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X-RAY DIFFRACTION
Materials and Methods page
4D8H
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 298.0
    Details ~15 mg/mL protein concentration, 1.5 M (NH4)2SO4, 0.11 M Li2SO4, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.58 α = 90
    b = 48.7 β = 90
    c = 64.88 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 IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Details Osmic Confocal Mirrors
    Collection Date 2011-12-10
     
    Diffraction Radiation
    Monochromator Multi-layer mirrors
    Diffraction Protocol Single Wavelength
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU
    Wavelength List 1.541
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 1.9
    Resolution(Low) 20
    Number Reflections(All) 12143
    Number Reflections(Observed) 11803
    Percent Possible(Observed) 97.2
    R Merge I(Observed) 0.095
    Redundancy 12.3
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.96
    Percent Possible(All) 76.2
    R Merge I(Observed) 0.342
    Redundancy 5.8
    Number Unique Reflections(All) 756
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.901
    Resolution(Low) 19.99
    Cut-off Sigma(F) 2.01
    Number of Reflections(all) 12143
    Number of Reflections(Observed) 11533
    Number of Reflections(R-Free) 579
    Percent Reflections(Observed) 95.24
    R-Factor(Observed) 0.1671
    R-Work 0.1647
    R-Free 0.2139
    R-Free Selection Details Random 5%
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.2147
    Anisotropic B[1][1] 0.0261
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.2013
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.1752
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9008
    Shell Resolution(Low) 2.0919
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2414
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2711
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0919
    Shell Resolution(Low) 2.3942
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2778
    R-Factor(R-Work) 0.1413
    R-Factor(R-Free) 0.1895
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3942
    Shell Resolution(Low) 3.0147
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2819
    R-Factor(R-Work) 0.1543
    R-Factor(R-Free) 0.2206
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0147
    Shell Resolution(Low) 19.9909
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2943
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.639
    f_plane_restr 0.006
    f_chiral_restr 0.071
    f_angle_d 1.066
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 939
    Nucleic Acid Atoms 0
    Heterogen Atoms 13
    Solvent Atoms 177
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK