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X-RAY DIFFRACTION
Materials and Methods page
3VAK
  •   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 = 166.41 α = 90
    b = 37.73 β = 125.43
    c = 101.63 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
    Monochromator Horizontal focusing 5.05? asymmetric cut Si(111)
    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) 2.16
    Resolution(Low) 50
    Number Reflections(Observed) 27427
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.14
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 2.16
    Resolution(Low) 2.24
    Percent Possible(All) 92.1
    R Merge I(Observed) 0.365
    Redundancy 4.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.17
    Resolution(Low) 41.42
    Number of Reflections(all) 29877
    Number of Reflections(Observed) 24457
    Number of Reflections(R-Free) 2710
    Percent Reflections(Observed) 97.69
    R-Factor(Observed) 0.1924
    R-Work 0.18837
    R-Free 0.22944
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.7193
    Anisotropic B[1][1] -0.7
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.01
    Anisotropic B[2][2] -1.33
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.21
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.17
    Shell Resolution(Low) 2.226
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 1506
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.269
    Percent Reflections(Observed) 82.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.917
    r_scbond_it 1.152
    r_mcangle_it 0.653
    r_mcbond_it 0.571
    r_nbd_refined 0.176
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.003
    r_dihedral_angle_4_deg 16.451
    r_dihedral_angle_3_deg 13.951
    r_dihedral_angle_2_deg 34.638
    r_dihedral_angle_1_deg 5.249
    r_angle_other_deg 1.187
    r_angle_refined_deg 1.257
    r_bond_other_d 0.001
    r_bond_refined_d 0.008
    r_nbd_other 0.179
    r_nbtor_refined 0.174
    r_nbtor_other 0.08
    r_xyhbond_nbd_refined 0.133
    r_symmetry_vdw_refined 0.123
    r_symmetry_vdw_other 0.152
    r_symmetry_hbond_refined 0.179
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2686
    Nucleic Acid Atoms 262
    Heterogen Atoms 116
    Solvent Atoms 272
     
     
  •   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