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SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a4
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 8.5 289 Sitting drops consisted of 0.23 uL A:0.23 uL B:
A) 5.3 mg/mL Mpro + 0.9 mM ML2006a4 in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO
B) 0.1 M BICINE pH 8.5, 8% w/v mPEG 5000
Crystal Properties Matthews coefficient Solvent content 2.21 44.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.649 α = 90 b = 63.231 β = 90 c = 103.798 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 0.97946 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 2 37.04 97.9 0.123 0.057 0.997 5.5 4.3 20441
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) 2 2.11 99.6 2.19 1.021 0.255 4.3
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 2 37.04 19391 1032 97.28 0.19297 0.18974 0.1988 0.25476 0.2554 RANDOM 51.68
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] -0.81 1.94 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.311 r_long_range_B_other 9.513 r_long_range_B_refined 9.511 r_dihedral_angle_2_deg 9.334 r_dihedral_angle_1_deg 7.827 r_scangle_other 7.369 r_mcangle_other 5.741 r_mcangle_it 5.74 r_scbond_it 4.94 r_scbond_other 4.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.311 r_long_range_B_other 9.513 r_long_range_B_refined 9.511 r_dihedral_angle_2_deg 9.334 r_dihedral_angle_1_deg 7.827 r_scangle_other 7.369 r_mcangle_other 5.741 r_mcangle_it 5.74 r_scbond_it 4.94 r_scbond_other 4.937 r_mcbond_it 4.035 r_mcbond_other 4.013 r_angle_refined_deg 1.52 r_angle_other_deg 0.492 r_chiral_restr 0.065 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 49 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing