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X-RAY DIFFRACTION
Materials and Methods page
3VAI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details 1.6M M 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 = 166.03 α = 90
    b = 37.44 β = 125.5
    c = 100.56 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 210
    Details Rh coated Si vertical focus mirror
    Collection Date 2007-01-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CHESS BEAMLINE A1
    Wavelength List 0.987
    Site CHESS
    Beamline A1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -1.0
    Resolution(High) 2.2
    Resolution(Low) 50
    Number Reflections(Observed) 25485
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.103
    Redundancy 4.4
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.28
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.454
    Redundancy 2.9
    Number Unique Reflections(All) 2480
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.2
    Resolution(Low) 41.59
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 27004
    Number of Reflections(Observed) 24563
    Number of Reflections(R-Free) 2441
    Percent Reflections(Observed) 94.09
    R-Factor(Observed) 0.2023
    R-Work 0.1972
    R-Free 0.2496
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.4621
    Anisotropic B[1][1] -1.2
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.32
    Anisotropic B[2][2] -0.13
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.7
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.257
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 1075
    R-Factor(R-Work) 0.289
    R-Factor(R-Free) 0.322
    Percent Reflections(Observed) 63.79
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.073
    r_scbond_it 1.315
    r_mcangle_it 0.705
    r_mcbond_other 0.084
    r_mcbond_it 0.641
    r_symmetry_hbond_refined 0.199
    r_symmetry_vdw_other 0.282
    r_symmetry_vdw_refined 0.199
    r_xyhbond_nbd_refined 0.174
    r_nbtor_other 0.082
    r_nbtor_refined 0.178
    r_nbd_other 0.192
    r_bond_refined_d 0.011
    r_bond_other_d 0.009
    r_angle_refined_deg 1.416
    r_angle_other_deg 0.99
    r_dihedral_angle_1_deg 5.799
    r_dihedral_angle_2_deg 33.556
    r_dihedral_angle_3_deg 15.733
    r_dihedral_angle_4_deg 12.88
    r_chiral_restr 0.076
    r_gen_planes_refined 0.004
    r_gen_planes_other 0.001
    r_nbd_refined 0.179
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2686
    Nucleic Acid Atoms 186
    Heterogen Atoms 98
    Solvent Atoms 167
     
     
  •   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