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Structure of SARS-CoV-2 Mpro complexed with 5bf
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MLF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350
Crystal Properties Matthews coefficient Solvent content 1.95 36.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.875 α = 90 b = 53.263 β = 102.885 c = 44.55 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 PILATUS 12M 2024-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.97918 SSRF BL17UM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.8 48.1 99.3 0.139 0.98 7.8 6.6 23980
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 0.416 0.7
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 7MLF 1.802 48.067 23980 1203 99.148 0.174 0.1709 0.1855 0.2362 0.2446 23.886
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] 1.976 -1.331 0.108 -1.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.402 r_dihedral_angle_4_deg 16.797 r_dihedral_angle_3_deg 13.745 r_dihedral_angle_1_deg 7.542 r_lrange_it 7.364 r_lrange_other 7.135 r_scangle_other 4.867 r_scangle_it 4.863 r_mcangle_it 3.299 r_mcangle_other 3.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.402 r_dihedral_angle_4_deg 16.797 r_dihedral_angle_3_deg 13.745 r_dihedral_angle_1_deg 7.542 r_lrange_it 7.364 r_lrange_other 7.135 r_scangle_other 4.867 r_scangle_it 4.863 r_mcangle_it 3.299 r_mcangle_other 3.298 r_scbond_it 3.283 r_scbond_other 3.265 r_dihedral_angle_other_3_deg 2.973 r_mcbond_it 2.281 r_mcbond_other 2.277 r_angle_refined_deg 1.875 r_angle_other_deg 1.487 r_symmetry_xyhbond_nbd_refined 0.336 r_xyhbond_nbd_refined 0.33 r_nbd_other 0.244 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.224 r_symmetry_xyhbond_nbd_other 0.212 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.174 r_xyhbond_nbd_other 0.1 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing