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Crystal structure of SARS-CoV-2 main protease treated with ebselen
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, HANGING DROP 292 200mM ammonium chloride, 5%glycerol and 16% polyethylene glycol mw.3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.2 α = 90 b = 53.78 β = 101.45 c = 44.92 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 EIGER2 XE 16M mirrors 2020-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.05 48.44 99.5 0.048 0.058 0.031 0.998 12.4 3.4 16661
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 2.05 2.11 100 0.688 0.814 0.43 0.699 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6y2e 2.05 48.39 15831 829 99.42 0.201 0.2 0.207 0.2193 0.2222 RANDOM 46.883
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] 1.09 -1.13 0.86 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.055 r_dihedral_angle_4_deg 16.774 r_dihedral_angle_3_deg 15.451 r_dihedral_angle_1_deg 7.924 r_angle_refined_deg 1.505 r_angle_other_deg 1.364 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.055 r_dihedral_angle_4_deg 16.774 r_dihedral_angle_3_deg 15.451 r_dihedral_angle_1_deg 7.924 r_angle_refined_deg 1.505 r_angle_other_deg 1.364 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 2324 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing