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Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1
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 7.5 294 0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 2.5 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.3 α = 90 b = 212.79 β = 91.08 c = 52.91 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2017-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 70.93 99.9 0.103 0.122 0.065 0.998 9.6 6.9 71658
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 2.05 99.7 1.31 1.546 0.815 0.681 7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4KBB 2 53.25 68048 3555 99.86 0.19568 0.19361 0.23545 0.2347 RANDOM 43.992
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] -1.8 -0.73 -2.41 4.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.149 r_dihedral_angle_4_deg 18.231 r_dihedral_angle_3_deg 13.509 r_long_range_B_refined 8.265 r_long_range_B_other 8.255 r_dihedral_angle_1_deg 7.294 r_scangle_other 4.799 r_mcangle_other 4.528 r_mcangle_it 4.527 r_scbond_it 2.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.149 r_dihedral_angle_4_deg 18.231 r_dihedral_angle_3_deg 13.509 r_long_range_B_refined 8.265 r_long_range_B_other 8.255 r_dihedral_angle_1_deg 7.294 r_scangle_other 4.799 r_mcangle_other 4.528 r_mcangle_it 4.527 r_scbond_it 2.979 r_scbond_other 2.979 r_mcbond_it 2.825 r_mcbond_other 2.823 r_angle_refined_deg 1.089 r_angle_other_deg 0.785 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 7455 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing