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An Information Portal to 109093 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DXO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.7
    Temperature 298.0
    Details 0.07M tris, 0.2 M magnesium chloride, 16% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.65 α = 90
    b = 78.34 β = 90
    c = 119.43 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Collection Date 2009-06-04
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU300
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.5
    Resolution(Low) 39.16
    Number Reflections(All) 8009
    Number Reflections(Observed) 7913
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.058
    Redundancy 4.8
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.64
    Percent Possible(All) 98.4
    R Merge I(Observed) 0.363
    Mean I Over Sigma(Observed) 4.1
    Redundancy 4.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 30.55
    Number of Reflections(Observed) 7527
    Number of Reflections(R-Free) 382
    Percent Reflections(Observed) 98.02
    R-Factor(Observed) 0.19021
    R-Work 0.18706
    R-Free 0.25257
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.523
    Anisotropic B[1][1] 0.13
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.06
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.07
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.565
    Number of Reflections(R-Free) 34
    Number of Reflections(R-Work) 534
    R-Factor(R-Work) 0.279
    R-Factor(R-Free) 0.459
    Percent Reflections(Observed) 97.43
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 2.598
    r_sphericity_free 11.076
    r_rigid_bond_restr 2.01
    r_scangle_it 5.356
    r_scbond_it 3.508
    r_mcangle_it 2.553
    r_mcbond_other 0.437
    r_mcbond_it 1.501
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.01
    r_chiral_restr 0.123
    r_dihedral_angle_4_deg 10.244
    r_dihedral_angle_3_deg 19.737
    r_dihedral_angle_2_deg 36.708
    r_dihedral_angle_1_deg 7.861
    r_angle_other_deg 1.065
    r_angle_refined_deg 2.07
    r_bond_other_d 0.001
    r_bond_refined_d 0.025
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1726
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 60
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) MOSFLM
    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