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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DXI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.7
    Temperature 277.0
    Details 0.06M Tris, 0.1M magnesium sulfate, 20% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 106.49 α = 90
    b = 93.06 β = 92.72
    c = 89 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Collection Date 2008-02-01
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU200
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.6
    Resolution(Low) 28.35
    Number Reflections(All) 274833
    Number Reflections(Observed) 112134
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.043
    Redundancy 2.45
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 28.12
    Number of Reflections(all) 114028
    Number of Reflections(Observed) 106316
    Number of Reflections(R-Free) 5612
    Percent Reflections(Observed) 98.16
    R-Factor(Observed) 0.17484
    R-Work 0.17294
    R-Free 0.20981
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 11.434
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.01
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.641
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6806
    R-Factor(R-Work) 0.46
    R-Factor(R-Free) 0.498
    Percent Reflections(Observed) 85.57
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 1.238
    r_sphericity_free 3.394
    r_rigid_bond_restr 1.065
    r_scangle_it 3.048
    r_scbond_it 2.054
    r_mcangle_it 1.307
    r_mcbond_other 0.31
    r_bond_refined_d 0.011
    r_bond_other_d 0.001
    r_angle_refined_deg 1.402
    r_angle_other_deg 0.851
    r_dihedral_angle_1_deg 6.908
    r_dihedral_angle_2_deg 34.373
    r_dihedral_angle_3_deg 11.243
    r_dihedral_angle_4_deg 11.778
    r_chiral_restr 0.085
    r_gen_planes_refined 0.01
    r_gen_planes_other 0.002
    r_mcbond_it 0.812
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7116
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 907
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building PHASER
    data collection CrystalClear