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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VQE
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.5
    Details SEE WIMBERLY ET AL., NATURE 2000, pH 6.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402 α = 90
    b = 402 β = 90
    c = 175.65 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2006-02-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength 1
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.5
    Resolution(Low) 50
    Number Reflections(Observed) 587336
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.16
    B(Isotropic) From Wilson Plot 53.2
    Redundancy 7.5
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.6
    Percent Possible(All) 97.3
    R Merge I(Observed) 0.77
    Mean I Over Sigma(Observed) 2.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 49.5
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 487131
    Number of Reflections(R-Free) 24512
    Percent Reflections(Observed) 99.8
    R-Factor(Observed) 0.257
    R-Work 0.257
    R-Free 0.283
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 61.1
    Anisotropic B[1][1] -2.5
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.5
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.99
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.66
    Number of Reflections(R-Free) 4005
    Number of Reflections(R-Work) 76381
    R-Factor(R-Work) 0.442
    R-Factor(R-Free) 0.444
    R-Free Error 0.007
    Percent Reflections(Observed) 99.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 1.64
    c_bond_d 0.081
    c_angle_deg 1.5
    c_dihedral_angle_d 28.5
     
    Coordinate Error
    Luzzati ESD(Observed) 0.42
    Luzzati Sigma A(Observed) 0.79
    Luzzati Resolution Cutoff(Low) 30.0
    Luzzati ESD(R-Free Set) 0.46
    Luzzati Sigma A(R-Free Set) 0.78
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19210
    Nucleic Acid Atoms 32723
    Heterogen Atoms 312
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building CNS