6QNS

Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1a receptors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294.1520% v/v PEG6000, 0.1 M MES pH 6.0, 0.2 M sodium chloride
Crystal Properties
Matthews coefficientSolvent content
2.653.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.344α = 90
b = 78.491β = 90
c = 149.103γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.474.61000.1170.1290.0540.9989.910.423939
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)RedundancyNumber Unique Reflections (All)
12.42.461001.4691.620.6760.9071.210.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4KBB2.474.5522656120399.760.200980.199450.22872RANDOM65.14
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]
4.382.92-7.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.455
r_dihedral_angle_4_deg14.004
r_dihedral_angle_3_deg12.935
r_dihedral_angle_1_deg9.921
r_long_range_B_other9.497
r_long_range_B_refined9.495
r_scangle_other6.676
r_mcangle_it6.103
r_mcangle_other6.102
r_scbond_it4.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.455
r_dihedral_angle_4_deg14.004
r_dihedral_angle_3_deg12.935
r_dihedral_angle_1_deg9.921
r_long_range_B_other9.497
r_long_range_B_refined9.495
r_scangle_other6.676
r_mcangle_it6.103
r_mcangle_other6.102
r_scbond_it4.031
r_scbond_other4.031
r_mcbond_it3.759
r_mcbond_other3.755
r_angle_refined_deg1.543
r_angle_other_deg1.201
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3813
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing