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X-RAY DIFFRACTION
Materials and Methods page
3VB3
  •   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 = 52.43 α = 90
    b = 96.74 β = 102.73
    c = 67.72 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 2009-09-16
     
    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) 27.28
    Number Reflections(Observed) 33503
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 30.32
     
    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) 27.278
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 33470
    Number of Reflections(R-Free) 2000
    Percent Reflections(Observed) 99.96
    R-Factor(All) 0.206
    R-Factor(Observed) 0.1916
    R-Work 0.1891
    R-Free 0.2306
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 34.3825
    Anisotropic B[1][1] 1.7066
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 3.9283
    Anisotropic B[2][2] 3.2846
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.9912
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2001
    Shell Resolution(Low) 2.2551
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2236
    R-Factor(R-Work) 0.2015
    R-Factor(R-Free) 0.2629
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2551
    Shell Resolution(Low) 2.316
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2221
    R-Factor(R-Work) 0.1948
    R-Factor(R-Free) 0.2588
    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) 143
    Number of Reflections(R-Work) 2250
    R-Factor(R-Work) 0.2023
    R-Factor(R-Free) 0.262
    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) 143
    Number of Reflections(R-Work) 2234
    R-Factor(R-Work) 0.194
    R-Factor(R-Free) 0.267
    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) 2244
    R-Factor(R-Work) 0.1978
    R-Factor(R-Free) 0.2571
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5489
    Shell Resolution(Low) 2.6509
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2218
    R-Factor(R-Work) 0.1901
    R-Factor(R-Free) 0.2421
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6509
    Shell Resolution(Low) 2.7714
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2254
    R-Factor(R-Work) 0.1894
    R-Factor(R-Free) 0.2491
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7714
    Shell Resolution(Low) 2.9174
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2259
    R-Factor(R-Work) 0.1851
    R-Factor(R-Free) 0.259
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9174
    Shell Resolution(Low) 3.0999
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2244
    R-Factor(R-Work) 0.1825
    R-Factor(R-Free) 0.2247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0999
    Shell Resolution(Low) 3.3389
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2244
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3389
    Shell Resolution(Low) 3.6742
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2239
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2014
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6742
    Shell Resolution(Low) 4.2042
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2272
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.198
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2042
    Shell Resolution(Low) 5.2905
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2259
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.2163
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2905
    Shell Resolution(Low) 27.2799
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2296
    R-Factor(R-Work) 0.2059
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.062
    f_dihedral_angle_d 15.812
    f_angle_d 0.919
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4703
    Nucleic Acid Atoms 0
    Heterogen Atoms 35
    Solvent Atoms 168
     
     
  •   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)
     
    Software
    refinement PHENIX version: (phenix.refine)
    model building PHASES
    data collection CrystalClear