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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z126932614
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 1.89 35.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.952 α = 90 b = 52.63 β = 102.98 c = 44.657 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 2020-03-06 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 1.41 54.59 94.2 0.079 0.094 0.05 0.996 6.6 3.2 45926
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 1.41 1.43 78.9 1.154 1.509 0.957 0.309 2.2 1885
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6LU7 1.41 54.55 43624 2211 93.79 0.1793 0.1776 0.211 0.2244 RANDOM 18.514
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] 0.75 -0.89 -0.05 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.445 r_dihedral_angle_4_deg 15.568 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 7.29 r_mcangle_it 2.384 r_angle_refined_deg 1.626 r_mcbond_other 1.572 r_mcbond_it 1.565 r_angle_other_deg 1.521 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.445 r_dihedral_angle_4_deg 15.568 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 7.29 r_mcangle_it 2.384 r_angle_refined_deg 1.626 r_mcbond_other 1.572 r_mcbond_it 1.565 r_angle_other_deg 1.521 r_chiral_restr 0.085 r_bond_refined_d 0.011 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 332 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing