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Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR04
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 HEPES pH7, 0.1M Calcium chloride dihydrate, 20% w/vPEG 6000, 10% v/vEthylene glycol
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.86 α = 90 b = 64.08 β = 93.74 c = 98.48 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 2021-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0032 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 1.69 42.561 99.11 0.998 13.8 6.9 426239
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 0.817
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 1.696 42.561 62409 2101 98.772 0.168 0.1671 0.1774 0.2011 0.2128 24.767
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] -0.941 0.24 1.361 -0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.958 r_dihedral_angle_3_deg 15.09 r_dihedral_angle_2_deg 9.85 r_dihedral_angle_1_deg 7.173 r_lrange_it 7.108 r_lrange_other 7.033 r_scangle_it 5.822 r_scangle_other 5.821 r_scbond_it 3.808 r_scbond_other 3.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.958 r_dihedral_angle_3_deg 15.09 r_dihedral_angle_2_deg 9.85 r_dihedral_angle_1_deg 7.173 r_lrange_it 7.108 r_lrange_other 7.033 r_scangle_it 5.822 r_scangle_other 5.821 r_scbond_it 3.808 r_scbond_other 3.808 r_mcangle_other 3.66 r_mcangle_it 3.659 r_mcbond_it 2.496 r_mcbond_other 2.496 r_dihedral_angle_other_3_deg 2.242 r_angle_refined_deg 1.65 r_angle_other_deg 0.631 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_refined 0.211 r_chiral_restr 0.202 r_symmetry_nbd_other 0.198 r_nbd_other 0.198 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_other 0.124 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4705 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing