4EL4

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S double mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293reservoir: 29% MPEG2K, 0.04 M Li2SO4, 0.1 M imidazole-HCl pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, 0.050 M bicine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.0640.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.3α = 90
b = 66.3β = 99.1
c = 64.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9395ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.246.0898.70.0720.06611.113.97130060128420-317.075
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2796.50.8050.6951.993.8621021

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODYTHROUGHOUTPDB entry 4EJ51.246.08-3123808121332638699.280.168870.167120.20224RANDOM21.829
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]
0.50.14-0.06-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.365
r_dihedral_angle_4_deg15.71
r_dihedral_angle_3_deg13.852
r_dihedral_angle_1_deg7.004
r_scangle_it5.354
r_scbond_it3.97
r_mcangle_it3.706
r_rigid_bond_restr2.937
r_mcbond_it2.56
r_angle_refined_deg1.643
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.365
r_dihedral_angle_4_deg15.71
r_dihedral_angle_3_deg13.852
r_dihedral_angle_1_deg7.004
r_scangle_it5.354
r_scbond_it3.97
r_mcangle_it3.706
r_rigid_bond_restr2.937
r_mcbond_it2.56
r_angle_refined_deg1.643
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3444
Nucleic Acid Atoms
Solvent Atoms565
Heterogen Atoms27

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing