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SARS-CoV-2 Mpro (Omicron, P132H+T169S) free enzyme
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 296 PEG 3350 25%
Crystal Properties Matthews coefficient Solvent content 1.96 37.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.746 α = 90 b = 53.384 β = 102.38 c = 44.804 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 6M 2022-11-23 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 1.8 33.98 98.58 1 19.85 4 24113
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 1.8 1.86 98.72 0.592 1.39 4.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 33.98 22927 1184 98.59 0.21224 0.20949 0.2154 0.26422 0.2647 RANDOM 43.519
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] 1.25 0.06 -0.33 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.87 r_dihedral_angle_2_deg 10.497 r_long_range_B_other 9.433 r_long_range_B_refined 9.425 r_dihedral_angle_1_deg 7.701 r_scangle_other 7.509 r_mcangle_it 5.392 r_mcangle_other 5.391 r_scbond_it 5.206 r_scbond_other 5.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.87 r_dihedral_angle_2_deg 10.497 r_long_range_B_other 9.433 r_long_range_B_refined 9.425 r_dihedral_angle_1_deg 7.701 r_scangle_other 7.509 r_mcangle_it 5.392 r_mcangle_other 5.391 r_scbond_it 5.206 r_scbond_other 5.204 r_mcbond_it 4.383 r_mcbond_other 4.378 r_angle_refined_deg 1.575 r_angle_other_deg 0.526 r_chiral_restr 0.073 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHENIX refinement SCALA data scaling PHASER phasing