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X-RAY DIFFRACTION
Materials and Methods page
4IKH
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 298.0
    Details Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione), Reservoir (35 % v/v pentaerythritol ethoxylate (15/4 EO/OH) 0.2 M CaCl2, 0.1 M HEPES-NaOH pH 6.5), Cryoprotection (harvested straight from drop), VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.19 α = 90
    b = 88.19 β = 90
    c = 159.83 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Details MIRRORS
    Collection Date 2012-11-08
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 31-ID
    Wavelength List 0.9793
    Site APS
    Beamline 31-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.1
    Resolution(Low) 79.92
    Number Reflections(All) 22195
    Number Reflections(Observed) 22195
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.122
    B(Isotropic) From Wilson Plot 36.77
    Redundancy 15.2
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.21
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.76
    Mean I Over Sigma(Observed) 1.0
    R-Sym I(Observed) 0.76
    Redundancy 15.5
    Number Unique Reflections(All) 3152
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.1
    Resolution(Low) 38.608
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 22054
    Number of Reflections(Observed) 22054
    Number of Reflections(R-Free) 1123
    Percent Reflections(Observed) 99.5
    R-Factor(All) 0.2085
    R-Factor(Observed) 0.2085
    R-Work 0.2072
    R-Free 0.234
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 49.6903
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.1956
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2534
    R-Factor(R-Work) 0.2841
    R-Factor(R-Free) 0.3249
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1956
    Shell Resolution(Low) 2.3113
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2558
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.3045
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3113
    Shell Resolution(Low) 2.4561
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2565
    R-Factor(R-Work) 0.2291
    R-Factor(R-Free) 0.3037
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4561
    Shell Resolution(Low) 2.6457
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.2188
    R-Factor(R-Free) 0.2698
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6457
    Shell Resolution(Low) 2.9119
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2727
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9119
    Shell Resolution(Low) 3.3331
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2413
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3331
    Shell Resolution(Low) 4.1985
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.2048
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1985
    Shell Resolution(Low) 38.6142
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2826
    R-Factor(R-Work) 0.1956
    R-Factor(R-Free) 0.1989
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.801
    f_plane_restr 0.005
    f_chiral_restr 0.071
    f_angle_d 0.996
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1810
    Nucleic Acid Atoms 0
    Heterogen Atoms 41
    Solvent Atoms 60
     
     
  •   Software and Computing Hide
    Computing
    Data Collection UNKNOWN
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALA version: 3.3.20