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X-RAY DIFFRACTION
Materials and Methods page
3VB5
  •   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 = 52.27 α = 90
    b = 96.4 β = 103.26
    c = 67.7 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 2009-10-12
     
    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) 1.95
    Resolution(Low) 27.2
    Number Reflections(Observed) 47614
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 25.39
     
    High Resolution Shell Details
    Resolution(High) 1.95
    Resolution(Low) 2.06
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.95
    Resolution(Low) 26.276
    Cut-off Sigma(F) 1.41
    Number of Reflections(Observed) 47564
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 99.93
    R-Factor(All) 0.218
    R-Factor(Observed) 0.2057
    R-Work 0.2045
    R-Free 0.232
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.8581
    Anisotropic B[1][1] -0.0079
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 8.2318
    Anisotropic B[2][2] 4.567
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.5591
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.95
    Shell Resolution(Low) 1.9988
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3265
    R-Factor(R-Work) 0.2484
    R-Factor(R-Free) 0.2839
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9988
    Shell Resolution(Low) 2.0528
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3217
    R-Factor(R-Work) 0.2287
    R-Factor(R-Free) 0.2774
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0528
    Shell Resolution(Low) 2.1132
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3244
    R-Factor(R-Work) 0.2122
    R-Factor(R-Free) 0.2433
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1132
    Shell Resolution(Low) 2.1813
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3257
    R-Factor(R-Work) 0.2092
    R-Factor(R-Free) 0.2518
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1813
    Shell Resolution(Low) 2.2593
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3246
    R-Factor(R-Work) 0.2093
    R-Factor(R-Free) 0.2955
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2593
    Shell Resolution(Low) 2.3497
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3238
    R-Factor(R-Work) 0.2107
    R-Factor(R-Free) 0.2324
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3497
    Shell Resolution(Low) 2.4565
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3238
    R-Factor(R-Work) 0.2153
    R-Factor(R-Free) 0.2294
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4565
    Shell Resolution(Low) 2.5859
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3252
    R-Factor(R-Work) 0.2148
    R-Factor(R-Free) 0.246
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5859
    Shell Resolution(Low) 2.7478
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3268
    R-Factor(R-Work) 0.2233
    R-Factor(R-Free) 0.2738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7478
    Shell Resolution(Low) 2.9597
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3240
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.2562
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9597
    Shell Resolution(Low) 3.257
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3271
    R-Factor(R-Work) 0.2128
    R-Factor(R-Free) 0.2193
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.257
    Shell Resolution(Low) 3.7272
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3254
    R-Factor(R-Work) 0.2005
    R-Factor(R-Free) 0.2294
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7272
    Shell Resolution(Low) 4.6915
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3276
    R-Factor(R-Work) 0.1751
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6915
    Shell Resolution(Low) 26.2788
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3299
    R-Factor(R-Work) 0.1956
    R-Factor(R-Free) 0.1923
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.075
    f_dihedral_angle_d 14.736
    f_angle_d 1.203
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4781
    Nucleic Acid Atoms 0
    Heterogen Atoms 12
    Solvent Atoms 312
     
     
  •   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