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X-RAY DIFFRACTION
Materials and Methods page
4K67
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 291.0
    Details 25% PEG 1500, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.63 α = 90
    b = 70.63 β = 90
    c = 494.52 γ = 120
     
    Space Group
    Space Group Name:    P 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2012-11-22
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-17A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline BL-17A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.7
    Resolution(Low) 50
    Number Reflections(All) 72276
    Number Reflections(Observed) 72276
    Percent Possible(Observed) 95.3
    B(Isotropic) From Wilson Plot 51.0
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.8
    Percent Possible(All) 95.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 49.117
    Cut-off Sigma(F) 1.97
    Number of Reflections(all) 72239
    Number of Reflections(Observed) 72239
    Number of Reflections(R-Free) 3629
    Percent Reflections(Observed) 95.24
    R-Factor(All) 0.2287
    R-Factor(Observed) 0.2287
    R-Work 0.2273
    R-Free 0.2554
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 77.8937
    Anisotropic B[1][1] -8.6607
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -8.6607
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 17.3213
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6999
    Shell Resolution(Low) 2.7354
    Number of Reflections(R-Free) 102
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.351
    R-Factor(R-Free) 0.3626
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7354
    Shell Resolution(Low) 2.7729
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.3206
    R-Factor(R-Free) 0.369
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7729
    Shell Resolution(Low) 2.8125
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.2998
    R-Factor(R-Free) 0.3294
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8125
    Shell Resolution(Low) 2.8545
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.3051
    R-Factor(R-Free) 0.3371
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8545
    Shell Resolution(Low) 2.8991
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.2824
    R-Factor(R-Free) 0.3189
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8991
    Shell Resolution(Low) 2.9466
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.2986
    R-Factor(R-Free) 0.3213
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9466
    Shell Resolution(Low) 2.9974
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.2829
    R-Factor(R-Free) 0.3322
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9974
    Shell Resolution(Low) 3.0519
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.2624
    R-Factor(R-Free) 0.3111
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0519
    Shell Resolution(Low) 3.1106
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.2508
    R-Factor(R-Free) 0.2683
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1106
    Shell Resolution(Low) 3.1741
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2600
    R-Factor(R-Work) 0.2282
    R-Factor(R-Free) 0.2364
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1741
    Shell Resolution(Low) 3.2431
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2604
    R-Factor(R-Work) 0.2341
    R-Factor(R-Free) 0.2517
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2431
    Shell Resolution(Low) 3.3185
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.2921
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3185
    Shell Resolution(Low) 3.4015
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.2526
    R-Factor(R-Free) 0.3033
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4015
    Shell Resolution(Low) 3.4934
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.2349
    R-Factor(R-Free) 0.2807
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4934
    Shell Resolution(Low) 3.5962
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2578
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.2425
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5962
    Shell Resolution(Low) 3.7122
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.2394
    R-Factor(R-Free) 0.2687
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7122
    Shell Resolution(Low) 3.8449
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.2345
    R-Factor(R-Free) 0.2909
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8449
    Shell Resolution(Low) 3.9987
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.2257
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9987
    Shell Resolution(Low) 4.1806
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2083
    R-Factor(R-Free) 0.2512
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1806
    Shell Resolution(Low) 4.4009
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.234
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4009
    Shell Resolution(Low) 4.6765
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2645
    R-Factor(R-Work) 0.1944
    R-Factor(R-Free) 0.2019
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6765
    Shell Resolution(Low) 5.0372
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1927
    R-Factor(R-Free) 0.2314
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0372
    Shell Resolution(Low) 5.5435
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.22
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5435
    Shell Resolution(Low) 6.3442
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2747
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2304
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3442
    Shell Resolution(Low) 7.9875
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2775
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9875
    Shell Resolution(Low) 49.1248
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.2124
    R-Factor(R-Free) 0.2445
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.136
    f_dihedral_angle_d 18.767
    f_angle_d 1.08
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 15480
    Nucleic Acid Atoms 0
    Heterogen Atoms 212
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHASER
    data collection ADSC version: Quantum