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X-RAY DIFFRACTION
Materials and Methods page
3BHD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 3.8
    Temperature 300.0
    Details 50mM Citric acid, 0.2M Ammonium sulfate, 3mM Sodium tungstenate, 10mg/ml Protein, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.77 α = 90
    b = 46.81 β = 113.97
    c = 71.87 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2007-09-13
     
    Diffraction Radiation
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.97915
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.5
    Resolution(Low) 20
    Number Reflections(Observed) 115663
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.061
    B(Isotropic) From Wilson Plot 20.28
    Redundancy 3.51
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.6
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.421
    Mean I Over Sigma(Observed) 3.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.5
    Resolution(Low) 19.96
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 59035
    Number of Reflections(Observed) 59035
    Number of Reflections(R-Free) 2983
    Percent Reflections(Observed) 99.5
    R-Factor(Observed) 0.17774
    R-Work 0.17648
    R-Free 0.20117
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.948
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.01
    Anisotropic B[2][2] -0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.539
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 4048
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.275
    Percent Reflections(Observed) 98.38
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.217
    r_scbond_it 2.691
    r_mcangle_it 1.639
    r_mcbond_it 0.94
    r_nbd_refined 0.244
    r_gen_planes_refined 0.008
    r_chiral_restr 0.104
    r_dihedral_angle_4_deg 20.614
    r_dihedral_angle_3_deg 13.269
    r_dihedral_angle_2_deg 31.093
    r_dihedral_angle_1_deg 6.567
    r_angle_refined_deg 1.605
    r_bond_refined_d 0.014
    r_nbtor_refined 0.309
    r_xyhbond_nbd_refined 0.142
    r_metal_ion_refined 0.884
    r_symmetry_vdw_refined 0.209
    r_symmetry_hbond_refined 0.175
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3261
    Nucleic Acid Atoms 0
    Heterogen Atoms 77
    Solvent Atoms 225
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ProDC
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    Structure Solution SHELXD
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.004
    refinement REFMAC5
    phasing SHELX
    data processing Xscale