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X-RAY DIFFRACTION
Materials and Methods page
4AFK
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Details 0.1 M TRIS-HCL, PH 7.5, 0.1 M SODIUM CITRATE, 18 %(W/V) PEG 400. PROTEIN WAS MIXED WITH 7.8 MAG AT RATIO 1:1 (W:W) TO FORM CUBIC PHASE.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 57.25 α = 90
    b = 74.42 β = 101.56
    c = 115.53 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2008-04-22
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTAL CRYO-COOLED
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength 0.97934
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.9
    Resolution(Low) 113.18
    Number Reflections(Observed) 37703
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.14
    B(Isotropic) From Wilson Plot 15.42
    Redundancy 6.4
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 84.9
    R Merge I(Observed) 0.35
    Mean I Over Sigma(Observed) 2.9
    Redundancy 2.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.897
    Resolution(Low) 19.77
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 35580
    Number of Reflections(R-Free) 1788
    Percent Reflections(Observed) 94.51
    R-Factor(Observed) 0.1656
    R-Work 0.1633
    R-Free 0.2086
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.505
    Anisotropic B[1][1] 1.0359
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.7468
    Anisotropic B[2][2] 2.2185
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.2544
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8973
    Shell Resolution(Low) 1.9486
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 1972
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.3114
    Percent Reflections(Observed) 71.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9486
    Shell Resolution(Low) 2.0059
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2306
    R-Factor(R-Work) 0.1739
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0059
    Shell Resolution(Low) 2.0705
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2526
    R-Factor(R-Work) 0.1611
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0705
    Shell Resolution(Low) 2.1444
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2591
    R-Factor(R-Work) 0.1574
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1444
    Shell Resolution(Low) 2.2302
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.1961
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2302
    Shell Resolution(Low) 2.3315
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.2298
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3315
    Shell Resolution(Low) 2.4543
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4543
    Shell Resolution(Low) 2.6077
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2719
    R-Factor(R-Work) 0.1547
    R-Factor(R-Free) 0.1984
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6077
    Shell Resolution(Low) 2.8085
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.2182
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8085
    Shell Resolution(Low) 3.0902
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.1917
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0902
    Shell Resolution(Low) 3.5352
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.1601
    R-Factor(R-Free) 0.2039
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5352
    Shell Resolution(Low) 4.4456
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2770
    R-Factor(R-Work) 0.1543
    R-Factor(R-Free) 0.1976
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4456
    Shell Resolution(Low) 19.7712
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2814
    R-Factor(R-Work) 0.1763
    R-Factor(R-Free) 0.1942
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.099
    f_dihedral_angle_d 19.379
    f_angle_d 1.344
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3415
    Nucleic Acid Atoms 0
    Heterogen Atoms 342
    Solvent Atoms 242
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building PHASER