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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1JYJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9.1
    Temperature 289.0
    Details Sodium Chloride, Tris/HCl buffer, beta-octyl-glucoside, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 102.76 α = 90
    b = 102.76 β = 90
    c = 72.72 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MARRESEARCH
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type EMBL/DESY, HAMBURG BEAMLINE X31
    Wavelength List 1.09
    Site EMBL/DESY, HAMBURG
    Beamline X31
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 40
    Number Reflections(Observed) 18890
    Percent Possible(Observed) 98.0
    B(Isotropic) From Wilson Plot 18.8
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 92.7
    Mean I Over Sigma(Observed) 3.19
    R-Sym I(Observed) 0.37
    Number Unique Reflections(All) 1798
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 19.66
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 18890
    Number of Reflections(Observed) 18890
    Number of Reflections(R-Free) 900
    Percent Reflections(Observed) 97.8
    R-Factor(Observed) 0.209
    R-Work 0.205
    R-Free 0.229
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 22.4
    Anisotropic B[1][1] 0.94
    Anisotropic B[1][2] 1.44
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.94
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.89
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.13
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2851
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.269
    R-Free Error 0.023
    Percent Reflections(Observed) 93.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.69
    c_dihedral_angle_d 24.7
    c_angle_deg 1.4
    c_bond_d 0.006
     
    Coordinate Error
    Luzzati ESD(Observed) 0.23
    Luzzati Sigma A(Observed) 0.19
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.26
    Luzzati Sigma A(R-Free Set) 0.22
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1397
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 218
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0
    model building AMoRE
    data reduction SCALEPACK
    data collection DENZO