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X-RAY DIFFRACTION
Materials and Methods page
4DNR
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7
    Temperature 298.0
    Details PEG3350, NH4SO4, JM600, pH 7, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 159.59 α = 90
    b = 159.59 β = 90
    c = 689.65 γ = 120
     
    Space Group
    Space Group Name:    H 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type ADSC QUANTUM 315r
    Collection Date 2011-01-01
     
    Diffraction Radiation
    Monochromator Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9798
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 3.68
    Resolution(Low) 114.94
    Number Reflections(All) 37324
    Number Reflections(Observed) 37324
    Percent Possible(Observed) 99.9
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 3.68
    Resolution(Low) 3.78
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.625
    Mean I Over Sigma(Observed) 1.1
    R-Sym I(Observed) 0.625
    Redundancy 4.0
    Number Unique Reflections(All) 2715
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.68
    Resolution(Low) 97.6654
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 33612
    Number of Reflections(Observed) 33612
    Number of Reflections(R-Free) 1703
    Percent Reflections(Observed) 89.93
    R-Factor(All) 0.2457
    R-Factor(Observed) 0.2457
    R-Work 0.2443
    R-Free 0.2719
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 95.6005
    Anisotropic B[1][1] 4.2364
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 4.2364
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -8.4729
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.68
    Shell Resolution(Low) 3.7883
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2296
    R-Factor(R-Work) 0.3524
    R-Factor(R-Free) 0.3818
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7883
    Shell Resolution(Low) 3.9106
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 2350
    R-Factor(R-Work) 0.3179
    R-Factor(R-Free) 0.3274
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9106
    Shell Resolution(Low) 4.0504
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2457
    R-Factor(R-Work) 0.2877
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0504
    Shell Resolution(Low) 4.2125
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2546
    R-Factor(R-Work) 0.2599
    R-Factor(R-Free) 0.296
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2125
    Shell Resolution(Low) 4.4043
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.2325
    R-Factor(R-Free) 0.2588
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4043
    Shell Resolution(Low) 4.6365
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.2069
    R-Factor(R-Free) 0.217
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6365
    Shell Resolution(Low) 4.9269
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2756
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.2671
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9269
    Shell Resolution(Low) 5.3073
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2760
    R-Factor(R-Work) 0.2242
    R-Factor(R-Free) 0.2685
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3073
    Shell Resolution(Low) 5.8414
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2740
    R-Factor(R-Work) 0.2402
    R-Factor(R-Free) 0.3009
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8414
    Shell Resolution(Low) 6.6865
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2784
    R-Factor(R-Work) 0.2415
    R-Factor(R-Free) 0.3234
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6865
    Shell Resolution(Low) 8.4235
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2813
    R-Factor(R-Work) 0.2135
    R-Factor(R-Free) 0.2385
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.4235
    Shell Resolution(Low) 97.6654
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3099
    R-Factor(R-Work) 0.2477
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.955
    f_plane_restr 0.003
    f_chiral_restr 0.041
    f_angle_d 0.635
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12881
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 5
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALA
    Structure Solution phaser
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALA version: 3.3.9