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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3DYT
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.15
    Details 1.8M Ammonium sulfate, 0.1M Tris-HCl pH 8.5, 5% PEG 400, 0.05M MgSO4, 15% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 67 α = 90
    b = 144.01 β = 90
    c = 103.33 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Details Mirrors
    Collection Date 2006-11-11
     
    Diffraction Radiation
    Monochromator Horizontal focusing 5.05 degrees asymmetric cut Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CHESS BEAMLINE A1
    Wavelength List 0.9792
    Site CHESS
    Beamline A1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.08
    Resolution(Low) 50
    Number Reflections(All) 30311
    Number Reflections(Observed) 30311
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.112
    B(Isotropic) From Wilson Plot 27.22
    Redundancy 14.4
     
    High Resolution Shell Details
    Resolution(High) 2.08
    Resolution(Low) 2.15
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.35
    Mean I Over Sigma(Observed) 9.6
    R-Sym I(Observed) 0.316
    Redundancy 14.0
    Number Unique Reflections(All) 2984
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.08
    Resolution(Low) 50.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 28804
    Number of Reflections(Observed) 28804
    Number of Reflections(R-Free) 2071
    Percent Reflections(Observed) 95.05
    R-Factor(All) 0.219
    R-Factor(Observed) 0.219
    R-Work 0.217
    R-Free 0.2453
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 2.97
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.08
    Shell Resolution(Low) 2.13
    Number of Reflections(Observed) 1724
    Number of Reflections(R-Free) 127
    R-Factor(R-Work) 0.2099
    R-Factor(R-Free) 0.2447
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.012
    f_angle_deg 1.099
    f_bond_d 0.009
     
    Coordinate Error
    Luzzati ESD(Observed) 0.48
    Luzzati Sigma A(Observed) 0.47
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.51
    Luzzati Sigma A(R-Free Set) 0.48
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2884
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 143
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE
    Structure Refinement PHENIX
     
    Software
    refinement PHENIX version: (phenix.refine)