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X-RAY DIFFRACTION
Materials and Methods page
2D01
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 6.5
    Temperature 293.0
    Details 40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.42 α = 90
    b = 40.42 β = 90
    c = 118.13 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Details bending magnet
    Collection Date 2004-03-26
     
    Diffraction Radiation
    Monochromator fixed-exit double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL40B2
    Wavelength List 1.000
    Site SPRING-8
    Beamline BL40B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.34
    Resolution(Low) 20.09
    Number Reflections(Observed) 23170
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.053
    Redundancy 11.1
     
    High Resolution Shell Details
    Resolution(High) 1.34
    Resolution(Low) 1.39
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.303
    Mean I Over Sigma(Observed) 9.09
    Redundancy 11.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.34
    Resolution(Low) 20.0
    Number of Reflections(Observed) 23170
    Number of Reflections(R-Free) 1244
    Percent Reflections(Observed) 99.91
    R-Factor(Observed) 0.15397
    R-Work 0.15209
    R-Free 0.18915
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.989
    Anisotropic B[1][1] 0.53
    Anisotropic B[1][2] 0.27
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.53
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.8
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.34
    Number of Reflections(R-Work) 1706
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 4.264
    r_sphericity_free 5.36
    r_rigid_bond_restr 2.094
    r_scangle_it 3.615
    r_scbond_it 2.857
    r_mcangle_it 2.289
    r_mcbond_it 1.596
    r_symmetry_hbond_refined 0.164
    r_bond_refined_d 0.012
    r_angle_refined_deg 1.487
    r_dihedral_angle_1_deg 6.074
    r_dihedral_angle_2_deg 36.474
    r_dihedral_angle_3_deg 15.769
    r_dihedral_angle_4_deg 12.98
    r_chiral_restr 0.102
    r_gen_planes_refined 0.008
    r_nbd_refined 0.257
    r_nbtor_refined 0.316
    r_xyhbond_nbd_refined 0.185
    r_symmetry_vdw_refined 0.21
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 968
    Nucleic Acid Atoms 0
    Heterogen Atoms 11
    Solvent Atoms 210
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement REFMAC 5.2.0005
     
    Software
    refinement REFMAC version: 5.2.0005