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PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease screened against DSI poised (Enamine), Fraglites and Peplites (Newcastle university), Mini Frags (Astex), York 3D (York university), electrophile cysteine covalent (Weizman institute) fragment libraries
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 293.15 15% PEG 4K, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 1.9 35.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.207 α = 90 b = 52.596 β = 102.99 c = 44.631 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 2020-03-03 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 1.27 54.69 86.1 0.065 0.078 0.041 0.998 7.1 2.8 57493
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 1.27 1.29 31.9 0.708 0.994 0.696 0.392 1.2 1051
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 1.27 54.67 54097 2729 85.04 0.1852 0.1841 0.192 0.2081 0.2191 RANDOM 16.473
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] 0.79 -0.49 -0.3 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.924 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_3_deg 12.236 r_dihedral_angle_1_deg 7.272 r_mcangle_it 2.185 r_angle_refined_deg 1.676 r_angle_other_deg 1.561 r_mcbond_it 1.416 r_mcbond_other 1.415 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.924 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_3_deg 12.236 r_dihedral_angle_1_deg 7.272 r_mcangle_it 2.185 r_angle_refined_deg 1.676 r_angle_other_deg 1.561 r_mcbond_it 1.416 r_mcbond_other 1.415 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 341 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing