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X-RAY DIFFRACTION
Materials and Methods page
3GDE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9
    Temperature 294.0
    Details 100mM Tris-HCl, pH9.0, 0.4M sodium dihydrogen phosphate, 1.2M dipotassium hydrogen phosphate, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 94.36 α = 90
    b = 94.36 β = 90
    c = 197.42 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2006-01-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PAL/PLS BEAMLINE 4A
    Wavelength List 1.0000
    Site PAL/PLS
    Beamline 4A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.3
    Resolution(Low) 20
    Number Reflections(Observed) 40500
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.089
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 5.1
    R-Sym I(Observed) 0.44
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 20.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 36294
    Number of Reflections(R-Free) 4007
    Percent Reflections(Observed) 99.84
    R-Factor(Observed) 0.221
    R-Work 0.215
    R-Free 0.277
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 37.035
    Anisotropic B[1][1] 1.62
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.62
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.25
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.359
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.351
    Percent Reflections(Observed) 99.79
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.765
    r_scbond_it 1.622
    r_mcangle_it 1.189
    r_mcbond_it 0.683
    r_symmetry_hbond_refined 0.187
    r_bond_refined_d 0.01
    r_angle_refined_deg 1.314
    r_dihedral_angle_1_deg 7.246
    r_dihedral_angle_2_deg 36.166
    r_dihedral_angle_3_deg 18.92
    r_dihedral_angle_4_deg 19.356
    r_chiral_restr 0.098
    r_gen_planes_refined 0.004
    r_nbd_refined 0.198
    r_nbtor_refined 0.299
    r_xyhbond_nbd_refined 0.153
    r_symmetry_vdw_refined 0.235
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4423
    Nucleic Acid Atoms 0
    Heterogen Atoms 20
    Solvent Atoms 458
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution PHASE
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.006
    refinement REFMAC5 version: 5.2.0019
    data processing HKL