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X-RAY DIFFRACTION
Materials and Methods page
3QDK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 298.0
    Details 30% PEG4K, 0.2M Sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 56.68 α = 90
    b = 88.84 β = 92.75
    c = 230.52 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details mirrors
    Collection Date 2009-08-28
    Detector CCD
    Type ADSC QUANTUM 315
    Details mirrors
    Collection Date 2009-08-27
     
    Diffraction Radiation
    Monochromator SI-III
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator SI-III
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 0.9791
    Site NSLS
    Beamline X25
    Source SYNCHROTRON
    Type NSLS BEAMLINE X12C
    Wavelength List 0.9791
    Site NSLS
    Beamline X12C
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.31
    Resolution(Low) 50
    Number Reflections(All) 99100
    Number Reflections(Observed) 99100
    Percent Possible(Observed) 98.1
    R Merge I(Observed) 0.065
    B(Isotropic) From Wilson Plot 29.7
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 2.31
    Resolution(Low) 2.35
    Percent Possible(All) 87.8
    R Merge I(Observed) 0.165
    Mean I Over Sigma(Observed) 4.0
    Redundancy 2.7
    Number Unique Reflections(All) 4458
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.31
    Resolution(Low) 48.31
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 99100
    Number of Reflections(Observed) 97059
    Number of Reflections(R-Free) 2940
    Percent Reflections(Observed) 96.6
    R-Factor(Observed) 0.224
    R-Work 0.224
    R-Free 0.274
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 36.0
    Anisotropic B[1][1] 2.09
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.62
    Anisotropic B[2][2] 4.09
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.17
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.31
    Shell Resolution(Low) 2.45
    Number of Reflections(R-Free) 481
    Number of Reflections(R-Work) 14861
    R-Factor(R-Work) 0.28
    R-Factor(R-Free) 0.34
    R-Free Error 0.015
    Percent Reflections(Observed) 91.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.52
    c_scbond_it 1.79
    c_mcangle_it 1.67
    c_mcbond_it 1.11
    c_improper_angle_d 0.88
    c_dihedral_angle_d 23.5
    c_angle_deg 1.5
    c_bond_d 0.009
     
    Coordinate Error
    Luzzati ESD(Observed) 0.3
    Luzzati Sigma A(Observed) 0.27
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.39
    Luzzati Sigma A(R-Free Set) 0.38
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16759
    Nucleic Acid Atoms 0
    Heterogen Atoms 10
    Solvent Atoms 395
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution ShelxD, Sharp,
    Structure Refinement CNS 1.1, Coot, CCP4
     
    Software
    refinement CCP4
    refinement Coot
    refinement CNS version: 1.1
    model building Sharp
    model building ShelxD
    data collection CBASS