4KS6

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 166-174 stretch


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293protein complex - 6 microL LCA C134S at 145 microM + 1.4 microL KG23 at 1.25 milli-M, Reservoir - 17.5% PEG 600, 0.065 M HEPES pH 7.5. Cryoprotectant - CryoProtX CM1, 10% PEG 20K, 100 milliM CHC (citric acid, HEPES, CHES - 40% pH 4 / 60% pH 10), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.634α = 90
b = 65.634β = 90
c = 201.725γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2011-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97240ESRFID23-1

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
11.795099.20.3770.3659.7915.44267342323-3
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)
11.791.994.94.8864.7260.8615.42

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4ELC1.9362.414232332454172499.960.195610.192550.25199RANDOM26.766
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]
-0.09-0.090.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.606
r_dihedral_angle_3_deg14.553
r_dihedral_angle_4_deg13.167
r_dihedral_angle_1_deg6.166
r_scangle_it5.592
r_scbond_it3.786
r_mcangle_it2.691
r_mcbond_it1.731
r_angle_refined_deg1.514
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.606
r_dihedral_angle_3_deg14.553
r_dihedral_angle_4_deg13.167
r_dihedral_angle_1_deg6.166
r_scangle_it5.592
r_scbond_it3.786
r_mcangle_it2.691
r_mcbond_it1.731
r_angle_refined_deg1.514
r_chiral_restr0.117
r_bond_refined_d0.02
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3502
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms53

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing