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X-RAY DIFFRACTION
Materials and Methods page
3VXV
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.4
    Temperature 293.0
    Details pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.4
    Temperature 293.0
    Details pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 89.07 α = 90
    b = 94.99 β = 90
    c = 54.74 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
    Diffrn ID 2
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2009-10-14
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2010-01-27
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Site PHOTON FACTORY
    Beamline AR-NE3A
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-5A
    Wavelength List 1.000
    Site PHOTON FACTORY
    Beamline BL-5A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(All) 16110
    Number Reflections(Observed) 16062
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.031
    B(Isotropic) From Wilson Plot 36.36
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.365
    Mean I Over Sigma(Observed) 4.3
    Redundancy 7.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.0
    Resolution(Low) 23.747
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 16002
    Number of Reflections(R-Free) 801
    Percent Reflections(Observed) 99.44
    R-Factor(Observed) 0.1892
    R-Work 0.1875
    R-Free 0.2235
     
    Temperature Factor Modeling
    Mean Isotropic B Value 40.4743
    Anisotropic B[1][1] -12.9528
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 10.7675
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.1853
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9989
    Shell Resolution(Low) 2.124
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2475
    R-Factor(R-Work) 0.2332
    R-Factor(R-Free) 0.2707
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.124
    Shell Resolution(Low) 2.2879
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2493
    R-Factor(R-Work) 0.2553
    R-Factor(R-Free) 0.3677
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2879
    Shell Resolution(Low) 2.5179
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2500
    R-Factor(R-Work) 0.2338
    R-Factor(R-Free) 0.2924
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5179
    Shell Resolution(Low) 2.8817
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.2178
    R-Factor(R-Free) 0.2713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8817
    Shell Resolution(Low) 3.6286
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.2235
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6286
    Shell Resolution(Low) 23.7489
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.1633
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.01
    f_chiral_restr 0.119
    f_dihedral_angle_d 23.326
    f_angle_d 2.071
    f_bond_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 525
    Nucleic Acid Atoms 570
    Heterogen Atoms 36
    Solvent Atoms 154
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building SOLVE
    data collection HKL-2000