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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GJI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.3
    Temperature 293.0
    Details 7-8% (w/v) PEG 20000, 50mM MES pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.12 α = 90
    b = 104.92 β = 106.01
    c = 112.38 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Details mirrors
    Collection Date 2011-06-17
     
    Diffraction Radiation
    Monochromator Si(111) double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Wavelength List 1.0
    Site PHOTON FACTORY
    Beamline AR-NE3A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 182769
    Number Reflections(Observed) 182769
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.091
    B(Isotropic) From Wilson Plot 19.1
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.73
    Percent Possible(All) 97.8
    R Merge I(Observed) 0.321
    Mean I Over Sigma(Observed) 3.9
    Redundancy 3.4
    Number Unique Reflections(All) 9074
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 31.48
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 173095
    Number of Reflections(Observed) 173095
    Number of Reflections(R-Free) 17191
    Percent Reflections(Observed) 94.2
    R-Factor(All) 0.177
    R-Factor(Observed) 0.175
    R-Work 0.175
    R-Free 0.195
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 20.7
    Anisotropic B[1][1] -2.5
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.3
    Anisotropic B[2][2] -1.15
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.65
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.81
    Number of Reflections(Observed) 24342
    Number of Reflections(R-Free) 2620
    Number of Reflections(R-Work) 24342
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.256
    R-Free Error 0.005
    Percent Reflections(Observed) 88.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.76
    c_dihedral_angle_d 21.3
    c_angle_deg 1.2
    c_bond_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.17
    Luzzati Sigma A(Observed) 0.11
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.19
    Luzzati Sigma A(R-Free Set) 0.15
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13056
    Nucleic Acid Atoms 0
    Heterogen Atoms 131
    Solvent Atoms 1964
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molrep
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building Molrep
    data collection ADSC version: Quantum