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Structure of SARS-CoV-2 Mpro complexed with 4bf
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 PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.308 α = 90 b = 53.611 β = 101.574 c = 44.687 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 2024-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.21 33.96 99.1 0.06 0.94 0.06 5.8 13407
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 2.21 2.27 0.5 3.5
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 2.21 31.682 13382 664 98.899 0.182 0.1778 0.1861 0.2587 0.2618 37.484
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] 1.312 -0.305 -0.709 -0.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.421 r_dihedral_angle_3_deg 15.909 r_dihedral_angle_4_deg 13.923 r_dihedral_angle_1_deg 9.721 r_lrange_it 9.018 r_lrange_other 9.006 r_dihedral_angle_other_3_deg 6.49 r_scangle_it 6.365 r_scangle_other 6.363 r_mcangle_it 4.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.421 r_dihedral_angle_3_deg 15.909 r_dihedral_angle_4_deg 13.923 r_dihedral_angle_1_deg 9.721 r_lrange_it 9.018 r_lrange_other 9.006 r_dihedral_angle_other_3_deg 6.49 r_scangle_it 6.365 r_scangle_other 6.363 r_mcangle_it 4.91 r_mcangle_other 4.909 r_scbond_it 4.337 r_scbond_other 4.336 r_mcbond_other 3.493 r_mcbond_it 3.492 r_angle_refined_deg 1.758 r_angle_other_deg 1.367 r_xyhbond_nbd_refined 0.239 r_nbd_other 0.234 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.209 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.161 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 162 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing