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X-RAY DIFFRACTION
Materials and Methods page
3VD1
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.1
    Temperature 298.0
    Details 0.1M MES, 0.1M Na acetate, pH 6.1, temperature 298.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 82.54 α = 90
    b = 104.2 β = 96.55
    c = 123.22 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 200
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details MIRROR
    Collection Date 2010-01-01
     
    Diffraction Radiation
    Monochromator RH COATED FLAT MIRROR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL7-1
    Wavelength 0.98
    Site SSRL
    Beamline BL7-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.95
    Resolution(Low) 100
    Number Reflections(Observed) 41946
    Percent Possible(Observed) 96.1
    B(Isotropic) From Wilson Plot 35.6
    Redundancy 6.2
     
    High Resolution Shell Details
    Resolution(High) 2.95
    Resolution(Low) 3.06
    Percent Possible(All) 96.5
    Mean I Over Sigma(Observed) 3.2
    R-Sym I(Observed) 0.4
    Redundancy 4.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.95
    Resolution(Low) 19.99
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 41946
    Number of Reflections(Observed) 41779
    Number of Reflections(R-Free) 843
    Percent Reflections(Observed) 95.6
    R-Factor(Observed) 0.239
    R-Work 0.239
    R-Free 0.285
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 74.5
    Anisotropic B[1][1] 5.31
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -8.29
    Anisotropic B[2][2] 12.41
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -17.72
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.95
    Shell Resolution(Low) 3.13
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 6596
    R-Factor(R-Work) 0.362
    R-Factor(R-Free) 0.431
    R-Free Error 0.039
    Percent Reflections(Observed) 93.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 1.38
    c_bond_d 0.009
    c_angle_deg 1.7
    c_dihedral_angle_d 25.6
     
    Coordinate Error
    Luzzati ESD(Observed) 0.43
    Luzzati Sigma A(Observed) 0.58
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.52
    Luzzati Sigma A(R-Free Set) 0.71
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12576
    Nucleic Acid Atoms 1944
    Heterogen Atoms 8
    Solvent Atoms 188
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement CNS 1.3
     
    Software
    refinement CNS version: 1.3
    model building phaser
    data collection HKL-2000