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SARS-CoV2 major protease in complex with a covalent inhibitor SLL12.
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 293 20% w/v PEG3350
0.2M potassium-thiocyanate
0.1M bis-tris propane pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.827 α = 78.96 b = 85.558 β = 87.18 c = 93.668 γ = 83.17
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 0.976254 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 2.25 43.91 58.8 0.157 0.186 0.098 0.989 6.7 3.5 58705
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 2.25 2.44 13.9 0.683 0.812 0.433 0.597 1.8 3.4
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 2.25 43.91 55787 2918 58.8 0.24322 0.24084 0.2435 0.28912 0.2894 RANDOM 33.558
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] 0.08 0.15 0.1 0.01 -0.16 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.505 r_dihedral_angle_3_deg 17.45 r_long_range_B_refined 9.77 r_long_range_B_other 9.77 r_dihedral_angle_1_deg 6.998 r_scangle_other 5.562 r_mcangle_it 5.103 r_mcangle_other 5.103 r_scbond_it 3.489 r_scbond_other 3.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.505 r_dihedral_angle_3_deg 17.45 r_long_range_B_refined 9.77 r_long_range_B_other 9.77 r_dihedral_angle_1_deg 6.998 r_scangle_other 5.562 r_mcangle_it 5.103 r_mcangle_other 5.103 r_scbond_it 3.489 r_scbond_other 3.489 r_mcbond_it 3.243 r_mcbond_other 3.239 r_angle_refined_deg 1.257 r_angle_other_deg 0.436 r_chiral_restr 0.057 r_bond_refined_d 0.007 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 14262 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing