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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1RA6
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 289.0
    Details sodium acetate, cacodylate, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 127.59 α = 90
    b = 127.59 β = 90
    c = 112.97 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details Pt-coated toroidal Si mirror for horizontal and vertical focussing
    Collection Date 2003-04-09
     
    Diffraction Radiation
    Monochromator double flat Si crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2
    Resolution(Low) 30
    Number Reflections(All) 67110
    Number Reflections(Observed) 67110
    Percent Possible(Observed) 96.3
    R Merge I(Observed) 0.054
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 93.7
    R Merge I(Observed) 0.456
    Mean I Over Sigma(Observed) 2.5
    Redundancy 3.1
    Number Unique Reflections(All) 6514
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 30.0
    Number of Reflections(all) 67110
    Number of Reflections(Observed) 67110
    Number of Reflections(R-Free) 6807
    Percent Reflections(Observed) 96.1
    R-Work 0.231
    R-Free 0.247
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic
    Mean Isotropic B Value 51.9
    Anisotropic B[1][1] 6.25
    Anisotropic B[1][2] 4.57
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 6.25
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -12.49
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.07
    Number of Reflections(Observed) 5256
    Number of Reflections(R-Free) 469
    R-Factor(R-Work) 0.393
    R-Factor(R-Free) 0.394
    Percent Reflections(Observed) 93.7
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_angle_deg 1.3
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.33
    Luzzati Sigma A(Observed) 0.45
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.35
    Luzzati Sigma A(R-Free Set) 0.45
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3707
    Nucleic Acid Atoms 0
    Heterogen Atoms 32
    Solvent Atoms 297
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building CNS
    data reduction SCALEPACK
    data collection DENZO