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PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00025058
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 pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.9 35.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.605 α = 90 b = 52.589 β = 102.94 c = 44.578 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 1.63 54.9 99.7 0.127 0.15 0.078 0.995 5.9 3.5 31775
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 1.63 1.66 97.4 1.461 1.8 1.033 0.311 2.8 1519
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 1.63 54.87 30184 1570 99.7 0.1853 0.1831 0.1959 0.2283 0.2408 RANDOM 19.964
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] -0.08 0.05 0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.644 r_dihedral_angle_3_deg 14.047 r_dihedral_angle_4_deg 12.43 r_dihedral_angle_1_deg 7.74 r_mcangle_it 2.174 r_angle_refined_deg 1.522 r_angle_other_deg 1.433 r_mcbond_other 1.394 r_mcbond_it 1.385 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.644 r_dihedral_angle_3_deg 14.047 r_dihedral_angle_4_deg 12.43 r_dihedral_angle_1_deg 7.74 r_mcangle_it 2.174 r_angle_refined_deg 1.522 r_angle_other_deg 1.433 r_mcbond_other 1.394 r_mcbond_it 1.385 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing