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Crystal structure of SARS CoV2 main protease in complex with FSP007
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 6.5 293 0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock FSP007 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM FSP007 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
Crystal Properties Matthews coefficient Solvent content 2.68912506 54.2886314
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.175 α = 90 b = 102.171 β = 90 c = 104.38 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2020-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000035 SLS X06SA
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 2.85 46.48 98.9 0.181 0.227 0.135 0.987 6.3 4.6 17362
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 2.85 3 1.12 1.405 0.835 0.478 4.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6lu7 2.85 46.48 17333 874 98.343 0.208 0.2041 0.2047 0.2784 0.2703 56.792
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] -3.432 7.202 -3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_3_deg 18.255 r_dihedral_angle_4_deg 15.14 r_lrange_it 9.998 r_lrange_other 9.997 r_dihedral_angle_1_deg 7.698 r_mcangle_it 6.923 r_mcangle_other 6.923 r_scangle_it 6.473 r_scangle_other 6.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_3_deg 18.255 r_dihedral_angle_4_deg 15.14 r_lrange_it 9.998 r_lrange_other 9.997 r_dihedral_angle_1_deg 7.698 r_mcangle_it 6.923 r_mcangle_other 6.923 r_scangle_it 6.473 r_scangle_other 6.472 r_mcbond_it 4.28 r_mcbond_other 4.259 r_scbond_it 3.937 r_scbond_other 3.936 r_angle_refined_deg 1.494 r_angle_other_deg 1.197 r_symmetry_xyhbond_nbd_refined 0.3 r_nbd_other 0.214 r_nbd_refined 0.202 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.155 r_ncsr_local_group_1 0.132 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4705 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data processing Aimless data scaling Aimless data reduction PHASER phasing Coot model building