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Crystal Structure of the Human Coronavirus SARS HR1 motif in complex with pan-CoVs inhibitor EK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.5 293 0.2M Li2SO4, 0.1M BIS-Tris, pH 5.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.958 α = 90 b = 100.958 β = 90 c = 73.425 γ = 90
Symmetry Space Group P 43 21 2
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 2017-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 3.3 34.5 99.9 0.172 0.06 11.9 8.1 6070 97.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.42 100 1 0.363 0.74 1.5 7.8
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 2bez 3.3 34.5 6060 307 99.75 0.2507 0.2476 0.2507 0.3014 0.3011 RANDOM 112
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] 1.36 1.36 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.487 r_dihedral_angle_3_deg 17.245 r_long_range_B_refined 11.898 r_long_range_B_other 11.896 r_dihedral_angle_4_deg 9.673 r_scangle_other 8.236 r_mcangle_it 7.207 r_mcangle_other 7.205 r_scbond_it 4.708 r_scbond_other 4.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.487 r_dihedral_angle_3_deg 17.245 r_long_range_B_refined 11.898 r_long_range_B_other 11.896 r_dihedral_angle_4_deg 9.673 r_scangle_other 8.236 r_mcangle_it 7.207 r_mcangle_other 7.205 r_scbond_it 4.708 r_scbond_other 4.706 r_dihedral_angle_1_deg 4.546 r_mcbond_it 4.337 r_mcbond_other 4.331 r_angle_other_deg 1.381 r_angle_refined_deg 1.138 r_chiral_restr 0.054 r_bond_refined_d 0.009 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2438 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing