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X-RAY DIFFRACTION
Materials and Methods page
3KS8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 295.5
    Details 365mM ammonium acetate, 100mM trisodium citrate, 18.5% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 85.68 α = 90
    b = 85.68 β = 90
    c = 108.81 γ = 120
     
    Space Group
    Space Group Name:    P 31
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2009-05-12
     
    Diffraction Radiation
    Monochromator single crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL11-1
    Wavelength List 0.9795
    Site SSRL
    Beamline BL11-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.28
    Resolution(Low) 37.1
    Number Reflections(All) 40821
    Number Reflections(Observed) 33227
    Percent Possible(Observed) 81.4
    R Merge I(Observed) 0.061
    B(Isotropic) From Wilson Plot 42.2
    Redundancy 4.3
     
    High Resolution Shell Details
    Resolution(High) 2.28
    Resolution(Low) 2.38
    Percent Possible(All) 35.3
    R Merge I(Observed) 0.254
    Mean I Over Sigma(Observed) 5.03
    Redundancy 1.43
    Number Unique Reflections(All) 1751
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.401
    Resolution(Low) 35.117
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 29669
    Number of Reflections(R-Free) 1499
    Percent Reflections(Observed) 84.93
    R-Factor(Observed) 0.2
    R-Work 0.198
    R-Free 0.239
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 42.743
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4011
    Shell Resolution(Low) 2.4869
    Number of Reflections(Observed) 1101
    Number of Reflections(R-Free) 55
    Number of Reflections(R-Work) 1101
    R-Factor(R-Work) 0.2424
    R-Factor(R-Free) 0.3286
    Percent Reflections(Observed) 33.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4869
    Shell Resolution(Low) 2.5864
    Number of Reflections(Observed) 1658
    Number of Reflections(R-Free) 90
    Number of Reflections(R-Work) 1658
    R-Factor(R-Work) 0.2774
    R-Factor(R-Free) 0.3403
    Percent Reflections(Observed) 51.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5864
    Shell Resolution(Low) 2.7041
    Number of Reflections(Observed) 2507
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2507
    R-Factor(R-Work) 0.2706
    R-Factor(R-Free) 0.3459
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7041
    Shell Resolution(Low) 2.8466
    Number of Reflections(Observed) 3058
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3058
    R-Factor(R-Work) 0.2631
    R-Factor(R-Free) 0.3379
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8466
    Shell Resolution(Low) 3.0249
    Number of Reflections(Observed) 3310
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3310
    R-Factor(R-Work) 0.2523
    R-Factor(R-Free) 0.2924
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0249
    Shell Resolution(Low) 3.2583
    Number of Reflections(Observed) 3277
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3277
    R-Factor(R-Work) 0.2204
    R-Factor(R-Free) 0.3027
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2583
    Shell Resolution(Low) 3.5859
    Number of Reflections(Observed) 3314
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3314
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2535
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5859
    Shell Resolution(Low) 4.1041
    Number of Reflections(Observed) 3317
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3317
    R-Factor(R-Work) 0.1717
    R-Factor(R-Free) 0.2107
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1041
    Shell Resolution(Low) 5.168
    Number of Reflections(Observed) 3301
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3301
    R-Factor(R-Work) 0.1551
    R-Factor(R-Free) 0.1701
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.168
    Shell Resolution(Low) 35.1211
    Number of Reflections(Observed) 3327
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3327
    R-Factor(R-Work) 0.1681
    R-Factor(R-Free) 0.1746
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.06
    f_dihedral_angle_d 18.229
    f_angle_d 1.304
    f_bond_d 0.021
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3846
    Nucleic Acid Atoms 761
    Heterogen Atoms 0
    Solvent Atoms 150
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blue-ice
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) XPREP
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_222)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_222)
    model building PHASER
    data collection Blue-ice