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Crystal structure of SARS-CoV-2 Mpro in complex with RK-411
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 0.1 M SPG pH 6.0, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.99 38.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.361 α = 90 b = 53.938 β = 102.038 c = 44.709 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 2023-09-26 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 1.7 48.58 98.88 0.999 15.95 6.9 29117
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 1.7 1.761 0.704
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 1.7 48.58 29117 1419 98.882 0.196 0.1938 0.2006 0.2431 0.2441 39.106
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] 0.465 1.466 -1.745 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.354 r_dihedral_angle_3_deg 16.072 r_dihedral_angle_2_deg 11.001 r_lrange_other 8.102 r_lrange_it 8.093 r_dihedral_angle_1_deg 7.261 r_scangle_it 6.537 r_scangle_other 6.535 r_scbond_it 4.478 r_scbond_other 4.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.354 r_dihedral_angle_3_deg 16.072 r_dihedral_angle_2_deg 11.001 r_lrange_other 8.102 r_lrange_it 8.093 r_dihedral_angle_1_deg 7.261 r_scangle_it 6.537 r_scangle_other 6.535 r_scbond_it 4.478 r_scbond_other 4.477 r_mcangle_it 4.287 r_mcangle_other 4.286 r_dihedral_angle_other_3_deg 3.251 r_mcbond_it 3.19 r_mcbond_other 3.187 r_angle_refined_deg 1.534 r_angle_other_deg 0.533 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.22 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.188 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_refined 0.085 r_chiral_restr 0.073 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 2367 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing