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X-RAY DIFFRACTION
Materials and Methods page
3OL6
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 283.0
    Details 95 mM trisodium citrate, pH 5.6-5.9, 6.5-7.0% (v/v) isopropanol, 16.5-18.0% (w/v) PEG4000, 5% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 283K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.4 α = 83.72
    b = 60.41 β = 83.69
    c = 191.43 γ = 77.85
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type NOIR-1
    Collection Date 2009-05-24
     
    Diffraction Radiation
    Monochromator Rosenbaum-Rock Si(111) sagitally focused monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength List 1.00
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 40.27
    Number Reflections(Observed) 112942
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.073
    Redundancy 2.09
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 96.4
    R Merge I(Observed) 0.495
    Mean I Over Sigma(Observed) 1.4
    Redundancy 1.91
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 38.622
    Cut-off Sigma(F) 0.01
    Number of Reflections(Observed) 85118
    Number of Reflections(R-Free) 4278
    Percent Reflections(Observed) 93.94
    R-Factor(Observed) 0.2146
    R-Work 0.2116
    R-Free 0.2688
    R-Free Selection Details 5% random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 60.0349
    Anisotropic B[1][1] 4.4844
    Anisotropic B[1][2] 4.0547
    Anisotropic B[1][3] 2.8808
    Anisotropic B[2][2] 0.2494
    Anisotropic B[2][3] -0.0586
    Anisotropic B[3][3] -4.7338
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.5284
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.429
    R-Factor(R-Free) 0.4681
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5284
    Shell Resolution(Low) 2.5581
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2521
    R-Factor(R-Work) 0.4289
    R-Factor(R-Free) 0.4733
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5581
    Shell Resolution(Low) 2.5893
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2564
    R-Factor(R-Work) 0.3787
    R-Factor(R-Free) 0.482
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5893
    Shell Resolution(Low) 2.6221
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.3795
    R-Factor(R-Free) 0.4562
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6221
    Shell Resolution(Low) 2.6566
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2469
    R-Factor(R-Work) 0.3951
    R-Factor(R-Free) 0.473
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6566
    Shell Resolution(Low) 2.693
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2557
    R-Factor(R-Work) 0.3653
    R-Factor(R-Free) 0.4887
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.693
    Shell Resolution(Low) 2.7314
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.346
    R-Factor(R-Free) 0.4625
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7314
    Shell Resolution(Low) 2.7722
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2589
    R-Factor(R-Work) 0.3274
    R-Factor(R-Free) 0.3591
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7722
    Shell Resolution(Low) 2.8155
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.3285
    R-Factor(R-Free) 0.4054
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8155
    Shell Resolution(Low) 2.8617
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2761
    R-Factor(R-Work) 0.3064
    R-Factor(R-Free) 0.3996
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8617
    Shell Resolution(Low) 2.911
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2823
    R-Factor(R-Free) 0.3776
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.911
    Shell Resolution(Low) 2.9639
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.2749
    R-Factor(R-Free) 0.3836
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9639
    Shell Resolution(Low) 3.0209
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2807
    R-Factor(R-Work) 0.2589
    R-Factor(R-Free) 0.3682
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0209
    Shell Resolution(Low) 3.0825
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.2408
    R-Factor(R-Free) 0.3017
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0825
    Shell Resolution(Low) 3.1495
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2728
    R-Factor(R-Work) 0.2366
    R-Factor(R-Free) 0.2918
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1495
    Shell Resolution(Low) 3.2227
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.2433
    R-Factor(R-Free) 0.2975
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2227
    Shell Resolution(Low) 3.3033
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2785
    R-Factor(R-Work) 0.2266
    R-Factor(R-Free) 0.2845
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3033
    Shell Resolution(Low) 3.3926
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2730
    R-Factor(R-Work) 0.2236
    R-Factor(R-Free) 0.2631
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3926
    Shell Resolution(Low) 3.4923
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.2173
    R-Factor(R-Free) 0.3005
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4923
    Shell Resolution(Low) 3.605
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2793
    R-Factor(R-Work) 0.2035
    R-Factor(R-Free) 0.3048
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.605
    Shell Resolution(Low) 3.7337
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2732
    R-Factor(R-Work) 0.1832
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7337
    Shell Resolution(Low) 3.8831
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2343
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8831
    Shell Resolution(Low) 4.0596
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2767
    R-Factor(R-Work) 0.1555
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0596
    Shell Resolution(Low) 4.2734
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2833
    R-Factor(R-Work) 0.1442
    R-Factor(R-Free) 0.1774
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2734
    Shell Resolution(Low) 4.5408
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2757
    R-Factor(R-Work) 0.1395
    R-Factor(R-Free) 0.1918
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5408
    Shell Resolution(Low) 4.8907
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2810
    R-Factor(R-Work) 0.1466
    R-Factor(R-Free) 0.1711
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8907
    Shell Resolution(Low) 5.3817
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2801
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.2041
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3817
    Shell Resolution(Low) 6.1578
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2753
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1578
    Shell Resolution(Low) 7.7478
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2795
    R-Factor(R-Work) 0.1903
    R-Factor(R-Free) 0.2356
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7478
    Shell Resolution(Low) 38.6261
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.2101
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.08
    f_dihedral_angle_d 16.771
    f_angle_d 1.162
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14788
    Nucleic Acid Atoms 3014
    Heterogen Atoms 68
    Solvent Atoms 759
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLUE-ICE
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) d*TREK
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASER
    data collection BLUE-ICE