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X-RAY DIFFRACTION
Materials and Methods page
2AGG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 298.0
    Details ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 61.39 α = 90
    b = 63.59 β = 90
    c = 68.85 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 ADSC QUANTUM 4
    Collection Date 2005-05-26
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.00000
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.28
    Resolution(Low) 46.63
    Number Reflections(All) 59870
    Number Reflections(Observed) 59870
    Percent Possible(Observed) 96.27
    R Merge I(Observed) 0.075
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 1.28
    Resolution(Low) 1.35
    R Merge I(Observed) 0.475
    Mean I Over Sigma(Observed) 1.7
    R-Sym I(Observed) 0.475
    Redundancy 2.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.28
    Resolution(Low) 46.63
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 59869
    Number of Reflections(Observed) 59869
    Number of Reflections(R-Free) 3027
    Percent Reflections(Observed) 96.27
    R-Factor(All) 0.125
    R-Factor(Observed) 0.125
    R-Work 0.124
    R-Free 0.158
    R-Free Selection Details inherited from PDB entry 2AGE
     
    Temperature Factor Modeling
    Isotropic Thermal Model anisotropic
    Mean Isotropic B Value 8.963
    Anisotropic B[1][1] 0.83
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.74
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.28
    Shell Resolution(Low) 1.313
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2211
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.369
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 7.134
    r_sphericity_free 16.795
    r_rigid_bond_restr 5.198
    r_nbd_refined 0.386
    r_gen_planes_other 0.002
    r_gen_planes_refined 0.009
    r_chiral_restr 0.125
    r_dihedral_angle_4_deg 20.84
    r_dihedral_angle_3_deg 10.63
    r_dihedral_angle_2_deg 39.459
    r_dihedral_angle_1_deg 6.679
    r_angle_other_deg 0.933
    r_angle_refined_deg 1.742
    r_bond_other_d 0.006
    r_bond_refined_d 0.018
    r_nbd_other 0.264
    r_nbtor_other 0.094
    r_xyhbond_nbd_refined 0.22
    r_metal_ion_refined 0.143
    r_symmetry_vdw_refined 0.032
    r_symmetry_vdw_other 0.325
    r_symmetry_hbond_refined 0.283
    r_mcbond_it 3.455
    r_mcbond_other 2.264
    r_mcangle_it 4.354
    r_scbond_it 5.464
    r_scangle_it 6.747
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1648
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 357
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution EPMR
    Structure Refinement REFMAC 5.2
     
    Software
    refinement REFMAC version: 5.2
    model building EPMR
    data reduction SCALA
    data collection MOSFLM