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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4KDP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 298.0
    Details 40 % ethylene glycol, 0.1 M Tris , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 91.9 α = 90
    b = 91.9 β = 90
    c = 261.53 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type Bruker DIP-6040
    Details mirrors
    Collection Date 2012-01-28
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 1
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.6
    Resolution(Low) 30
    Number Reflections(All) 15185
    Number Reflections(Observed) 15179
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.052
    Redundancy 3.0
     
    High Resolution Shell Details
    Resolution(High) 3.6
    Resolution(Low) 3.73
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.526
    Mean I Over Sigma(Observed) 2.1
    Redundancy 3.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.6
    Resolution(Low) 16.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 14084
    Number of Reflections(R-Free) 706
    R-Factor(Observed) 0.274
    R-Work 0.274
    R-Free 0.285
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic
    Mean Isotropic B Value 112.238
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6
    Shell Resolution(Low) 3.73
    Number of Reflections(R-Free) 57
    R-Factor(R-Work) 0.373
    R-Factor(R-Free) 0.438
    Percent Reflections(Observed) 84.12
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_bond_d 0.02
    c_angle_deg 1.985
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8509
    Nucleic Acid Atoms 420
    Heterogen Atoms 64
    Solvent Atoms 91
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building CNS
    data collection HKL-2000