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Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1a receptors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 20% v/v PEG6000, 0.1 M MES pH 6.0, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.6 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.344 α = 90 b = 78.491 β = 90 c = 149.103 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 PILATUS3 S 6M 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
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 2.4 74.6 100 0.117 0.129 0.054 0.998 9.9 10.4 23939
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 2.4 2.46 100 1.469 1.62 0.676 0.907 1.2 10.5
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 4KBB 2.4 74.55 22656 1203 99.76 0.20098 0.19945 0.2032 0.22872 0.2323 RANDOM 65.14
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] 4.38 2.92 -7.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.455 r_dihedral_angle_4_deg 14.004 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 9.921 r_long_range_B_other 9.497 r_long_range_B_refined 9.495 r_scangle_other 6.676 r_mcangle_it 6.103 r_mcangle_other 6.102 r_scbond_it 4.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.455 r_dihedral_angle_4_deg 14.004 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 9.921 r_long_range_B_other 9.497 r_long_range_B_refined 9.495 r_scangle_other 6.676 r_mcangle_it 6.103 r_mcangle_other 6.102 r_scbond_it 4.031 r_scbond_other 4.031 r_mcbond_it 3.759 r_mcbond_other 3.755 r_angle_refined_deg 1.543 r_angle_other_deg 1.201 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 3813 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing