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X-RAY DIFFRACTION
Materials and Methods page
4GKL
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.6
    Temperature 287.0
    Details 0.1M Sodium acetate, 2M sodium formate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.88 α = 90
    b = 74.45 β = 107.77
    c = 108.9 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 173
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2011-10-08
     
    Diffraction Radiation
    Monochromator Double MIRRORS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Wavelength List 1.0
    Site PHOTON FACTORY
    Beamline AR-NE3A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.4
    Resolution(Low) 20
    Number Reflections(All) 37665
    Number Reflections(Observed) 35640
    Percent Possible(Observed) 94.1
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.44
    Percent Possible(All) 86.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 19.98
    Cut-off Sigma(F) 1.54
    Number of Reflections(all) 37665
    Number of Reflections(Observed) 35640
    Number of Reflections(R-Free) 1981
    Percent Reflections(Observed) 93.93
    R-Factor(Observed) 0.201
    R-Work 0.1974
    R-Free 0.2633
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 7.3982
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 10.6891
    Anisotropic B[2][2] -11.9694
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.5713
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.4577
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2236
    R-Factor(R-Work) 0.2671
    R-Factor(R-Free) 0.3274
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4577
    Shell Resolution(Low) 2.524
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2360
    R-Factor(R-Work) 0.2437
    R-Factor(R-Free) 0.349
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.524
    Shell Resolution(Low) 2.5982
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2369
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.2623
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5982
    Shell Resolution(Low) 2.6818
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2422
    R-Factor(R-Work) 0.2327
    R-Factor(R-Free) 0.3149
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6818
    Shell Resolution(Low) 2.7774
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2476
    R-Factor(R-Work) 0.2369
    R-Factor(R-Free) 0.3064
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7774
    Shell Resolution(Low) 2.8883
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2571
    R-Factor(R-Work) 0.2403
    R-Factor(R-Free) 0.3441
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8883
    Shell Resolution(Low) 3.0194
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2592
    R-Factor(R-Work) 0.2223
    R-Factor(R-Free) 0.2852
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0194
    Shell Resolution(Low) 3.178
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.2065
    R-Factor(R-Free) 0.2745
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.178
    Shell Resolution(Low) 3.3762
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2785
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3762
    Shell Resolution(Low) 3.6354
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.1854
    R-Factor(R-Free) 0.2459
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6354
    Shell Resolution(Low) 3.9986
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.1744
    R-Factor(R-Free) 0.2369
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9986
    Shell Resolution(Low) 4.5712
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2116
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5712
    Shell Resolution(Low) 5.7365
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.1791
    R-Factor(R-Free) 0.1921
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7365
    Shell Resolution(Low) 19.9803
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2753
    R-Factor(R-Work) 0.22
    R-Factor(R-Free) 0.2659
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.091
    f_dihedral_angle_d 18.052
    f_angle_d 1.278
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7021
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 244
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) HKL-2000
    Structure Solution CCP4
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building CCP4
    data collection HKL-2000