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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1587220559
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 35.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.398 α = 90 b = 52.72 β = 102.89 c = 44.4 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 1.73 54.84 99.6 0.121 0.143 0.075 0.996 5.9 3.5 26494
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 1.73 1.76 97.5 1.425 1.73 0.965 0.315 3.1 1468
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 1.73 54.78 25121 1314 99.42 0.1853 0.1826 0.1937 0.2371 0.2483 RANDOM 26.783
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] 2.2 -1.3 -0.74 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.872 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_4_deg 11.798 r_dihedral_angle_1_deg 7.736 r_mcangle_it 2.779 r_mcbond_it 1.785 r_mcbond_other 1.785 r_angle_refined_deg 1.456 r_angle_other_deg 1.363 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.872 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_4_deg 11.798 r_dihedral_angle_1_deg 7.736 r_mcangle_it 2.779 r_mcbond_it 1.785 r_mcbond_other 1.785 r_angle_refined_deg 1.456 r_angle_other_deg 1.363 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 329 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing