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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1IVO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.4
    Temperature 293.0
    Details PEG4000, PEG6000, sodium acetate, sodium chloride, TRIS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 220.16 α = 90
    b = 220.16 β = 90
    c = 113.12 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details mirrors
    Collection Date 2001-01-01
    Detector CCD
    Type MARRESEARCH
    Details mirrors
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol MAD
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 0.9795, 0.9798, 0.9733, 0.9839
    Site SPRING-8
    Beamline BL41XU
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.00
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.5
    Resolution(Low) 50
    Number Reflections(All) 293584
    Number Reflections(Observed) 293584
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.075
    B(Isotropic) From Wilson Plot 71.3
     
    High Resolution Shell Details
    Resolution(High) 3.5
    Resolution(Low) 3.71
    Percent Possible(All) 98.6
    R Merge I(Observed) 0.27
    Mean I Over Sigma(Observed) 5.1
    R-Sym I(Observed) 0.27
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 3.3
    Resolution(Low) 10.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 44854
    Number of Reflections(R-Free) 2239
    Percent Reflections(Observed) 98.0
    R-Factor(Observed) 0.258
    R-Work 0.255
    R-Free 0.326
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 82.5
    Anisotropic B[1][1] -9.51
    Anisotropic B[1][2] 15.74
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -9.51
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 19.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3
    Shell Resolution(Low) 3.5
    Number of Reflections(Observed) 6103
    Number of Reflections(R-Free) 360
    Number of Reflections(R-Work) 6616
    R-Factor(R-Work) 0.31
    R-Factor(R-Free) 0.37
    R-Free Error 0.02
    Percent Reflections(Observed) 91.7
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.78
    c_bond_d 0.006
    c_angle_deg 1.4
    c_dihedral_angle_d 25.1
     
    Coordinate Error
    Luzzati ESD(Observed) 0.39
    Luzzati Sigma A(Observed) 0.5
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.54
    Luzzati Sigma A(R-Free Set) 0.75
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8673
    Nucleic Acid Atoms 0
    Heterogen Atoms 140
    Solvent Atoms 79
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MLPHARE
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0
    model building MLPHARE
    data reduction SCALEPACK
    data collection DENZO