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SARS-CoV-2 Main Protease (Mpro) in Complex with ML3006a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LZE 6LZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289.15 Sitting drops consisted of 0.23 uL A:0.23 uL B:
A) 5.3 mg/mL Mpro + 0.9 mM ML3006a in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO
B) 0.1 M MES pH 6.5, 4% PEG 35000
Crystal Properties Matthews coefficient Solvent content 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.576 α = 90 b = 63.846 β = 90 c = 104.384 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 Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2022-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979460 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 37.09 99.1 0.134 0.067 0.996 7.1 3.5 22645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.06 99.3 1.895 0.975 0.312 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6LZE 1.95 34.98 21542 1086 98.69 0.19871 0.19552 0.26683 0.2329 RANDOM 40.453
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] -2.73 2.48 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.51 r_dihedral_angle_2_deg 8.028 r_dihedral_angle_1_deg 7.703 r_long_range_B_other 7.7 r_long_range_B_refined 7.695 r_scangle_other 5.804 r_mcangle_other 4.599 r_mcangle_it 4.589 r_scbond_it 3.998 r_scbond_other 3.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.51 r_dihedral_angle_2_deg 8.028 r_dihedral_angle_1_deg 7.703 r_long_range_B_other 7.7 r_long_range_B_refined 7.695 r_scangle_other 5.804 r_mcangle_other 4.599 r_mcangle_it 4.589 r_scbond_it 3.998 r_scbond_other 3.997 r_mcbond_it 3.276 r_mcbond_other 3.266 r_angle_refined_deg 1.515 r_angle_other_deg 0.489 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 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing