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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1G2D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 298.0
    Details PEG 400, NaCl, Bis-Tris Propane, CoCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 105.1 α = 90
    b = 105.1 β = 90
    c = 104.6 γ = 120
     
    Space Group
    Space Group Name:    P 64
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 130
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV
    Details Yale mirrors
    Collection Date 2000-04-27
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU200
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.2
    Resolution(Low) 20
    Number Reflections(All) 32875
    Number Reflections(Observed) 358651
    Percent Possible(Observed) 99.5
    B(Isotropic) From Wilson Plot 31.0
    Redundancy 10.91
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.28
    Percent Possible(All) 95.5
    Mean I Over Sigma(Observed) 9.35
    R-Sym I(Observed) 44.8
    Redundancy 9.0
    Number Unique Reflections(All) 3182
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 20.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 32465
    Number of Reflections(Observed) 31492
    Number of Reflections(R-Free) 3081
    Percent Reflections(Observed) 94.6
    R-Work 0.225
    R-Free 0.262
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 38.6
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.34
    Number of Reflections(R-Free) 442
    Number of Reflections(R-Work) 4110
    R-Factor(R-Work) 0.362
    R-Factor(R-Free) 0.397
    R-Free Error 0.019
    Percent Reflections(Observed) 82.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    x_scangle_it 5.95
    x_scbond_it 3.92
    x_mcangle_it 3.85
    x_mcbond_it 2.46
    x_improper_angle_d 1.17
    x_dihedral_angle_d 20.1
    x_angle_deg 1.1
    x_bond_d 0.006
     
    Coordinate Error
    Luzzati ESD(Observed) 0.33
    Luzzati Sigma A(Observed) 0.39
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.37
    Luzzati Sigma A(R-Free Set) 0.42
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1467
    Nucleic Acid Atoms 1300
    Heterogen Atoms 6
    Solvent Atoms 224
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) R-AXIS
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MLPHARE
    Structure Refinement X-PLOR 3.851
     
    Software
    refinement X-PLOR(ONLINE) version: 3.851
    model building MLPHARE