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PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1619978933 (Mpro-x0395)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 15% PEG 4K, 5% DMSO, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.045 α = 90 b = 52.891 β = 102.99 c = 44.402 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 PILATUS 6M 2020-02-27 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9126 Diamond I04-1
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 1.7 55.07 99.6 0.111 0.131 0.069 0.993 8.4 3.5 28162
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 1.7 1.73 97 0.978 1.197 0.678 0.425 3 1465
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 FOURIER SYNTHESIS THROUGHOUT 6LU7 1.7 55.08 26705 1394 99.43 0.1675 0.1654 0.1794 0.2076 0.2199 RANDOM 21.507
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] 0.96 -0.51 0.15 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.851 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_4_deg 13.788 r_dihedral_angle_1_deg 7.451 r_mcangle_it 2.549 r_mcbond_other 1.658 r_mcbond_it 1.649 r_angle_refined_deg 1.605 r_angle_other_deg 1.49 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.851 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_4_deg 13.788 r_dihedral_angle_1_deg 7.451 r_mcangle_it 2.549 r_mcbond_other 1.658 r_mcbond_it 1.649 r_angle_refined_deg 1.605 r_angle_other_deg 1.49 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing