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X-RAY DIFFRACTION
Materials and Methods page
3VSZ
  •   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 = 107.79 α = 90
    b = 122.6 β = 90
    c = 405.08 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 2012-03-21
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97930
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.89
    Resolution(Low) 50
    Number Reflections(All) 114675
    Number Reflections(Observed) 114675
    Percent Possible(Observed) 95.4
    R Merge I(Observed) 0.175
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 95.4
    R Merge I(Observed) 0.805
    Redundancy 5.9
    Number Unique Reflections(All) 11309
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.893
    Resolution(Low) 48.884
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 109164
    Number of Reflections(R-Free) 1949
    Percent Reflections(Observed) 90.52
    R-Factor(Observed) 0.2395
    R-Work 0.2391
    R-Free 0.2618
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 72.3225
    Anisotropic B[1][1] 21.3315
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.3531
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -24.2773
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8934
    Shell Resolution(Low) 2.9658
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 6243
    R-Factor(R-Work) 0.3707
    R-Factor(R-Free) 0.3582
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9658
    Shell Resolution(Low) 3.046
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 7004
    R-Factor(R-Work) 0.3577
    R-Factor(R-Free) 0.3495
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.046
    Shell Resolution(Low) 3.1356
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 7328
    R-Factor(R-Work) 0.3435
    R-Factor(R-Free) 0.3757
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1356
    Shell Resolution(Low) 3.2368
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7289
    R-Factor(R-Work) 0.3224
    R-Factor(R-Free) 0.3672
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2368
    Shell Resolution(Low) 3.3524
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 7534
    R-Factor(R-Work) 0.2909
    R-Factor(R-Free) 0.3235
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3524
    Shell Resolution(Low) 3.4866
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 7531
    R-Factor(R-Work) 0.2771
    R-Factor(R-Free) 0.2879
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4866
    Shell Resolution(Low) 3.6453
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 7697
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.3104
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6453
    Shell Resolution(Low) 3.8374
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 7838
    R-Factor(R-Work) 0.2379
    R-Factor(R-Free) 0.2688
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8374
    Shell Resolution(Low) 4.0777
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 7830
    R-Factor(R-Work) 0.2174
    R-Factor(R-Free) 0.2474
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0777
    Shell Resolution(Low) 4.3923
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 7954
    R-Factor(R-Work) 0.2029
    R-Factor(R-Free) 0.1885
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3923
    Shell Resolution(Low) 4.834
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 8014
    R-Factor(R-Work) 0.1881
    R-Factor(R-Free) 0.2003
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.834
    Shell Resolution(Low) 5.5327
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 8075
    R-Factor(R-Work) 0.2026
    R-Factor(R-Free) 0.2308
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5327
    Shell Resolution(Low) 6.9674
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 8162
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.2534
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9674
    Shell Resolution(Low) 48.8908
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 8716
    R-Factor(R-Work) 0.2295
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 9.663
    f_plane_restr 0.002
    f_chiral_restr 0.035
    f_angle_d 0.559
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22127
    Nucleic Acid Atoms 0
    Heterogen Atoms 253
    Solvent Atoms 19
     
     
  •   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