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X-RAY DIFFRACTION
Materials and Methods page
3VTR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.4
    Temperature 277.0
    Details 100MM HEPES, 200MM MGCL2, 33% PEG 400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 107.94 α = 90
    b = 107.94 β = 90
    c = 174.95 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 180
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Collection Date 2012-01-05
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.5
    Resolution(Low) 53.97
    Number Reflections(Observed) 41167
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.11
    B(Isotropic) From Wilson Plot 40.8
    Redundancy 4.22
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.59
    Percent Possible(All) 98.7
    R Merge I(Observed) 0.376
    Mean I Over Sigma(Observed) 2.2
    R-Sym I(Observed) 0.376
    Redundancy 4.27
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 49.477
    Cut-off Sigma(F) 1.37
    Number of Reflections(Observed) 41052
    Number of Reflections(R-Free) 2070
    Percent Reflections(Observed) 99.02
    R-Factor(Observed) 0.2184
    R-Work 0.217
    R-Free 0.244
     
    Temperature Factor Modeling
    Mean Isotropic B Value 73.277
    Anisotropic B[1][1] 3.35
    Anisotropic B[1][2] 1.67
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.35
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.02
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5001
    Shell Resolution(Low) 2.5583
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2529
    R-Factor(R-Work) 0.2734
    R-Factor(R-Free) 0.3181
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5583
    Shell Resolution(Low) 2.6222
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2537
    R-Factor(R-Work) 0.2584
    R-Factor(R-Free) 0.3067
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6222
    Shell Resolution(Low) 2.6931
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.2781
    R-Factor(R-Free) 0.2925
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6931
    Shell Resolution(Low) 2.7724
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.2672
    R-Factor(R-Free) 0.3112
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7724
    Shell Resolution(Low) 2.8618
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.2345
    R-Factor(R-Free) 0.2841
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8618
    Shell Resolution(Low) 2.9641
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.2328
    R-Factor(R-Free) 0.2471
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9641
    Shell Resolution(Low) 3.0828
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2544
    R-Factor(R-Work) 0.2501
    R-Factor(R-Free) 0.2771
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0828
    Shell Resolution(Low) 3.223
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2580
    R-Factor(R-Work) 0.2424
    R-Factor(R-Free) 0.2651
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.223
    Shell Resolution(Low) 3.3929
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.2468
    R-Factor(R-Free) 0.304
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3929
    Shell Resolution(Low) 3.6055
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2617
    R-Factor(R-Work) 0.2308
    R-Factor(R-Free) 0.2237
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6055
    Shell Resolution(Low) 3.8837
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.2354
    R-Factor(R-Free) 0.2746
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8837
    Shell Resolution(Low) 4.2744
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2744
    Shell Resolution(Low) 4.8924
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.1748
    R-Factor(R-Free) 0.2184
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8924
    Shell Resolution(Low) 6.1621
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2132
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1621
    Shell Resolution(Low) 49.4869
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2800
    R-Factor(R-Work) 0.1994
    R-Factor(R-Free) 0.1967
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.09
    f_dihedral_angle_d 15.696
    f_angle_d 1.137
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4611
    Nucleic Acid Atoms 0
    Heterogen Atoms 85
    Solvent Atoms 254
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement REFMAC version: 5.5.0109
    model building PHASER
    data collection HKL-2000