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X-RAY DIFFRACTION
Materials and Methods page
4JBM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 289.0
    Details 0.1M sodium malonate, 12%(w/v) polyethylene glycol 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 111.02 α = 90
    b = 39.12 β = 110.64
    c = 137.88 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-01-12
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.1
    Wavelength List 0.98
    Site ALS
    Beamline 5.0.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.22
    Resolution(Low) 50
    Number Reflections(All) 28054
    Number Reflections(Observed) 27608
    Percent Possible(Observed) 98.4
    B(Isotropic) From Wilson Plot 46.26
     
    High Resolution Shell Details
    Resolution(High) 2.23
    Resolution(Low) 2.31
    Percent Possible(All) 99.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.218
    Resolution(Low) 40.973
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 28054
    Number of Reflections(Observed) 27608
    Number of Reflections(R-Free) 1996
    Percent Reflections(Observed) 98.41
    R-Factor(All) 0.236
    R-Factor(Observed) 0.2371
    R-Work 0.2335
    R-Free 0.2827
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 83.6867
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2179
    Shell Resolution(Low) 2.2733
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1652
    R-Factor(R-Work) 0.339
    R-Factor(R-Free) 0.3835
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2733
    Shell Resolution(Low) 2.3348
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1806
    R-Factor(R-Work) 0.3168
    R-Factor(R-Free) 0.3686
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3348
    Shell Resolution(Low) 2.4035
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1825
    R-Factor(R-Work) 0.2962
    R-Factor(R-Free) 0.3568
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4035
    Shell Resolution(Low) 2.481
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1818
    R-Factor(R-Work) 0.309
    R-Factor(R-Free) 0.3746
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.481
    Shell Resolution(Low) 2.5697
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1839
    R-Factor(R-Work) 0.3042
    R-Factor(R-Free) 0.3635
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5697
    Shell Resolution(Low) 2.6726
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1831
    R-Factor(R-Work) 0.2732
    R-Factor(R-Free) 0.391
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6726
    Shell Resolution(Low) 2.7942
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1851
    R-Factor(R-Work) 0.2879
    R-Factor(R-Free) 0.3324
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7942
    Shell Resolution(Low) 2.9415
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1819
    R-Factor(R-Work) 0.2684
    R-Factor(R-Free) 0.2892
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9415
    Shell Resolution(Low) 3.1257
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1837
    R-Factor(R-Work) 0.2678
    R-Factor(R-Free) 0.294
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1257
    Shell Resolution(Low) 3.3669
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1827
    R-Factor(R-Work) 0.2316
    R-Factor(R-Free) 0.267
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3669
    Shell Resolution(Low) 3.7055
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1842
    R-Factor(R-Work) 0.2292
    R-Factor(R-Free) 0.2742
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7055
    Shell Resolution(Low) 4.2413
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1870
    R-Factor(R-Work) 0.2124
    R-Factor(R-Free) 0.2549
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2413
    Shell Resolution(Low) 5.3417
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1897
    R-Factor(R-Work) 0.1888
    R-Factor(R-Free) 0.247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3417
    Shell Resolution(Low) 40.9804
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1898
    R-Factor(R-Work) 0.2
    R-Factor(R-Free) 0.2524
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.367
    f_plane_restr 0.006
    f_chiral_restr 0.079
    f_angle_d 1.367
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3004
    Nucleic Acid Atoms 486
    Heterogen Atoms 0
    Solvent Atoms 135
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building PHASES
    data collection HKL-2000