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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 Z2856434890 (Mpro-x0165)
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 1.9 35.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.03 α = 90 b = 52.76 β = 102.5 c = 44.57 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 2020-02-26 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 2.25 54.61 99.4 0.338 0.407 0.221 0.823 4.4 3.4 12065
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 2.25 2.33 97.1 2.445 3.016 1.727 0.061 3.3 1080
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 2.26 47.52 11423 553 99.3 0.1689 0.1665 0.1934 0.2165 0.2271 RANDOM 37.816
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] 3.04 0.46 -1.61 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.878 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_3_deg 13.822 r_dihedral_angle_1_deg 7.93 r_mcangle_it 3.65 r_mcbond_other 2.263 r_mcbond_it 2.252 r_angle_refined_deg 1.435 r_angle_other_deg 1.293 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.878 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_3_deg 13.822 r_dihedral_angle_1_deg 7.93 r_mcangle_it 3.65 r_mcbond_other 2.263 r_mcbond_it 2.252 r_angle_refined_deg 1.435 r_angle_other_deg 1.293 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 323 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing