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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102389
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 35.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.043 α = 90 b = 52.569 β = 103.02 c = 44.672 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 2020-03-05 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 1.64 54.63 99.4 0.134 0.158 0.083 0.994 4.8 3.4 30955
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 1.64 1.67 98.2 1.439 1.778 1.026 0.272 2.8 1561
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 1.64 54.58 29309 1520 98.99 0.1863 0.1843 0.1998 0.2247 0.2336 RANDOM 21.866
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] 0.7 -1.1 0.02 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.872 r_dihedral_angle_3_deg 14.187 r_dihedral_angle_4_deg 12.846 r_dihedral_angle_1_deg 7.219 r_mcangle_it 2.169 r_angle_refined_deg 1.474 r_angle_other_deg 1.4 r_mcbond_other 1.315 r_mcbond_it 1.277 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.872 r_dihedral_angle_3_deg 14.187 r_dihedral_angle_4_deg 12.846 r_dihedral_angle_1_deg 7.219 r_mcangle_it 2.169 r_angle_refined_deg 1.474 r_angle_other_deg 1.4 r_mcbond_other 1.315 r_mcbond_it 1.277 r_chiral_restr 0.072 r_bond_refined_d 0.012 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 328 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing