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SARS-CoV-2 Main Protease (Mpro) in Complex with ML104
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 ML104 in in 20 mM Tris pH 7.3 + 2 mM DTT + 5 % DMSO
B) 0.1 M MES pH 6 + 14 % w/v PEG 4000
Cryoprotectant was 30% v/v glycerol.
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.49 α = 90 b = 63.586 β = 90 c = 105.64 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 1.95 105.64 98.8 0.063 0.073 0.037 13 3.7 22730 22730
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 1.95 2.06 99.3 0.583 0.583 0.679 0.341 1.3 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6LZE 1.95 35.24 21592 1099 98.36 0.1973 0.1952 0.2386 0.2139 RANDOM 32.583
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] -1.4 2.3 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.653 r_dihedral_angle_4_deg 16.736 r_dihedral_angle_3_deg 13.985 r_dihedral_angle_1_deg 7.873 r_angle_refined_deg 1.573 r_angle_other_deg 1.317 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.653 r_dihedral_angle_4_deg 16.736 r_dihedral_angle_3_deg 13.985 r_dihedral_angle_1_deg 7.873 r_angle_refined_deg 1.573 r_angle_other_deg 1.317 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction