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X-RAY DIFFRACTION
Materials and Methods page
4HYK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 298.0
    Details 18% PEG-3350, 100 mM HEPES pH 7.55, 100mM Ca(OAc)2, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 122.64 α = 90
    b = 122.64 β = 90
    c = 69.92 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector STORAGE PHOSPHORS
    Type RIGAKU RAXIS IV++
    Details OSMICS confocal optics
    Collection Date 2005-08-29
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.8
    Resolution(Low) 30
    Number Reflections(All) 13622
    Number Reflections(Observed) 12423
    Percent Possible(Observed) 91.2
    R Merge I(Observed) 0.06
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.85
    Percent Possible(All) 57.4
    R Merge I(Observed) 0.216
    Mean I Over Sigma(Observed) 3.1
    Redundancy 1.8
    Number Unique Reflections(All) 378
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.802
    Resolution(Low) 29.745
    Cut-off Sigma(F) 1.53
    Number of Reflections(all) 13622
    Number of Reflections(Observed) 12411
    Number of Reflections(R-Free) 1241
    Percent Reflections(Observed) 91.31
    R-Factor(Observed) 0.2419
    R-Work 0.234
    R-Free 0.3134
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 11.3924
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 11.3924
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -22.7848
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.802
    Shell Resolution(Low) 2.9139
    Number of Reflections(R-Free) 101
    Number of Reflections(R-Work) 906
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.4022
    Percent Reflections(Observed) 68.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9139
    Shell Resolution(Low) 3.0464
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1141
    R-Factor(R-Work) 0.3001
    R-Factor(R-Free) 0.3529
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0464
    Shell Resolution(Low) 3.2069
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1188
    R-Factor(R-Work) 0.2713
    R-Factor(R-Free) 0.3431
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2069
    Shell Resolution(Low) 3.4075
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1235
    R-Factor(R-Work) 0.2511
    R-Factor(R-Free) 0.3067
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4075
    Shell Resolution(Low) 3.6702
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1278
    R-Factor(R-Work) 0.2345
    R-Factor(R-Free) 0.3573
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6702
    Shell Resolution(Low) 4.0387
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1313
    R-Factor(R-Work) 0.2353
    R-Factor(R-Free) 0.3393
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0387
    Shell Resolution(Low) 4.6213
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1329
    R-Factor(R-Work) 0.1882
    R-Factor(R-Free) 0.3053
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6213
    Shell Resolution(Low) 5.8152
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1366
    R-Factor(R-Work) 0.2189
    R-Factor(R-Free) 0.2841
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8152
    Shell Resolution(Low) 29.7467
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1414
    R-Factor(R-Work) 0.2359
    R-Factor(R-Free) 0.2842
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.08
    f_dihedral_angle_d 18.532
    f_angle_d 1.213
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2673
    Nucleic Acid Atoms 325
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER in PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHASER version: in PHENIX
    data collection CrystalClear