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Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JRA 4JRA chain C; 3BTA experimental model PDB 3BTA 4JRA chain C; 3BTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.714 α = 90 b = 122.108 β = 90 c = 47.657 γ = 90
Symmetry Space Group P 21 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 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.919908 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 47.66 99.8 0.242 0.996 9.4 13.2 40692
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 97.7 1.237 0.481 2.2 13.4
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 4JRA chain C; 3BTA 2 47.66 38627 2010 99.81 0.18387 0.18139 0.1895 0.22967 0.2339 RANDOM 27.539
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] 1.86 -0.7 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.602 r_dihedral_angle_3_deg 14.658 r_dihedral_angle_4_deg 14.271 r_dihedral_angle_1_deg 6.947 r_long_range_B_refined 4.758 r_long_range_B_other 4.758 r_mcangle_it 1.666 r_mcangle_other 1.665 r_angle_refined_deg 1.663 r_scangle_other 1.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.602 r_dihedral_angle_3_deg 14.658 r_dihedral_angle_4_deg 14.271 r_dihedral_angle_1_deg 6.947 r_long_range_B_refined 4.758 r_long_range_B_other 4.758 r_mcangle_it 1.666 r_mcangle_other 1.665 r_angle_refined_deg 1.663 r_scangle_other 1.633 r_scbond_it 0.979 r_scbond_other 0.979 r_mcbond_it 0.962 r_angle_other_deg 0.96 r_mcbond_other 0.959 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 4234 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing