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X-RAY DIFFRACTION
Materials and Methods page
3VSF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 289.0
    Details 2.9M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 107.6 α = 90
    b = 122.51 β = 90
    c = 405.53 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2011-12-17
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2011-07-11
     
    Diffraction Radiation
    Diffraction Protocol MAD
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-17A
    Wavelength List 0.97865, 0.97935
    Site PHOTON FACTORY
    Beamline BL-17A
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-5A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline BL-5A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.7
    Resolution(Low) 50
    Number Reflections(Observed) 146526
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.073
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.8
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.522
    Redundancy 5.7
    Number Unique Reflections(All) 14598
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.757
    Resolution(Low) 37.548
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 136168
    Number of Reflections(R-Free) 2468
    Percent Reflections(Observed) 98.07
    R-Factor(Observed) 0.2366
    R-Work 0.2362
    R-Free 0.257
     
    Temperature Factor Modeling
    Mean Isotropic B Value 68.5776
    Anisotropic B[1][1] 12.2218
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.3698
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -17.5917
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7575
    Shell Resolution(Low) 2.8105
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 6807
    R-Factor(R-Work) 0.3383
    R-Factor(R-Free) 0.3085
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8105
    Shell Resolution(Low) 2.8679
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 7434
    R-Factor(R-Work) 0.3484
    R-Factor(R-Free) 0.3902
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8679
    Shell Resolution(Low) 2.9302
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 7471
    R-Factor(R-Work) 0.3392
    R-Factor(R-Free) 0.3588
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9302
    Shell Resolution(Low) 2.9983
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 7501
    R-Factor(R-Work) 0.3248
    R-Factor(R-Free) 0.3495
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9983
    Shell Resolution(Low) 3.0733
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7491
    R-Factor(R-Work) 0.3154
    R-Factor(R-Free) 0.3358
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0733
    Shell Resolution(Low) 3.1563
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 7451
    R-Factor(R-Work) 0.3014
    R-Factor(R-Free) 0.2971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1563
    Shell Resolution(Low) 3.2492
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 7489
    R-Factor(R-Work) 0.2934
    R-Factor(R-Free) 0.3164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2492
    Shell Resolution(Low) 3.354
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 7471
    R-Factor(R-Work) 0.2742
    R-Factor(R-Free) 0.3239
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.354
    Shell Resolution(Low) 3.4738
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 7502
    R-Factor(R-Work) 0.2674
    R-Factor(R-Free) 0.27
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4738
    Shell Resolution(Low) 3.6127
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7489
    R-Factor(R-Work) 0.2575
    R-Factor(R-Free) 0.2867
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6127
    Shell Resolution(Low) 3.777
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 7440
    R-Factor(R-Work) 0.2407
    R-Factor(R-Free) 0.2738
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.777
    Shell Resolution(Low) 3.9759
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 7513
    R-Factor(R-Work) 0.2309
    R-Factor(R-Free) 0.2458
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9759
    Shell Resolution(Low) 4.2247
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 7435
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.2072
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2247
    Shell Resolution(Low) 4.5504
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 7421
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2382
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5504
    Shell Resolution(Low) 5.0074
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 7383
    R-Factor(R-Work) 0.1906
    R-Factor(R-Free) 0.2005
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0074
    Shell Resolution(Low) 5.7298
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 7489
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2483
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7298
    Shell Resolution(Low) 7.2105
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 7555
    R-Factor(R-Work) 0.2103
    R-Factor(R-Free) 0.221
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.2105
    Shell Resolution(Low) 37.5519
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 7358
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.2171
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 10.773
    f_plane_restr 0.002
    f_chiral_restr 0.036
    f_angle_d 0.488
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22127
    Nucleic Acid Atoms 0
    Heterogen Atoms 84
    Solvent Atoms 22
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SOLVE
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    density modification RESOLVE version: 2.15
    phasing SOLVE version: 2.13
    data reduction SCALEPACK
    data collection DENZO