POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1RA7
  •   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 = 128.05 α = 90
    b = 128.05 β = 90
    c = 112.76 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV
    Collection Date 2003-09-10
     
    Diffraction Radiation
    Monochromator Osmic
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.35
    Resolution(Low) 30
    Number Reflections(All) 43388
    Number Reflections(Observed) 43388
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.082
    Redundancy 5.0
     
    High Resolution Shell Details
    Resolution(High) 2.35
    Resolution(Low) 2.43
    Percent Possible(All) 96.2
    R Merge I(Observed) 0.557
    Mean I Over Sigma(Observed) 2.13
    Redundancy 3.88
    Number Unique Reflections(All) 4210
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.35
    Resolution(Low) 30.0
    Number of Reflections(all) 43126
    Number of Reflections(Observed) 43126
    Number of Reflections(R-Free) 4354
    Percent Reflections(Observed) 96.3
    R-Work 0.222
    R-Free 0.259
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic
    Mean Isotropic B Value 45.9
    Anisotropic B[1][1] 5.79
    Anisotropic B[1][2] 4.45
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.79
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -11.58
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.35
    Shell Resolution(Low) 2.43
    Number of Reflections(Observed) 4195
    Number of Reflections(R-Free) 428
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.35
    Percent Reflections(Observed) 96.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_angle_deg 1.3
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.32
    Luzzati Sigma A(Observed) 0.38
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.38
    Luzzati Sigma A(R-Free Set) 0.42
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3707
    Nucleic Acid Atoms 0
    Heterogen Atoms 60
    Solvent Atoms 263
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) R-AXIS
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building CNS
    data reduction SCALEPACK
    data collection R-AXIS