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X-RAY DIFFRACTION
Materials and Methods page
4GKP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 277.0
    Details 0.1M HEPES, 13% PEG-6000, 5% isopropanol, 75mM NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.74 α = 90
    b = 77.72 β = 90
    c = 107.74 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2008-10-05
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X6A
    Wavelength List 0.976
    Site NSLS
    Beamline X6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.42
    Resolution(Low) 20
    Number Reflections(All) 22019
    Number Reflections(Observed) 21752
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.035
    B(Isotropic) From Wilson Plot 49.904
    Redundancy 7.8
     
    High Resolution Shell Details
    Resolution(High) 2.42
    Resolution(Low) 2.5
    Percent Possible(All) 92.7
    R Merge I(Observed) 0.193
    Mean I Over Sigma(Observed) 8.17
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.42
    Resolution(Low) 19.83
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 22019
    Number of Reflections(Observed) 21751
    Number of Reflections(R-Free) 1088
    Percent Reflections(Observed) 98.79
    R-Factor(All) 0.212
    R-Factor(Observed) 0.212
    R-Work 0.2095
    R-Free 0.2593
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 43.2617
    Anisotropic B[1][1] 0.36
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.25
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.89
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.42
    Shell Resolution(Low) 2.482
    Number of Reflections(R-Free) 71
    Number of Reflections(R-Work) 1297
    R-Factor(R-Work) 0.272
    R-Factor(R-Free) 0.329
    Percent Reflections(Observed) 91.63
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.005
    r_chiral_restr 0.083
    r_dihedral_angle_4_deg 15.827
    r_dihedral_angle_3_deg 16.053
    r_dihedral_angle_2_deg 39.254
    r_dihedral_angle_1_deg 6.261
    r_angle_refined_deg 1.255
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3724
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 80
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blue-Ice
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution Phaser
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    data reduction Xscale