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Crystal structure of SARS CoV2 main protease in complex with inhibitor Telaprevir
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)
18% PEG 6000 (W/V)
300 uM Telaprevir
Crystal Properties Matthews coefficient Solvent content 2.09605575 41.3548126
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.678 α = 90 b = 54.989 β = 101.42 c = 47.932 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 2020-06-30 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 48.96 99.3 0.05 0.054 0.021 0.999 22.1 6.4 16331
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 98.5 0.549 0.594 0.226 0.91 6.7
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 47.03 15497 834 99.03 0.2007 0.1988 0.2029 0.2366 0.2386 RANDOM 39.607
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] -1.18 -1.61 0.9 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 15.251 r_dihedral_angle_1_deg 7.861 r_angle_refined_deg 1.594 r_angle_other_deg 1.345 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 15.251 r_dihedral_angle_1_deg 7.861 r_angle_refined_deg 1.594 r_angle_other_deg 1.345 r_chiral_restr 0.075 r_bond_refined_d 0.009 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 2340 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 53
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction