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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4KJI
  •   Crystallization Hide
    Crystallization Experiments
    Method EVAPORATION
    pH 4.5
    Details 0.08M Mg(OAc)2, 0.1M NaOAc pH 4.5, 4% benzamidine HCl, 4% PEG 8000., EVAPORATION
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 83.65 α = 90
    b = 83.65 β = 90
    c = 94.24 γ = 90
     
    Space Group
    Space Group Name:    P 43 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I24
    Wavelength List 0.9686
    Site DIAMOND
    Beamline I24
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.2
    Resolution(Low) 29.57
    Number Reflections(Observed) 5917
    R Merge I(Observed) 0.085
    Redundancy 8.8
     
    High Resolution Shell Details
    Resolution(High) 3.2
    Resolution(Low) 3.37
    Mean I Over Sigma(Observed) 18.6
    Redundancy 6.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.2
    Resolution(Low) 29.56
    Number of Reflections(Observed) 5628
    Number of Reflections(R-Free) 267
    Percent Reflections(Observed) 99.5
    R-Factor(Observed) 0.226
    R-Work 0.222
    R-Free 0.317
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 109.22
    Anisotropic B[1][1] 3.99
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.99
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -7.98
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2
    Shell Resolution(Low) 3.28
    Number of Reflections(R-Free) 14
    Number of Reflections(R-Work) 330
    R-Factor(R-Work) 0.372
    R-Factor(R-Free) 0.462
    Percent Reflections(Observed) 96.36
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.013
    r_chiral_restr 0.097
    r_dihedral_angle_4_deg 20.788
    r_dihedral_angle_3_deg 24.851
    r_dihedral_angle_2_deg 35.872
    r_dihedral_angle_1_deg 6.607
    r_angle_refined_deg 1.718
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1008
    Nucleic Acid Atoms 688
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution Molecular replacement
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building Molecular version: replacement
    data collection DNA