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Crystal structure of SARS CoV2 main protease in complex with FSP006
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 FSP006 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 2.65545678 53.7090645
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.155 α = 90 b = 100.588 β = 90 c = 104.726 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 2.14 46.45 98.1 0.132 0.149 0.069 0.997 9.8 7.8 39260
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 2.14 2.21 1.329 1.516 0.712 0.634 7.9
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 2.145 46.447 39220 1962 97.657 0.204 0.2019 0.2073 0.2514 0.2466 RANDOM 40.003
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] -2.693 2.82 -0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_3_deg 15.942 r_dihedral_angle_1_deg 7.942 r_lrange_it 7.812 r_lrange_other 7.783 r_scangle_it 5.54 r_scangle_other 5.539 r_mcangle_it 4.662 r_mcangle_other 4.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_3_deg 15.942 r_dihedral_angle_1_deg 7.942 r_lrange_it 7.812 r_lrange_other 7.783 r_scangle_it 5.54 r_scangle_other 5.539 r_mcangle_it 4.662 r_mcangle_other 4.661 r_scbond_it 3.736 r_scbond_other 3.735 r_mcbond_it 3.109 r_mcbond_other 3.102 r_angle_refined_deg 1.553 r_angle_other_deg 1.291 r_symmetry_nbd_refined 0.245 r_nbd_other 0.219 r_nbd_refined 0.199 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 r_bond_refined_d 0.008 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 4681 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction XDS data processing Aimless data scaling PHASER phasing Coot model building