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Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR02
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 7.5 293 0.1M Bis Tris Propane pH 7.50, 2M Sodium nitrate, 20% w/vPEG 3350 and 10% v/vEthylene glycol
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.852 α = 90 b = 63.688 β = 91.171 c = 103.506 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 2021-11-24 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) R Merge I (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 2.191 45.884 98.79 0.08664 0.997 19.9 6.9 208789
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 2.191 2.27 0.973
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 2.191 45.884 30460 1498 98.768 0.169 0.1667 0.1761 0.2091 0.2203 23.194
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] -1.203 0.394 0.634 0.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.412 r_dihedral_angle_6_deg 16.329 r_dihedral_angle_2_deg 8.006 r_dihedral_angle_1_deg 7.474 r_dihedral_angle_other_3_deg 6.765 r_lrange_it 6.304 r_lrange_other 6.303 r_scangle_it 4.656 r_scangle_other 4.655 r_mcangle_it 3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.412 r_dihedral_angle_6_deg 16.329 r_dihedral_angle_2_deg 8.006 r_dihedral_angle_1_deg 7.474 r_dihedral_angle_other_3_deg 6.765 r_lrange_it 6.304 r_lrange_other 6.303 r_scangle_it 4.656 r_scangle_other 4.655 r_mcangle_it 3.08 r_mcangle_other 3.08 r_scbond_it 2.9 r_scbond_other 2.899 r_mcbond_it 1.985 r_mcbond_other 1.983 r_angle_refined_deg 1.634 r_angle_other_deg 0.723 r_symmetry_nbd_refined 0.268 r_nbd_refined 0.208 r_symmetry_nbd_other 0.198 r_nbd_other 0.197 r_nbtor_refined 0.183 r_chiral_restr 0.154 r_xyhbond_nbd_refined 0.119 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4714 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing