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Crystal structure of SARS-CoV-2 Mpro in complex with RK-468
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M PTCP, pH 8.0, 30% w/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.666 α = 90 b = 100.11 β = 90 c = 103.52 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 EIGER X 16M 2024-03-19 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 1.689 49.345 99.76 0.999 13.45 13.5 79239
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 1.69 1.75 0.999
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.689 49.345 79239 3903 99.721 0.211 0.2094 0.2196 0.2418 0.2474 28.176
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] -1.895 2.702 -0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.26 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_1_deg 7.199 r_lrange_other 6.535 r_lrange_it 6.534 r_dihedral_angle_2_deg 6.087 r_scangle_it 5.134 r_scangle_other 5.134 r_mcangle_other 3.596 r_mcangle_it 3.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.26 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_1_deg 7.199 r_lrange_other 6.535 r_lrange_it 6.534 r_dihedral_angle_2_deg 6.087 r_scangle_it 5.134 r_scangle_other 5.134 r_mcangle_other 3.596 r_mcangle_it 3.595 r_scbond_it 3.377 r_scbond_other 3.376 r_dihedral_angle_other_2_deg 3.092 r_mcbond_it 2.521 r_mcbond_other 2.52 r_angle_refined_deg 1.597 r_dihedral_angle_other_3_deg 1.336 r_angle_other_deg 0.561 r_nbd_refined 0.211 r_nbd_other 0.199 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.19 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.079 r_gen_planes_refined 0.008 r_bond_refined_d 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 4673 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing