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Mpro of SARS COV-2 in complex with the RK-90 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 6 293 0.1MMES pH 6, 0.2MSodium chloride, 20% w/vPEG 6000, 10% v/vEthylene glycol
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.253 α = 90 b = 54.376 β = 101.38 c = 114.192 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 2022-05-28 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 2.519 48.959 98.6 0.988 6.4 4.9 18391
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 2.52 2.61 0.599
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 2.519 48.959 18391 950 98.654 0.19 0.1856 0.1926 0.2661 0.2662 30.904
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] -0.181 -0.062 0.271 -0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.589 r_dihedral_angle_3_deg 17.825 r_dihedral_angle_4_deg 17.28 r_dihedral_angle_1_deg 8.262 r_lrange_it 6.135 r_lrange_other 6.135 r_scangle_it 4.259 r_scangle_other 4.258 r_mcangle_it 3.611 r_mcangle_other 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.589 r_dihedral_angle_3_deg 17.825 r_dihedral_angle_4_deg 17.28 r_dihedral_angle_1_deg 8.262 r_lrange_it 6.135 r_lrange_other 6.135 r_scangle_it 4.259 r_scangle_other 4.258 r_mcangle_it 3.611 r_mcangle_other 3.61 r_scbond_it 2.714 r_scbond_other 2.713 r_dihedral_angle_other_3_deg 2.436 r_mcbond_it 2.305 r_mcbond_other 2.305 r_angle_refined_deg 1.671 r_angle_other_deg 1.28 r_metal_ion_refined 1.048 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.215 r_symmetry_nbd_other 0.188 r_nbd_other 0.181 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4662 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing