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Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FFZ 3FFZ, 5JLV, 6GLW experimental model PDB 5JLV 3FFZ, 5JLV, 6GLW experimental model PDB 6GLW 3FFZ, 5JLV, 6GLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M HEPES, pH 7.5, 0.2 M potassium sulfate, 20% PEG 3350, and 5% (v/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.85 56.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.742 α = 90 b = 172.335 β = 90 c = 137.162 γ = 90
Symmetry Space Group C 2 2 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 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.59 137.16 100 0.999 19.9 12.1 52103
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 2.59 2.67 0.894
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 3FFZ, 5JLV, 6GLW 2.59 109.01 49418 2660 99.93 0.22711 0.22595 0.2291 0.24897 0.2526 RANDOM 51.741
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] 4.94 -2.89 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.521 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 6.188 r_long_range_B_refined 5.175 r_long_range_B_other 5.153 r_mcangle_it 3.617 r_mcangle_other 3.617 r_scangle_other 3.3 r_mcbond_it 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.521 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 6.188 r_long_range_B_refined 5.175 r_long_range_B_other 5.153 r_mcangle_it 3.617 r_mcangle_other 3.617 r_scangle_other 3.3 r_mcbond_it 2.25 r_mcbond_other 2.25 r_scbond_it 2.044 r_scbond_other 2.032 r_angle_other_deg 1.254 r_angle_refined_deg 1.128 r_chiral_restr 0.041 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 10169 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing