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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2RD8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9
    Temperature 277.0
    Details 10-20% PEG 4000, 3mM potassium phosphate, 20mM 2-mercaptoethanol, 0.1M TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 120.74 α = 90
    b = 120.74 β = 90
    c = 129.77 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 MARMOSAIC 225 mm CCD
    Collection Date 2007-04-15
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 0.97243
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.4
    Resolution(Low) 33.8
    Number Reflections(Observed) 30034
    Percent Possible(Observed) 69.6
    R Merge I(Observed) 0.138
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.49
    Percent Possible(All) 15.3
    R Merge I(Observed) 0.465
    Mean I Over Sigma(Observed) 7.8
    Redundancy 2.7
    Number Unique Reflections(All) 651
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 2.5
    Resolution(Low) 33.8
    Cut-off Sigma(I) 1.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 30034
    Number of Reflections(Observed) 26954
    Number of Reflections(R-Free) 2711
    Percent Reflections(Observed) 70.4
    R-Work 0.228
    R-Free 0.271
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model overall
    Mean Isotropic B Value 46.036
    Anisotropic B[1][1] -10.356
    Anisotropic B[1][2] -13.846
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -10.356
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 20.712
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 4.869
    c_mcangle_it 2.977
    c_scbond_it 3.248
    c_mcbond_it 1.774
    c_angle_deg 1.33
    c_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4566
    Nucleic Acid Atoms 0
    Heterogen Atoms 14
    Solvent Atoms 88
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution AMoRE
    Structure Refinement CNS
     
    Software
    data extraction pdb_extract version: 3.000
    refinement CNS
    data processing HKL