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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3UDO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 297.0
    Details 25%PEG3350, 0.2M Na Chloride, 0.1MHEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 74.79 α = 90
    b = 74.79 β = 90
    c = 163.79 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-07-06
     
    Diffraction Radiation
    Monochromator Si 111 channel
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.9772
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.3
    Resolution(Low) 50
    Number Reflections(All) 21382
    Number Reflections(Observed) 21382
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.063
    B(Isotropic) From Wilson Plot 57.9
    Redundancy 7.8
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.34
    Percent Possible(All) 99.1
    R Merge I(Observed) 0.595
    Mean I Over Sigma(Observed) 3.7
    R-Sym I(Observed) 0.595
    Redundancy 7.8
    Number Unique Reflections(All) 1051
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.3
    Resolution(Low) 50.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 20207
    Number of Reflections(Observed) 20207
    Number of Reflections(R-Free) 1091
    Percent Reflections(Observed) 99.64
    R-Factor(All) 0.17836
    R-Factor(Observed) 0.17836
    R-Work 0.17633
    R-Free 0.21718
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 54.211
    Anisotropic B[1][1] 2.94
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.94
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.88
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.303
    Shell Resolution(Low) 2.362
    Number of Reflections(R-Free) 68
    Number of Reflections(R-Work) 1290
    R-Factor(R-Work) 0.235
    R-Factor(R-Free) 0.345
    Percent Reflections(Observed) 99.27
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.008
    r_chiral_restr 0.099
    r_dihedral_angle_4_deg 16.918
    r_dihedral_angle_3_deg 15.71
    r_dihedral_angle_2_deg 36.863
    r_dihedral_angle_1_deg 6.387
    r_angle_other_deg 0.987
    r_angle_refined_deg 1.786
    r_bond_other_d 0.006
    r_bond_refined_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2723
    Nucleic Acid Atoms 0
    Heterogen Atoms 28
    Solvent Atoms 92
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-3000
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution HKL-3000:SHELXD, SHELXE, DM, MLPHARE, RESOLVE, CCP4, ARP/WARP
    Structure Refinement REFMAC 5.6.0117, COOT
     
    Software
    refinement COOT
    refinement REFMAC version: 5.6.0117
    model building ARP/WARP
    model building CCP4
    model building RESOLVE
    model building MLPHARE
    model building DM
    model building SHELXE
    model building HKL-3000:SHELXD
    data collection HKL-3000