r_scangle_other 5.368 r_mcangle_other 3.626 r_mcangle_it 3.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.951 r_dihedral_angle_4_deg 16.182 r_dihedral_angle_3_deg 16.147 r_dihedral_angle_1_deg 7.605 r_lrange_other 6.761 r_lrange_it 6.758 r_scangle_it 5.37 r_scangle_other 5.368 r_mcangle_other 3.626 r_mcangle_it 3.624 r_scbond_it 3.57 r_scbond_other 3.568 r_dihedral_angle_other_3_deg 3.565 r_mcbond_it 2.608 r_mcbond_other 2.605 r_angle_refined_deg 1.508 r_angle_other_deg 1.335 r_nbd_refined 0.204 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.172 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.138 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing