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X-RAY DIFFRACTION
Materials and Methods page
3G93
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 291.0
    Details 0.1M HEPES, 8% 2-methyl-2,4-pentadediol, 13% PEG 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 86.91 α = 90
    b = 151.82 β = 90
    c = 181.58 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2008-12-13
     
    Diffraction Radiation
    Monochromator Si(311)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL7-1
    Wavelength List 0.98
    Site SSRL
    Beamline BL7-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 3.2
    Resolution(Low) 48.75
    Number Reflections(Observed) 73790
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.144
    B(Isotropic) From Wilson Plot 50.19
    Redundancy 4.1
     
    High Resolution Shell Details
    Resolution(High) 3.2
    Resolution(Low) 3.28
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.506
    Mean I Over Sigma(Observed) 1.4
    R-Sym I(Observed) 0.506
    Redundancy 4.1
    Number Unique Reflections(All) 2903
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.2
    Resolution(Low) 48.747
    Cut-off Sigma(F) 0.03
    Number of Reflections(Observed) 68907
    Number of Reflections(R-Free) 3452
    Percent Reflections(Observed) 90.03
    R-Factor(Observed) 0.239
    R-Work 0.237
    R-Free 0.27
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 44.89
    Anisotropic B[1][1] 16.201
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -6.201
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -9.999
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2
    Shell Resolution(Low) 3.244
    Number of Reflections(R-Free) 107
    Number of Reflections(R-Work) 2368
    R-Factor(R-Work) 0.31
    R-Factor(R-Free) 0.329
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.244
    Shell Resolution(Low) 3.29
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2426
    R-Factor(R-Work) 0.292
    R-Factor(R-Free) 0.331
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.29
    Shell Resolution(Low) 3.339
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2451
    R-Factor(R-Work) 0.287
    R-Factor(R-Free) 0.327
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.339
    Shell Resolution(Low) 3.391
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2436
    R-Factor(R-Work) 0.299
    R-Factor(R-Free) 0.334
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.391
    Shell Resolution(Low) 3.447
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2423
    R-Factor(R-Work) 0.352
    R-Factor(R-Free) 0.381
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.447
    Shell Resolution(Low) 3.507
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2373
    R-Factor(R-Work) 0.297
    R-Factor(R-Free) 0.354
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.507
    Shell Resolution(Low) 3.57
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2559
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.289
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.57
    Shell Resolution(Low) 3.639
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2573
    R-Factor(R-Work) 0.263
    R-Factor(R-Free) 0.306
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.639
    Shell Resolution(Low) 3.713
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2485
    R-Factor(R-Work) 0.295
    R-Factor(R-Free) 0.338
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.713
    Shell Resolution(Low) 3.794
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.255
    R-Factor(R-Free) 0.293
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.794
    Shell Resolution(Low) 3.882
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2552
    R-Factor(R-Work) 0.26
    R-Factor(R-Free) 0.318
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.882
    Shell Resolution(Low) 3.979
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2555
    R-Factor(R-Work) 0.288
    R-Factor(R-Free) 0.38
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.979
    Shell Resolution(Low) 4.087
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2755
    R-Factor(R-Work) 0.228
    R-Factor(R-Free) 0.274
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.087
    Shell Resolution(Low) 4.207
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.261
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.207
    Shell Resolution(Low) 4.343
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2795
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.343
    Shell Resolution(Low) 4.498
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2753
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.498
    Shell Resolution(Low) 4.677
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.17
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.677
    Shell Resolution(Low) 4.89
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2756
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.89
    Shell Resolution(Low) 5.148
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.193
    R-Factor(R-Free) 0.216
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.148
    Shell Resolution(Low) 5.47
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2739
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.245
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.47
    Shell Resolution(Low) 5.892
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.892
    Shell Resolution(Low) 6.483
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.483
    Shell Resolution(Low) 7.419
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2751
    R-Factor(R-Work) 0.209
    R-Factor(R-Free) 0.2
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.419
    Shell Resolution(Low) 9.336
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 2746
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.207
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.336
    Shell Resolution(Low) 48.753
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2778
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.296
    f_plane_restr 0.009
    f_chiral_restr 0.084
    f_angle_d 1.467
    f_bond_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13435
    Nucleic Acid Atoms 0
    Heterogen Atoms 244
    Solvent Atoms 34
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BlueIce
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine)
     
    Software
    refinement PHENIX version: (phenix.refine)
    model building PHASES
    data collection BlueIce