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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DIF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.75
    Temperature 295.0
    Details 3.1 M ammonium sulfate, 200 mM NaCl, 100 mM sodium cacodylate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 61.55 α = 72.92
    b = 63.72 β = 67.22
    c = 71.98 γ = 89.74
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-09-10
     
    Diffraction Radiation
    Monochromator Double-crystal, Si(111) liquid N2 cooled
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.2
    Wavelength List 1.2130
    Site ALS
    Beamline 5.0.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 8.2
    Observed Criterion Sigma(I) 8.2
    Resolution(High) 1.52
    Resolution(Low) 50
    Number Reflections(All) 146711
    Number Reflections(Observed) 127786
    Percent Possible(Observed) 87.1
    R Merge I(Observed) 0.064
    B(Isotropic) From Wilson Plot 15.2
    Redundancy 1.9
     
    High Resolution Shell Details
    Resolution(High) 1.52
    Resolution(Low) 1.55
    Percent Possible(All) 83.3
    R Merge I(Observed) 0.124
    Mean I Over Sigma(Observed) 8.2
    Redundancy 1.9
    Number Unique Reflections(All) 6093
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.521
    Resolution(Low) 50.0
    Number of Reflections(all) 127762
    Number of Reflections(Observed) 121327
    Number of Reflections(R-Free) 6435
    Percent Reflections(Observed) 86.94
    R-Factor(Observed) 0.19967
    R-Work 0.19838
    R-Free 0.2239
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.192
    Anisotropic B[1][1] 0.48
    Anisotropic B[1][2] 0.15
    Anisotropic B[1][3] -0.24
    Anisotropic B[2][2] -0.43
    Anisotropic B[2][3] -0.5
    Anisotropic B[3][3] 0.43
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.521
    Shell Resolution(Low) 1.56
    Number of Reflections(Observed) 8806
    Number of Reflections(R-Free) 421
    Number of Reflections(R-Work) 8806
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.277
    Percent Reflections(Observed) 85.05
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.022
    r_chiral_restr 0.221
    r_dihedral_angle_4_deg 15.2
    r_dihedral_angle_3_deg 12.394
    r_dihedral_angle_2_deg 32.901
    r_dihedral_angle_1_deg 6.879
    r_angle_refined_deg 1.023
    r_bond_refined_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6938
    Nucleic Acid Atoms 0
    Heterogen Atoms 102
    Solvent Atoms 613
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building Phaser
    data collection HKL-2000