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X-RAY DIFFRACTION
Materials and Methods page
3VB6
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 289.0
    Details 8.5% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 52.1 α = 90
    b = 96.43 β = 103.48
    c = 67.69 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV
    Collection Date 2009-10-14
     
    Diffraction Radiation
    Monochromator YALE MIRRORS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-E+ SUPERBRIGHT
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.5
    Resolution(Low) 29.61
    Number Reflections(Observed) 22586
    Percent Possible(Observed) 99.9
    B(Isotropic) From Wilson Plot 34.48
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.64
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 28.986
    Cut-off Sigma(F) 1.49
    Number of Reflections(Observed) 22556
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 99.94
    R-Factor(All) 0.212
    R-Factor(Observed) 0.1933
    R-Work 0.1881
    R-Free 0.2453
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 36.4448
    Anisotropic B[1][1] 3.6669
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 7.5477
    Anisotropic B[2][2] 5.4377
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -9.1046
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5001
    Shell Resolution(Low) 2.5626
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1443
    R-Factor(R-Work) 0.2172
    R-Factor(R-Free) 0.3077
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5626
    Shell Resolution(Low) 2.6318
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1462
    R-Factor(R-Work) 0.2324
    R-Factor(R-Free) 0.3094
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6318
    Shell Resolution(Low) 2.7092
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1470
    R-Factor(R-Work) 0.2431
    R-Factor(R-Free) 0.2938
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7092
    Shell Resolution(Low) 2.7966
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1454
    R-Factor(R-Work) 0.2219
    R-Factor(R-Free) 0.3298
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7966
    Shell Resolution(Low) 2.8964
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1481
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.3209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8964
    Shell Resolution(Low) 3.0123
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1443
    R-Factor(R-Work) 0.1788
    R-Factor(R-Free) 0.2401
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0123
    Shell Resolution(Low) 3.1492
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1473
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2445
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1492
    Shell Resolution(Low) 3.315
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1458
    R-Factor(R-Work) 0.1925
    R-Factor(R-Free) 0.2719
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.315
    Shell Resolution(Low) 3.5224
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1473
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5224
    Shell Resolution(Low) 3.7938
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1475
    R-Factor(R-Work) 0.1957
    R-Factor(R-Free) 0.2429
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7938
    Shell Resolution(Low) 4.1746
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1465
    R-Factor(R-Work) 0.169
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1746
    Shell Resolution(Low) 4.7763
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1482
    R-Factor(R-Work) 0.1504
    R-Factor(R-Free) 0.2242
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7763
    Shell Resolution(Low) 6.0089
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1473
    R-Factor(R-Work) 0.1874
    R-Factor(R-Free) 0.2164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0089
    Shell Resolution(Low) 28.9875
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1505
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2102
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.072
    f_dihedral_angle_d 14.232
    f_angle_d 1.129
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4761
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 134
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASES
    data collection CrystalClear