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X-RAY DIFFRACTION
Materials and Methods page
4K4X
  •   Crystallization Hide
    Crystallization Experiments
    pH 8.5
    Temperature 289.0
    Details 0.17 M sodium acetate, 0.085 M Tris, 25.5% PEG 4000, and 15% glycerol and directly frozen, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 61 α = 90.02
    b = 61.01 β = 89.98
    c = 195.14 γ = 78.36
     
    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
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength 1.00
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.37
    Resolution(Low) 48.78
    Number Reflections(Observed) 109647
    Percent Possible(Observed) 98.0
    R Merge I(Observed) 0.064
    B(Isotropic) From Wilson Plot 41.68
    Redundancy 1.99
     
    High Resolution Shell Details
    Resolution(High) 2.37
    Resolution(Low) 2.45
    Percent Possible(All) 96.6
    R Merge I(Observed) 0.302
    Mean I Over Sigma(Observed) 1.5
    Redundancy 1.94
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.37
    Resolution(Low) 44.01
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 109273
    Number of Reflections(R-Free) 5506
    Percent Reflections(Observed) 97.7
    R-Factor(Observed) 0.205
    R-Work 0.204
    R-Free 0.241
     
    Temperature Factor Modeling
    Mean Isotropic B Value 47.46
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.37
    Shell Resolution(Low) 2.3969
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3389
    R-Factor(R-Work) 0.3201
    R-Factor(R-Free) 0.3845
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3969
    Shell Resolution(Low) 2.4251
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3366
    R-Factor(R-Work) 0.2957
    R-Factor(R-Free) 0.3322
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4251
    Shell Resolution(Low) 2.4547
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3370
    R-Factor(R-Work) 0.297
    R-Factor(R-Free) 0.3487
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4547
    Shell Resolution(Low) 2.4858
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3432
    R-Factor(R-Work) 0.2927
    R-Factor(R-Free) 0.3505
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4858
    Shell Resolution(Low) 2.5185
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3402
    R-Factor(R-Work) 0.2866
    R-Factor(R-Free) 0.3282
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5185
    Shell Resolution(Low) 2.553
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3536
    R-Factor(R-Work) 0.3077
    R-Factor(R-Free) 0.3721
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.553
    Shell Resolution(Low) 2.5894
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3367
    R-Factor(R-Work) 0.2826
    R-Factor(R-Free) 0.311
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5894
    Shell Resolution(Low) 2.6281
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3409
    R-Factor(R-Work) 0.2714
    R-Factor(R-Free) 0.3533
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6281
    Shell Resolution(Low) 2.6692
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3483
    R-Factor(R-Work) 0.2635
    R-Factor(R-Free) 0.3245
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6692
    Shell Resolution(Low) 2.7129
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3428
    R-Factor(R-Work) 0.2637
    R-Factor(R-Free) 0.3006
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7129
    Shell Resolution(Low) 2.7597
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3556
    R-Factor(R-Work) 0.2562
    R-Factor(R-Free) 0.284
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7597
    Shell Resolution(Low) 2.8099
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3331
    R-Factor(R-Work) 0.2484
    R-Factor(R-Free) 0.3026
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8099
    Shell Resolution(Low) 2.8639
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3478
    R-Factor(R-Work) 0.2523
    R-Factor(R-Free) 0.3032
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8639
    Shell Resolution(Low) 2.9223
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3580
    R-Factor(R-Work) 0.2518
    R-Factor(R-Free) 0.3141
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9223
    Shell Resolution(Low) 2.9859
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3333
    R-Factor(R-Work) 0.2431
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9859
    Shell Resolution(Low) 3.0553
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3578
    R-Factor(R-Work) 0.2371
    R-Factor(R-Free) 0.2843
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0553
    Shell Resolution(Low) 3.1317
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3387
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.303
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1317
    Shell Resolution(Low) 3.2163
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3587
    R-Factor(R-Work) 0.2352
    R-Factor(R-Free) 0.2805
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2163
    Shell Resolution(Low) 3.311
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3362
    R-Factor(R-Work) 0.2169
    R-Factor(R-Free) 0.2492
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.311
    Shell Resolution(Low) 3.4178
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3554
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2336
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4178
    Shell Resolution(Low) 3.5399
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3453
    R-Factor(R-Work) 0.1973
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5399
    Shell Resolution(Low) 3.6816
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3505
    R-Factor(R-Work) 0.1885
    R-Factor(R-Free) 0.2138
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6816
    Shell Resolution(Low) 3.849
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 3477
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.224
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.849
    Shell Resolution(Low) 4.0518
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3539
    R-Factor(R-Work) 0.1695
    R-Factor(R-Free) 0.2067
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0518
    Shell Resolution(Low) 4.3055
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 3492
    R-Factor(R-Work) 0.155
    R-Factor(R-Free) 0.1802
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3055
    Shell Resolution(Low) 4.6376
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3463
    R-Factor(R-Work) 0.1459
    R-Factor(R-Free) 0.1562
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6376
    Shell Resolution(Low) 5.1036
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3550
    R-Factor(R-Work) 0.1553
    R-Factor(R-Free) 0.1892
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1036
    Shell Resolution(Low) 5.8407
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3462
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8407
    Shell Resolution(Low) 7.3531
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3482
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3531
    Shell Resolution(Low) 44.0195
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3416
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.2021
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.048
    f_dihedral_angle_d 15.495
    f_angle_d 1.1
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14772
    Nucleic Acid Atoms 2668
    Heterogen Atoms 28
    Solvent Atoms 729
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DTREK
    Data Reduction (data scaling) D*TREK
    Structure Solution PHENIX
    Structure Refinement PHENIX (PHENIX.REFINE: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data collection D*trek