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X-RAY DIFFRACTION
Materials and Methods page
3QA8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details 100mM N-(2-acetamido) iminodiacetic acid, 10%(w/v) polyethylene glycol (PEG)6000, 50mM Li2SO4, 300mM NaCl, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.17 α = 71.28
    b = 140.34 β = 79.56
    c = 161.17 γ = 86.04
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 298
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-07-08
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.97922
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.2
    Observed Criterion Sigma(I) 1.2
    Resolution(High) 3.6
    Resolution(Low) 50
    Number Reflections(All) 90090
    Number Reflections(Observed) 75637
    Percent Possible(Observed) 92.5
    R Merge I(Observed) 0.072
    Redundancy 1.9
     
    High Resolution Shell Details
    Resolution(High) 3.6
    Resolution(Low) 3.66
    Percent Possible(All) 76.6
    R Merge I(Observed) 0.432
    Mean I Over Sigma(Observed) 1.2
    R-Sym I(Observed) 0.261
    Redundancy 1.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.6
    Resolution(Low) 14.999
    Cut-off Sigma(F) 0.14
    Number of Reflections(all) 90090
    Number of Reflections(Observed) 75637
    Number of Reflections(R-Free) 3825
    Percent Reflections(Observed) 78.65
    R-Factor(Observed) 0.3097
    R-Work 0.3078
    R-Free 0.3435
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 6.972
    Anisotropic B[1][2] 29.7379
    Anisotropic B[1][3] -40.3815
    Anisotropic B[2][2] -47.6786
    Anisotropic B[2][3] -4.9605
    Anisotropic B[3][3] 26.1452
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6
    Shell Resolution(Low) 3.645
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 1834
    R-Factor(R-Work) 0.4447
    R-Factor(R-Free) 0.4917
    Percent Reflections(Observed) 55.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.645
    Shell Resolution(Low) 3.6922
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 1980
    R-Factor(R-Work) 0.4547
    R-Factor(R-Free) 0.4648
    Percent Reflections(Observed) 58.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6922
    Shell Resolution(Low) 3.7421
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 1934
    R-Factor(R-Work) 0.4377
    R-Factor(R-Free) 0.496
    Percent Reflections(Observed) 57.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7421
    Shell Resolution(Low) 3.7947
    Number of Reflections(R-Free) 92
    Number of Reflections(R-Work) 2023
    R-Factor(R-Work) 0.4241
    R-Factor(R-Free) 0.4586
    Percent Reflections(Observed) 59.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7947
    Shell Resolution(Low) 3.8504
    Number of Reflections(R-Free) 110
    Number of Reflections(R-Work) 2021
    R-Factor(R-Work) 0.4222
    R-Factor(R-Free) 0.4733
    Percent Reflections(Observed) 60.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8504
    Shell Resolution(Low) 3.9095
    Number of Reflections(R-Free) 111
    Number of Reflections(R-Work) 2142
    R-Factor(R-Work) 0.4064
    R-Factor(R-Free) 0.434
    Percent Reflections(Observed) 63.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9095
    Shell Resolution(Low) 3.9724
    Number of Reflections(R-Free) 105
    Number of Reflections(R-Work) 2179
    R-Factor(R-Work) 0.3968
    R-Factor(R-Free) 0.3954
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9724
    Shell Resolution(Low) 4.0396
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2264
    R-Factor(R-Work) 0.375
    R-Factor(R-Free) 0.4425
    Percent Reflections(Observed) 68.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0396
    Shell Resolution(Low) 4.1116
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2363
    R-Factor(R-Work) 0.363
    R-Factor(R-Free) 0.394
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1116
    Shell Resolution(Low) 4.189
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2418
    R-Factor(R-Work) 0.369
    R-Factor(R-Free) 0.38
    Percent Reflections(Observed) 72.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.189
    Shell Resolution(Low) 4.2726
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.3502
    R-Factor(R-Free) 0.3522
    Percent Reflections(Observed) 76.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2726
    Shell Resolution(Low) 4.3632
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.3341
    R-Factor(R-Free) 0.3896
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3632
    Shell Resolution(Low) 4.4621
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2774
    R-Factor(R-Work) 0.337
    R-Factor(R-Free) 0.3806
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4621
    Shell Resolution(Low) 4.5706
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.3242
    R-Factor(R-Free) 0.3466
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5706
    Shell Resolution(Low) 4.6905
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2880
    R-Factor(R-Work) 0.3155
    R-Factor(R-Free) 0.4082
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6905
    Shell Resolution(Low) 4.8241
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2885
    R-Factor(R-Work) 0.2998
    R-Factor(R-Free) 0.3435
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8241
    Shell Resolution(Low) 4.9743
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2897
    R-Factor(R-Work) 0.2938
    R-Factor(R-Free) 0.3245
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9743
    Shell Resolution(Low) 5.1452
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2973
    R-Factor(R-Work) 0.2938
    R-Factor(R-Free) 0.3014
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1452
    Shell Resolution(Low) 5.3422
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 2989
    R-Factor(R-Work) 0.3433
    R-Factor(R-Free) 0.3628
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3422
    Shell Resolution(Low) 5.5734
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3039
    R-Factor(R-Work) 0.3389
    R-Factor(R-Free) 0.4012
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5734
    Shell Resolution(Low) 5.8507
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3108
    R-Factor(R-Work) 0.3339
    R-Factor(R-Free) 0.3546
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8507
    Shell Resolution(Low) 6.1928
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3102
    R-Factor(R-Work) 0.3449
    R-Factor(R-Free) 0.3502
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1928
    Shell Resolution(Low) 6.6324
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 3139
    R-Factor(R-Work) 0.3227
    R-Factor(R-Free) 0.3743
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6324
    Shell Resolution(Low) 7.231
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 3193
    R-Factor(R-Work) 0.2943
    R-Factor(R-Free) 0.3493
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.231
    Shell Resolution(Low) 8.1284
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3113
    R-Factor(R-Work) 0.2769
    R-Factor(R-Free) 0.3339
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.1284
    Shell Resolution(Low) 9.7492
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3330
    R-Factor(R-Work) 0.2365
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.7492
    Shell Resolution(Low) 14.9987
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3225
    R-Factor(R-Work) 0.2038
    R-Factor(R-Free) 0.2416
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.139
    f_dihedral_angle_d 20.142
    f_angle_d 2.086
    f_bond_d 0.054
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 39026
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASES
    data collection HKL-2000