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Immune complex of HEV E2s and P1-5B nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GGQ experimental model PDB 7KN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 6% isopropanol, 0.1M sodium acetate pH 4.5, 20% PEG MME550
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.393 α = 90 b = 51.402 β = 92.74 c = 265.172 γ = 90
Symmetry Space Group P 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 EIGER X 9M 2024-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 66.22 98.6 0.314 0.12 0.929 4.9 6.9 70266
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.31 97.8 0.379
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 3GGQ,7KN5 2.2 66.22 68192 2000 85.35 0.27511 0.2168 0.2131 0.2452 0.2415 RANDOM 32.063
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] 4.77 -4.36 4.46 -9.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.372 r_dihedral_angle_2_deg 12.769 r_dihedral_angle_1_deg 8.585 r_long_range_B_refined 5.189 r_long_range_B_other 5.188 r_mcangle_it 4.308 r_mcangle_other 4.308 r_scangle_other 3.542 r_mcbond_it 3.106 r_mcbond_other 3.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.372 r_dihedral_angle_2_deg 12.769 r_dihedral_angle_1_deg 8.585 r_long_range_B_refined 5.189 r_long_range_B_other 5.188 r_mcangle_it 4.308 r_mcangle_other 4.308 r_scangle_other 3.542 r_mcbond_it 3.106 r_mcbond_other 3.105 r_scbond_it 2.492 r_scbond_other 2.492 r_angle_refined_deg 1.64 r_angle_other_deg 0.541 r_chiral_restr 0.072 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 7272 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction AutoProcess data scaling PHENIX phasing