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Crystal structure of SARS CoV2 main protease in complex with FSCU015
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 FSP006 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM FSCU015 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 2.65066648 53.6254044
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.005 α = 90 b = 101.348 β = 90 c = 103.982 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 2020-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000031 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 2.32 49.62 99.8 0.165 0.184 0.081 0.997 9.3 9.3 31612
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 2.32 2.41 1.748 1.956 0.866 0.606 9.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6lu7 2.325 46.302 31556 1626 99.769 0.21 0.2063 0.2072 0.2709 0.2649 RANDOM 49.324
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] -3.228 6.182 -2.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.731 r_dihedral_angle_3_deg 17.362 r_dihedral_angle_4_deg 16.127 r_lrange_other 9.088 r_lrange_it 9.084 r_dihedral_angle_1_deg 7.298 r_scangle_it 6.099 r_scangle_other 6.098 r_mcangle_it 5.721 r_mcangle_other 5.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.731 r_dihedral_angle_3_deg 17.362 r_dihedral_angle_4_deg 16.127 r_lrange_other 9.088 r_lrange_it 9.084 r_dihedral_angle_1_deg 7.298 r_scangle_it 6.099 r_scangle_other 6.098 r_mcangle_it 5.721 r_mcangle_other 5.712 r_scbond_it 3.774 r_scbond_other 3.773 r_mcbond_it 3.578 r_mcbond_other 3.566 r_dihedral_angle_other_2_deg 1.51 r_angle_refined_deg 1.474 r_angle_other_deg 1.25 r_symmetry_nbd_refined 0.272 r_nbd_other 0.259 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.191 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.149 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 45
Software Software Software Name Purpose XDS data processing Aimless data scaling Aimless data reduction PHASER phasing REFMAC refinement Coot model building