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X-RAY DIFFRACTION
Materials and Methods page
3VB4
  •   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 = 52.32 α = 90
    b = 97.1 β = 103.17
    c = 67.4 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 2009-09-18
     
    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) 2.2
    Resolution(Low) 34.1
    Number Reflections(Observed) 33359
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 33.25
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.32
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 32.816
    Cut-off Sigma(F) 1.43
    Number of Reflections(Observed) 33309
    Number of Reflections(R-Free) 1997
    Percent Reflections(Observed) 99.92
    R-Factor(All) 0.2
    R-Factor(Observed) 0.1849
    R-Work 0.1817
    R-Free 0.2354
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.8982
    Anisotropic B[1][1] -0.6346
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 5.8616
    Anisotropic B[2][2] 6.4174
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.7828
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.255
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2232
    R-Factor(R-Work) 0.2435
    R-Factor(R-Free) 0.3138
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.255
    Shell Resolution(Low) 2.316
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2219
    R-Factor(R-Work) 0.2191
    R-Factor(R-Free) 0.282
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.316
    Shell Resolution(Low) 2.3841
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2212
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.3016
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3841
    Shell Resolution(Low) 2.461
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2246
    R-Factor(R-Work) 0.2003
    R-Factor(R-Free) 0.2519
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.461
    Shell Resolution(Low) 2.5489
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2216
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2534
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5489
    Shell Resolution(Low) 2.651
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2218
    R-Factor(R-Work) 0.1851
    R-Factor(R-Free) 0.2658
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.651
    Shell Resolution(Low) 2.7715
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2266
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2564
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7715
    Shell Resolution(Low) 2.9176
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2229
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.2308
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9176
    Shell Resolution(Low) 3.1003
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2224
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.2334
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1003
    Shell Resolution(Low) 3.3394
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2235
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.2138
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3394
    Shell Resolution(Low) 3.6751
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2242
    R-Factor(R-Work) 0.1562
    R-Factor(R-Free) 0.2084
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6751
    Shell Resolution(Low) 4.2059
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2253
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.22
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2059
    Shell Resolution(Low) 5.2954
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2253
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.2169
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2954
    Shell Resolution(Low) 32.8198
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2267
    R-Factor(R-Work) 0.2201
    R-Factor(R-Free) 0.2407
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.069
    f_dihedral_angle_d 14.344
    f_angle_d 1.077
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4775
    Nucleic Acid Atoms 0
    Heterogen Atoms 38
    Solvent Atoms 201
     
     
  •   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