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SARS-CoV-2 Mpro in Complex with RK-107
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 7 293 0.1M PCTP pH7.0, 25% w/vPEG 1500
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.234 α = 90 b = 52.955 β = 102.806 c = 45.707 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 2021-12-06 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 2.6 47.793 98 0.996 7.1 3.5 8125
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 2.6 2.69 98 0.508
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 2.6 47.793 8124 397 98.246 0.2 0.1953 0.2036 0.2745 0.2831 69.138
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] 6.333 1.274 0.377 -6.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.032 r_dihedral_angle_3_deg 17.702 r_dihedral_angle_6_deg 13.969 r_lrange_it 10.82 r_lrange_other 10.819 r_scangle_it 7.555 r_scangle_other 7.553 r_dihedral_angle_1_deg 7.44 r_mcangle_it 6.769 r_mcangle_other 6.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.032 r_dihedral_angle_3_deg 17.702 r_dihedral_angle_6_deg 13.969 r_lrange_it 10.82 r_lrange_other 10.819 r_scangle_it 7.555 r_scangle_other 7.553 r_dihedral_angle_1_deg 7.44 r_mcangle_it 6.769 r_mcangle_other 6.768 r_scbond_it 4.728 r_scbond_other 4.727 r_mcbond_it 4.435 r_mcbond_other 4.431 r_dihedral_angle_other_3_deg 3.205 r_angle_refined_deg 1.122 r_angle_other_deg 0.381 r_nbd_refined 0.224 r_symmetry_nbd_other 0.205 r_nbd_other 0.196 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.127 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.066 r_symmetry_xyhbond_nbd_other 0.063 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing