☰ Navigation Tabs
SARS-CoV-2 Main Protease (Mpro) in Complex with ML1001
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 0.16 uL A:0.16 uL B:
A) 5 mg/mL Mpro + 1.5 mM ML1001 in in 20 mM Tris pH 7.3 + 2 mM DTT + 5 % DMSO
B) 0.1 M HEPES pH 7.5 + 0.2 M L-Proline + 24 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.97 37.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.548 α = 90 b = 52.925 β = 103.32 c = 45.19 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M Rh coated collimating mirrors, K-B focusing mirrors 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
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 1.85 55.733 98.8 0.083 0.096 0.048 6.9 3.9 22318 22318
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 1.85 1.95 99.2 0.611 0.611 0.708 0.353 1.2 3.9
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 1.85 39.22 21183 1122 98.61 0.1652 0.163 0.1715 0.2079 0.2125 RANDOM 38.363
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] 2.04 0.92 -0.55 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.23 r_dihedral_angle_4_deg 20.716 r_dihedral_angle_3_deg 14.215 r_dihedral_angle_1_deg 7.463 r_angle_refined_deg 1.543 r_angle_other_deg 1.364 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.23 r_dihedral_angle_4_deg 20.716 r_dihedral_angle_3_deg 14.215 r_dihedral_angle_1_deg 7.463 r_angle_refined_deg 1.543 r_angle_other_deg 1.364 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction