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X-RAY DIFFRACTION
Materials and Methods page
3VT2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 289.0
    Details 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 107.23 α = 90
    b = 121.97 β = 90
    c = 405.21 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-02-18
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.9791
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(Observed) 99156
    Percent Possible(Observed) 84.2
    R Merge I(Observed) 0.172
    Redundancy 5.3
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 86.8
    Redundancy 4.7
    Number Unique Reflections(All) 10058
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.002
    Resolution(Low) 44.714
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 88840
    Number of Reflections(R-Free) 1585
    Percent Reflections(Observed) 82.97
    R-Factor(Observed) 0.245
    R-Work 0.2446
    R-Free 0.2708
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 82.4269
    Anisotropic B[1][1] 18.8473
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.8306
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -21.6778
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0021
    Shell Resolution(Low) 3.099
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 7663
    R-Factor(R-Work) 0.3841
    R-Factor(R-Free) 0.3838
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.099
    Shell Resolution(Low) 3.2097
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 8094
    R-Factor(R-Work) 0.3619
    R-Factor(R-Free) 0.4089
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2097
    Shell Resolution(Low) 3.3382
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 8085
    R-Factor(R-Work) 0.3301
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3382
    Shell Resolution(Low) 3.49
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 8032
    R-Factor(R-Work) 0.2805
    R-Factor(R-Free) 0.2913
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.49
    Shell Resolution(Low) 3.674
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 8048
    R-Factor(R-Work) 0.2668
    R-Factor(R-Free) 0.3001
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.674
    Shell Resolution(Low) 3.904
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7993
    R-Factor(R-Work) 0.2416
    R-Factor(R-Free) 0.2806
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.904
    Shell Resolution(Low) 4.2053
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 8012
    R-Factor(R-Work) 0.2228
    R-Factor(R-Free) 0.2283
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2053
    Shell Resolution(Low) 4.6281
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 7902
    R-Factor(R-Work) 0.1997
    R-Factor(R-Free) 0.2507
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6281
    Shell Resolution(Low) 5.2968
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 7864
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2968
    Shell Resolution(Low) 6.6699
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 7840
    R-Factor(R-Work) 0.2235
    R-Factor(R-Free) 0.246
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6699
    Shell Resolution(Low) 44.719
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 7722
    R-Factor(R-Work) 0.226
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 77.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 9.81
    f_plane_restr 0.001
    f_chiral_restr 0.03
    f_angle_d 0.421
    f_bond_d 0.001
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22127
    Nucleic Acid Atoms 0
    Heterogen Atoms 147
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK