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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z44592329
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 1.89 35.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.267 α = 90 b = 52.583 β = 102.95 c = 44.535 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 1.58 54.65 99.6 0.1 0.118 0.061 0.997 6.7 3.4 34692
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 1.58 1.61 97.3 1.434 1.771 1.022 0.335 2.6 1688
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 1.58 54.71 32895 1714 99.39 0.1778 0.1758 0.1845 0.2149 0.2222 RANDOM 21.487
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] 1.26 -1.07 -0.41 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.308 r_dihedral_angle_3_deg 13.737 r_dihedral_angle_4_deg 13.198 r_dihedral_angle_1_deg 8.055 r_mcangle_it 2.493 r_mcbond_other 1.647 r_mcbond_it 1.638 r_angle_refined_deg 1.565 r_angle_other_deg 1.453 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.308 r_dihedral_angle_3_deg 13.737 r_dihedral_angle_4_deg 13.198 r_dihedral_angle_1_deg 8.055 r_mcangle_it 2.493 r_mcbond_other 1.647 r_mcbond_it 1.638 r_angle_refined_deg 1.565 r_angle_other_deg 1.453 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 328 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing