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Crystal structure of SARS-CoV-2 Mpro in complex with RK-496
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 7.5 293 0.1 M Sodium HEPES; MOPS (acid), 30% w/v (40% v/v PEG 500* MME; 20 % w/v PEG 20000), 0.1M Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.62 53.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.793 α = 90 b = 100.178 β = 90 c = 103.791 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 2024-05-03 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 1.6 49.38 99.94 0.999 16.5 26.5 93746
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 1.6 1.657 99.92 0.567
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 1.6 49.38 93742 4654 99.946 0.196 0.1942 0.2065 0.2242 0.2341 28.312
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] -1.728 2.569 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.134 r_dihedral_angle_6_deg 16.015 r_dihedral_angle_2_deg 9.038 r_dihedral_angle_1_deg 7.121 r_lrange_it 6.979 r_lrange_other 6.979 r_dihedral_angle_other_2_deg 6.414 r_scangle_it 5.932 r_scangle_other 5.932 r_scbond_other 3.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.134 r_dihedral_angle_6_deg 16.015 r_dihedral_angle_2_deg 9.038 r_dihedral_angle_1_deg 7.121 r_lrange_it 6.979 r_lrange_other 6.979 r_dihedral_angle_other_2_deg 6.414 r_scangle_it 5.932 r_scangle_other 5.932 r_scbond_other 3.957 r_scbond_it 3.956 r_mcangle_it 3.654 r_mcangle_other 3.654 r_mcbond_it 2.631 r_mcbond_other 2.615 r_dihedral_angle_other_3_deg 1.657 r_angle_refined_deg 1.58 r_angle_other_deg 0.542 r_symmetry_nbd_refined 0.213 r_nbd_refined 0.21 r_nbd_other 0.196 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4707 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing