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X-RAY DIFFRACTION
Materials and Methods page
3VX8
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 8
    Temperature 293.0
    Details 16% PEG 3350, 100mM Magnesium formate, 20mM Tris-HCl, 2mM DTT, NaCl, pH 8.0, vapor diffusion, sitting drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 101.52 α = 90
    b = 132.68 β = 90
    c = 102.81 γ = 90
     
    Space Group
    Space Group Name:    P 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2012-06-16
     
    Diffraction Radiation
    Monochromator Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline AR-NE3A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 3.1
    Resolution(Low) 50
    Number Reflections(Observed) 25356
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.162
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.15
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.492
    Redundancy 5.7
    Number Unique Reflections(All) 1241
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 3.11
    Resolution(Low) 34.85
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 24044
    Number of Reflections(R-Free) 1295
    Percent Reflections(Observed) 99.12
    R-Factor(All) 0.2288
    R-Factor(Observed) 0.2287
    R-Work 0.2261
    R-Free 0.2777
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 44.9797
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.113
    Shell Resolution(Low) 3.193
    Number of Reflections(R-Free) 88
    Number of Reflections(R-Work) 1589
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.415
    Percent Reflections(Observed) 91.69
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.003
    r_chiral_restr 0.065
    r_dihedral_angle_4_deg 15.644
    r_dihedral_angle_3_deg 17.364
    r_dihedral_angle_2_deg 35.608
    r_dihedral_angle_1_deg 4.924
    r_angle_refined_deg 0.974
    r_bond_refined_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7605
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 3
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SOLVE
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    density modification RESOLVE
    phasing SOLVE
    data reduction SCALEPACK
    data collection DENZO