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SARS-CoV2 major protease in complex with a covalent inhibitor SLL11.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 18% w/v PEG3350
0.2M KSCN
0.1M Bis-Tris Propanol pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.815 α = 79.25 b = 85.743 β = 87.44 c = 93.912 γ = 83.86
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 2021-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.11 46.16 63.1 0.129 0.152 0.08 0.991 7.3 3.6 76783
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.31 13.3 0.797 0.947 0.504 0.525 1.6
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 2.11 46.16 72978 3805 63.09 0.21063 0.20822 0.2124 0.2571 0.2583 RANDOM 32.107
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] -0.06 -0.04 -0.14 0.11 -0.19 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.8 r_dihedral_angle_2_deg 16.547 r_long_range_B_refined 8.642 r_long_range_B_other 8.639 r_dihedral_angle_1_deg 6.929 r_scangle_other 5.393 r_mcangle_it 4.533 r_mcangle_other 4.532 r_scbond_it 3.397 r_scbond_other 3.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.8 r_dihedral_angle_2_deg 16.547 r_long_range_B_refined 8.642 r_long_range_B_other 8.639 r_dihedral_angle_1_deg 6.929 r_scangle_other 5.393 r_mcangle_it 4.533 r_mcangle_other 4.532 r_scbond_it 3.397 r_scbond_other 3.397 r_mcbond_it 2.922 r_mcbond_other 2.922 r_angle_refined_deg 1.278 r_angle_other_deg 0.456 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 14249 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing