☰ Navigation Tabs
SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a
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 8 289 Sitting drops consisted of 0.23 uL A:0.23 uL B:
A) 5.3 mg/mL Mpro + 0.9 mM ML2006a in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO
B) 20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.829 α = 90 b = 64.071 β = 90 c = 104.422 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 1.03317 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 64.07 99.6 0.145 0.156 0.058 0.995 8 7.2 29174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.6 1.889 2.031 0.736 0.645 7.2
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 1.8 54.67 27728 1401 99.47 0.18074 0.17875 0.1903 0.22004 0.2279 RANDOM 27.621
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] -1.44 0.85 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.064 r_dihedral_angle_2_deg 11.906 r_dihedral_angle_1_deg 7.174 r_long_range_B_refined 6.508 r_long_range_B_other 6.407 r_scangle_other 4.673 r_mcangle_other 3.464 r_mcangle_it 3.462 r_scbond_it 3.13 r_scbond_other 3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.064 r_dihedral_angle_2_deg 11.906 r_dihedral_angle_1_deg 7.174 r_long_range_B_refined 6.508 r_long_range_B_other 6.407 r_scangle_other 4.673 r_mcangle_other 3.464 r_mcangle_it 3.462 r_scbond_it 3.13 r_scbond_other 3.13 r_mcbond_it 2.462 r_mcbond_other 2.461 r_angle_refined_deg 1.479 r_angle_other_deg 0.5 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 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 267 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing