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X-RAY DIFFRACTION
Materials and Methods page
2DC3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 293.0
    Details 1.4M sodium acetate, 100mM sodium cacodylate, 5mM KCN, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.53 α = 90
    b = 52.76 β = 87.75
    c = 83.44 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU JUPITER 210
    Collection Date 2004-07-02
     
    Diffraction Radiation
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL45PX
    Wavelength List 1.000
    Site SPRING-8
    Beamline BL45PX
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.68
    Resolution(Low) 50
    Number Reflections(All) 39043
    Number Reflections(Observed) 39043
    Percent Possible(Observed) 99.9
    B(Isotropic) From Wilson Plot 14.64
    Redundancy 4.9
     
    High Resolution Shell Details
    Resolution(High) 1.68
    Resolution(Low) 1.74
    Percent Possible(All) 99.5
    Mean I Over Sigma(Observed) 4.03
    R-Sym I(Observed) 0.286
    Redundancy 4.1
    Number Unique Reflections(All) 3849
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.68
    Resolution(Low) 20.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 37014
    Number of Reflections(R-Free) 1927
    Percent Reflections(Observed) 99.8
    R-Factor(Observed) 0.142
    R-Work 0.14
    R-Free 0.181
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.13
    Anisotropic B[1][1] 0.67
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.3
    Anisotropic B[2][2] -0.23
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.46
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.68
    Shell Resolution(Low) 1.724
    Number of Reflections(Observed) 3849
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.128
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 97.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 2.638
    r_sphericity_free 8.671
    r_rigid_bond_restr 2.259
    r_nbd_refined 0.229
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.008
    r_chiral_restr 0.108
    r_dihedral_angle_4_deg 21.24
    r_dihedral_angle_3_deg 13.768
    r_dihedral_angle_2_deg 32.06
    r_dihedral_angle_1_deg 4.677
    r_angle_other_deg 0.89
    r_angle_refined_deg 1.558
    r_bond_other_d 0.001
    r_bond_refined_d 0.018
    r_nbd_other 0.179
    r_nbtor_refined 0.189
    r_nbtor_other 0.085
    r_xyhbond_nbd_refined 0.182
    r_symmetry_vdw_refined 0.253
    r_symmetry_vdw_other 0.236
    r_symmetry_hbond_refined 0.315
    r_mcbond_it 1.973
    r_mcbond_other 0.605
    r_mcangle_it 2.215
    r_scbond_it 3.516
    r_scangle_it 4.751
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2710
    Nucleic Acid Atoms 0
    Heterogen Atoms 90
    Solvent Atoms 265
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0005
     
    Software
    refinement REFMAC version: 5.2.0005