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SARS-CoV-2 Main Protease (Mpro) in Complex with ML101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 Sitting drops consisted of 0.19 uL A:0.19 uL B:
A) 5.5 mg/mL Mpro + 0.5 mM ML101 in in 20 mM Tris pH 7.3 + 2 mM DTT + 5 % DMSO
B) 0.1 M di-sodium malonate + 12 % w/v PEG 3350
The cryoprotectant was 30% v/v PEG200
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.054 α = 90 b = 63.91 β = 90 c = 105.77 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 6M Rh coated collimating mirrors, K-B focusing mirrors 2021-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.9 105.77 98.3 0.052 0.057 0.023 16.7 5.9 24308 24308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98.4 0.752 0.752 0.824 0.332 1 5.9
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 6LZE 1.9 35.28 23104 1190 97.85 0.1858 0.1834 0.1939 0.2315 0.2365 RANDOM 37.525
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] -1.11 1.73 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.156 r_dihedral_angle_4_deg 19.306 r_dihedral_angle_3_deg 14.326 r_dihedral_angle_1_deg 7.417 r_angle_refined_deg 1.592 r_angle_other_deg 1.384 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.156 r_dihedral_angle_4_deg 19.306 r_dihedral_angle_3_deg 14.326 r_dihedral_angle_1_deg 7.417 r_angle_refined_deg 1.592 r_angle_other_deg 1.384 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction