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X-RAY DIFFRACTION
Materials and Methods page
4DPB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 277.0
    Details 2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 29.19 α = 90
    b = 46.4 β = 90
    c = 56.81 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Details MIRRORS
    Collection Date 2002-03-04
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type MPG/DESY, HAMBURG BEAMLINE BW6
    Wavelength List 1.05
    Site MPG/DESY, HAMBURG
    Beamline BW6
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1
    Resolution(Low) 15.94
    Number Reflections(All) 42532
    Number Reflections(Observed) 41299
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.048
    B(Isotropic) From Wilson Plot 5.52
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 1.0
    Resolution(Low) 1.02
    Percent Possible(All) 88.2
    R Merge I(Observed) 0.271
    Mean I Over Sigma(Observed) 3.0
    Redundancy 2.5
    Number Unique Reflections(All) 2087
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.0
    Resolution(Low) 15.94
    Number of Reflections(all) 40302
    Number of Reflections(Observed) 39177
    Number of Reflections(R-Free) 2080
    Percent Reflections(Observed) 97.21
    R-Factor(Observed) 0.11771
    R-Work 0.11673
    R-Free 0.13629
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ANISOTROPIC
    Mean Isotropic B Value 10.2
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.02
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0
    Shell Resolution(Low) 1.026
    Number of Reflections(Observed) 2643
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.286
    Percent Reflections(Observed) 91.34
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 5.999
    r_sphericity_free 15.633
    r_rigid_bond_restr 2.75
    r_scangle_it 7.116
    r_scbond_it 5.188
    r_mcangle_it 3.228
    r_mcbond_it 2.468
    r_nbd_refined 0.442
    r_gen_planes_refined 0.012
    r_chiral_restr 0.154
    r_dihedral_angle_3_deg 12.087
    r_dihedral_angle_2_deg 29.515
    r_dihedral_angle_1_deg 7.187
    r_angle_refined_deg 2.415
    r_bond_refined_d 0.025
    r_nbtor_refined 0.324
    r_xyhbond_nbd_refined 0.505
    r_metal_ion_refined 0.041
    r_symmetry_vdw_refined 0.221
    r_symmetry_hbond_refined 0.328
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 738
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 228
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Marccd
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution Molrep
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building Molrep
    data collection Marccd