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X-RAY DIFFRACTION
Materials and Methods page
4JAP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 289.0
    Details 0.2 M Sodium iodide, 20% w/v Polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 72.01 α = 90
    b = 48.63 β = 97.57
    c = 193.66 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 120
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details mirrors
    Collection Date 2008-01-12
     
    Diffraction Radiation
    Monochromator Graphite
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 1
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 6.34
    Observed Criterion Sigma(I) 0.22
    Resolution(High) 1.83
    Resolution(Low) 50
    Number Reflections(Observed) 90986
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.833
    Resolution(Low) 44.803
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 90962
    Number of Reflections(R-Free) 4291
    Percent Reflections(Observed) 77.37
    R-Factor(Observed) 0.2368
    R-Work 0.2341
    R-Free 0.289
    R-Free Selection Details 5%
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.5629
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -5.7934
    Anisotropic B[2][2] -1.5784
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0154
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.833
    Shell Resolution(Low) 1.8537
    Number of Reflections(R-Free) 1
    Number of Reflections(R-Work) 2
    R-Factor(R-Work) 0.9066
    R-Factor(R-Free) 0.9832
    Percent Reflections(Observed) 1.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8537
    Shell Resolution(Low) 1.8755
    Number of Reflections(R-Free) 41
    Number of Reflections(R-Work) 929
    R-Factor(R-Work) 0.6374
    R-Factor(R-Free) 0.6447
    Percent Reflections(Observed) 25.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8755
    Shell Resolution(Low) 1.8983
    Number of Reflections(R-Free) 32
    Number of Reflections(R-Work) 539
    R-Factor(R-Work) 0.5747
    R-Factor(R-Free) 0.5361
    Percent Reflections(Observed) 29.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8983
    Shell Resolution(Low) 1.9224
    Number of Reflections(R-Free) 65
    Number of Reflections(R-Work) 1075
    R-Factor(R-Work) 0.4807
    R-Factor(R-Free) 0.5038
    Percent Reflections(Observed) 34.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9224
    Shell Resolution(Low) 1.9477
    Number of Reflections(R-Free) 66
    Number of Reflections(R-Work) 1217
    R-Factor(R-Work) 0.4488
    R-Factor(R-Free) 0.4693
    Percent Reflections(Observed) 33.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9477
    Shell Resolution(Low) 1.9744
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 1688
    R-Factor(R-Work) 0.4587
    R-Factor(R-Free) 0.4686
    Percent Reflections(Observed) 46.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9744
    Shell Resolution(Low) 2.0026
    Number of Reflections(R-Free) 102
    Number of Reflections(R-Work) 1894
    R-Factor(R-Work) 0.4464
    R-Factor(R-Free) 0.4373
    Percent Reflections(Observed) 52.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0026
    Shell Resolution(Low) 2.0325
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2291
    R-Factor(R-Work) 0.425
    R-Factor(R-Free) 0.4204
    Percent Reflections(Observed) 62.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0325
    Shell Resolution(Low) 2.0642
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2448
    R-Factor(R-Work) 0.4326
    R-Factor(R-Free) 0.4422
    Percent Reflections(Observed) 67.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0642
    Shell Resolution(Low) 2.0981
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.4123
    R-Factor(R-Free) 0.361
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0981
    Shell Resolution(Low) 2.1342
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2908
    R-Factor(R-Work) 0.407
    R-Factor(R-Free) 0.4083
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1342
    Shell Resolution(Low) 2.173
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3021
    R-Factor(R-Work) 0.4005
    R-Factor(R-Free) 0.4255
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.173
    Shell Resolution(Low) 2.2148
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3212
    R-Factor(R-Work) 0.3875
    R-Factor(R-Free) 0.4217
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2148
    Shell Resolution(Low) 2.26
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3326
    R-Factor(R-Work) 0.3849
    R-Factor(R-Free) 0.3812
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.26
    Shell Resolution(Low) 2.3092
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3487
    R-Factor(R-Work) 0.3578
    R-Factor(R-Free) 0.414
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3092
    Shell Resolution(Low) 2.3629
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3546
    R-Factor(R-Work) 0.3456
    R-Factor(R-Free) 0.3699
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3629
    Shell Resolution(Low) 2.422
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3693
    R-Factor(R-Work) 0.3294
    R-Factor(R-Free) 0.4002
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.422
    Shell Resolution(Low) 2.4875
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 3623
    R-Factor(R-Work) 0.3231
    R-Factor(R-Free) 0.3982
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4875
    Shell Resolution(Low) 2.5606
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3704
    R-Factor(R-Work) 0.3177
    R-Factor(R-Free) 0.3676
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5606
    Shell Resolution(Low) 2.6433
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3613
    R-Factor(R-Work) 0.3019
    R-Factor(R-Free) 0.389
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6433
    Shell Resolution(Low) 2.7378
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3700
    R-Factor(R-Work) 0.2841
    R-Factor(R-Free) 0.3439
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7378
    Shell Resolution(Low) 2.8473
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 3690
    R-Factor(R-Work) 0.2707
    R-Factor(R-Free) 0.3699
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8473
    Shell Resolution(Low) 2.9769
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3681
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.3256
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9769
    Shell Resolution(Low) 3.1338
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3735
    R-Factor(R-Work) 0.2502
    R-Factor(R-Free) 0.2795
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1338
    Shell Resolution(Low) 3.3301
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3735
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.3416
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3301
    Shell Resolution(Low) 3.5871
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3718
    R-Factor(R-Work) 0.2163
    R-Factor(R-Free) 0.2535
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5871
    Shell Resolution(Low) 3.9479
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3752
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2579
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9479
    Shell Resolution(Low) 4.5187
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3768
    R-Factor(R-Work) 0.1649
    R-Factor(R-Free) 0.2341
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5187
    Shell Resolution(Low) 5.6913
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3763
    R-Factor(R-Work) 0.1746
    R-Factor(R-Free) 0.2211
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6913
    Shell Resolution(Low) 44.803
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 3905
    R-Factor(R-Work) 0.1664
    R-Factor(R-Free) 0.2177
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.089
    f_dihedral_angle_d 17.337
    f_angle_d 1.354
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10582
    Nucleic Acid Atoms 0
    Heterogen Atoms 174
    Solvent Atoms 185
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MLPHARE
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.2_869)
    model building MLPHARE
    data collection HKL-2000