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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2737076969
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
Crystal Properties Matthews coefficient Solvent content 1.9 35.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.962 α = 90 b = 52.752 β = 102.99 c = 44.174 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 1.81 55.05 99.8 0.171 0.201 0.105 0.992 4.6 3.6 23171
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 1.81 1.85 99.8 1.891 2.226 1.158 0.302 3.6 1347
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 1.81 55.03 21974 1164 99.62 0.1932 0.1903 0.2057 0.2483 0.2583 RANDOM 28.913
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] 2.7 -0.53 -1.73 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.45 r_dihedral_angle_3_deg 14.027 r_dihedral_angle_4_deg 10.454 r_dihedral_angle_1_deg 8.097 r_mcangle_it 2.975 r_mcbond_other 1.907 r_mcbond_it 1.905 r_angle_refined_deg 1.474 r_angle_other_deg 1.326 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.45 r_dihedral_angle_3_deg 14.027 r_dihedral_angle_4_deg 10.454 r_dihedral_angle_1_deg 8.097 r_mcangle_it 2.975 r_mcbond_other 1.907 r_mcbond_it 1.905 r_angle_refined_deg 1.474 r_angle_other_deg 1.326 r_chiral_restr 0.064 r_bond_refined_d 0.008 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 334 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing