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Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.75 291 100 mM MES pH 6.75
5% DMSO (V/V)
16% PEG 6000 (W/V)
300 uM Boceprevir
Crystal Properties Matthews coefficient Solvent content 2.02 39.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.763 α = 90 b = 53.535 β = 101.52 c = 45.876 γ = 90
Symmetry Space Group I 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 PSI PILATUS 6M 2020-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033200 PETRA III, DESY P11
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 2.1 48.26 100 0.04 0.044 0.017 1 23.9 6.8 15941
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 2.1 2.16 100 0.702 0.758 0.284 0.83 7
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 MOLECULAR REPLACEMENT THROUGHOUT 6LU7 2.1 44.96 15173 766 99.97 0.189 0.1876 0.1948 0.2154 0.2225 RANDOM 50.982
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] 1.66 0.12 -0.4 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_4_deg 13.524 r_dihedral_angle_1_deg 8.117 r_angle_refined_deg 1.654 r_angle_other_deg 1.325 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_4_deg 13.524 r_dihedral_angle_1_deg 8.117 r_angle_refined_deg 1.654 r_angle_other_deg 1.325 r_chiral_restr 0.07 r_bond_refined_d 0.009 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 2340 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction