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X-RAY DIFFRACTION
Materials and Methods page
4DM1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 295.0
    Details 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 163.1 α = 90
    b = 58.34 β = 109.65
    c = 137.91 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.75
    Resolution(Low) 50
    Number Reflections(Observed) 121695
    Percent Possible(Observed) 98.7
    R Merge I(Observed) 0.073
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.81
    Percent Possible(All) 87.5
    R Merge I(Observed) 0.434
    Redundancy 3.2
    Number Unique Reflections(All) 10747
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.75
    Resolution(Low) 44.69
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 121183
    Number of Reflections(R-Free) 6097
    Percent Reflections(Observed) 98.19
    R-Factor(Observed) 0.1621
    R-Work 0.1596
    R-Free 0.2087
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.6904
    Anisotropic B[1][1] 0.28
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.13
    Anisotropic B[2][2] -0.12
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.07
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.751
    Shell Resolution(Low) 1.796
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6713
    R-Factor(R-Work) 0.242
    R-Factor(R-Free) 0.277
    Percent Reflections(Observed) 79.62
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.014
    r_chiral_restr 0.179
    r_dihedral_angle_4_deg 17.011
    r_dihedral_angle_3_deg 14.245
    r_dihedral_angle_2_deg 36.073
    r_dihedral_angle_1_deg 6.965
    r_angle_refined_deg 2.276
    r_bond_refined_d 0.024
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9207
    Nucleic Acid Atoms 0
    Heterogen Atoms 75
    Solvent Atoms 1082
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.6.0117
    data reduction HKL