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Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CLpro
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.7 M sodium malonate (pH 7.0), and 3-5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.668 α = 90 b = 45.16 β = 90 c = 53.967 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 CCD ADSC QUANTUM 210 Monochromator:Si (111) channel cut monochromator;
mirror: oxford Danfysik toroidal focusing mirror 2007-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9537 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.7 50 98.8 0.077 11.3 5 7556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 98.4 0.505 5.7 719
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 THROUGHOUT 2.7 34.46 7510 372 98.89 0.264 0.259 0.3092 0.363 0.3688 RANDOM 37.002
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] -0.55 1.86 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.257 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 17.962 r_dihedral_angle_1_deg 6.065 r_angle_refined_deg 1.112 r_scangle_it 0.884 r_scbond_it 0.693 r_mcangle_it 0.476 r_mcbond_it 0.313 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.257 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 17.962 r_dihedral_angle_1_deg 6.065 r_angle_refined_deg 1.112 r_scangle_it 0.884 r_scbond_it 0.693 r_mcangle_it 0.476 r_mcbond_it 0.313 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.172 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling AMoRE phasing