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Crystal structure of SARS-CoV-2 Mpro in complex with RK-325
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 293 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH8.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.257 α = 90 b = 62.879 β = 94.083 c = 97.495 γ = 90
Symmetry Space Group P 1 21 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 2023-04-25 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 2.15 48.62 99.18 0.997 6.3 7 29646
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 2.15 2.227 0.559
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 2.15 48.62 29645 1438 99.197 0.213 0.2101 0.2144 0.2784 0.2827 34.372
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] -1.921 0.887 1.324 0.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.135 r_dihedral_angle_6_deg 14.698 r_dihedral_angle_2_deg 9.477 r_dihedral_angle_1_deg 8.209 r_lrange_other 7.234 r_lrange_it 7.23 r_dihedral_angle_other_3_deg 5.51 r_scangle_it 5.28 r_scangle_other 5.279 r_mcangle_it 4.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.135 r_dihedral_angle_6_deg 14.698 r_dihedral_angle_2_deg 9.477 r_dihedral_angle_1_deg 8.209 r_lrange_other 7.234 r_lrange_it 7.23 r_dihedral_angle_other_3_deg 5.51 r_scangle_it 5.28 r_scangle_other 5.279 r_mcangle_it 4.308 r_mcangle_other 4.308 r_scbond_it 3.372 r_scbond_other 3.371 r_mcbond_it 2.909 r_mcbond_other 2.905 r_dihedral_angle_other_2_deg 2.631 r_angle_refined_deg 1.443 r_angle_other_deg 0.473 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.222 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.19 r_nbd_other 0.171 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.168 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.067 r_chiral_restr 0.062 r_xyhbond_nbd_other 0.046 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing