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Crystal structure of SARS-CoV-2 main protease E166V (Apo structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.069 α = 90 b = 53.764 β = 100.91 c = 44.642 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 EIGER X 16M 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 55.51 98.1 0.04638 23.33 7 20488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.901 1.969 0.3108
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 1.9 55.51 19469 1005 98.12 0.21286 0.21012 0.2193 0.26538 0.2673 RANDOM 37.559
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] 1.28 -0.78 0.4 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.489 r_dihedral_angle_3_deg 13.637 r_long_range_B_other 7.861 r_long_range_B_refined 7.848 r_dihedral_angle_1_deg 7.732 r_scangle_other 5.982 r_mcangle_it 5.434 r_mcangle_other 5.432 r_scbond_it 4.085 r_scbond_other 4.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.489 r_dihedral_angle_3_deg 13.637 r_long_range_B_other 7.861 r_long_range_B_refined 7.848 r_dihedral_angle_1_deg 7.732 r_scangle_other 5.982 r_mcangle_it 5.434 r_mcangle_other 5.432 r_scbond_it 4.085 r_scbond_other 4.084 r_mcbond_it 3.792 r_mcbond_other 3.787 r_angle_refined_deg 1.716 r_angle_other_deg 0.579 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 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 2331 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction MOLREP phasing DIALS data scaling