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X-RAY DIFFRACTION
Materials and Methods page
4HHF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 277.0
    Details 1 uL 20 mg/mL lyophilized toxin in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, pH 7.5, 2% v/v dioxane, 56-60% v/v MPD) against 500 uL reservoir (rod-shaped crystals appeared after 24 hours, grew to 0.5 x 0.1 x 0.1 mm), VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.73 α = 90
    b = 48.73 β = 90
    c = 63.24 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU SATURN 944
    Collection Date 2012-05-14
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-E+ SUPERBRIGHT
    Wavelength List 1.54
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.58
    Resolution(Low) 35.1
    Number Reflections(All) 8454
    Number Reflections(Observed) 8431
    Percent Possible(Observed) 97.2
    R Merge I(Observed) 0.039
    B(Isotropic) From Wilson Plot 11.76
    Redundancy 3.21
     
    High Resolution Shell Details
    Resolution(High) 1.58
    Resolution(Low) 1.64
    Percent Possible(All) 95.6
    R Merge I(Observed) 0.325
    Mean I Over Sigma(Observed) 1.5
    Redundancy 1.54
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 35.1
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 7763
    Number of Reflections(R-Free) 397
    Percent Reflections(Observed) 96.75
    R-Factor(Observed) 0.18593
    R-Work 0.18511
    R-Free 0.20192
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.213
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 23
    Number of Reflections(R-Work) 469
    R-Factor(R-Work) 0.251
    R-Factor(R-Free) 0.375
    Percent Reflections(Observed) 86.77
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.013
    r_chiral_restr 0.298
    r_dihedral_angle_4_deg 8.025
    r_dihedral_angle_3_deg 13.215
    r_dihedral_angle_2_deg 40.395
    r_dihedral_angle_1_deg 6.504
    r_angle_refined_deg 2.671
    r_bond_refined_d 0.027
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 501
    Nucleic Acid Atoms 0
    Heterogen Atoms 24
    Solvent Atoms 45
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) CrystalClear
    Data Reduction (data scaling) CrystalClear
    Structure Solution Phaser
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building Phaser
    data collection CrystalClear