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Crystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2
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 20% polyethylene glycol mw. 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.004 α = 90 b = 53.622 β = 100.892 c = 44.545 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 1.85 33.867 99.9 0.075 0.102 0.069 0.997 8.6 3.3 22635
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 1.85 1.89 99.9 1.079 1.456 0.971 0.446 1.6 3.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6y2e 1.85 33.867 22624 1159 99.81 0.225 0.2239 0.2248 0.249 0.2508 36.114
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] 2.401 0.48 -0.621 -1.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 15.983 r_dihedral_angle_3_deg 15.115 r_dihedral_angle_1_deg 7.769 r_lrange_it 7.584 r_scangle_it 5.721 r_mcangle_it 4.314 r_scbond_it 4.084 r_mcbond_it 3.288 r_angle_refined_deg 1.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 15.983 r_dihedral_angle_3_deg 15.115 r_dihedral_angle_1_deg 7.769 r_lrange_it 7.584 r_scangle_it 5.721 r_mcangle_it 4.314 r_scbond_it 4.084 r_mcbond_it 3.288 r_angle_refined_deg 1.572 r_symmetry_nbd_refined 0.426 r_nbtor_refined 0.321 r_symmetry_xyhbond_nbd_refined 0.249 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.103 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2307 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing