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X-RAY DIFFRACTION
Materials and Methods page
3VAJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details 1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 163.87 α = 90
    b = 36.97 β = 125.66
    c = 99.99 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2009-01-30
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL7-1
    Wavelength List 1.00
    Site SSRL
    Beamline BL7-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -1.0
    Resolution(High) 1.9
    Resolution(Low) 50
    Number Reflections(Observed) 38838
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.075
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 92.6
    R Merge I(Observed) 0.356
    Redundancy 3.2
    Number Unique Reflections(All) 3626
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.9
    Resolution(Low) 40.62
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 40660
    Number of Reflections(Observed) 37002
    Number of Reflections(R-Free) 3658
    Percent Reflections(Observed) 94.86
    R-Factor(Observed) 0.1954
    R-Work 0.1911
    R-Free 0.2356
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.3794
    Anisotropic B[1][1] -1.07
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.05
    Anisotropic B[2][2] -0.5
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.5
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.949
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 2089
    R-Factor(R-Work) 0.237
    R-Factor(R-Free) 0.288
    Percent Reflections(Observed) 81.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.358
    r_nbd_refined 0.191
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.004
    r_chiral_restr 0.11
    r_dihedral_angle_4_deg 17.072
    r_dihedral_angle_3_deg 13.847
    r_dihedral_angle_2_deg 32.863
    r_dihedral_angle_1_deg 5.98
    r_angle_other_deg 1.071
    r_angle_refined_deg 1.31
    r_bond_other_d 0.001
    r_bond_refined_d 0.009
    r_nbd_other 0.193
    r_nbtor_refined 0.182
    r_nbtor_other 0.085
    r_xyhbond_nbd_refined 0.139
    r_xyhbond_nbd_other 0.013
    r_symmetry_vdw_refined 0.106
    r_symmetry_vdw_other 0.209
    r_symmetry_hbond_refined 0.11
    r_mcbond_it 0.724
    r_mcbond_other 0.121
    r_mcangle_it 0.813
    r_scbond_it 1.673
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2686
    Nucleic Acid Atoms 262
    Heterogen Atoms 99
    Solvent Atoms 227
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.2.0019
    data reduction SCALEPACK
    data collection DENZO