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X-RAY DIFFRACTION
Materials and Methods page
4NDG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 7.5
    Temperature 277.0
    Details 100 mM sodium formate, 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.28 α = 90
    b = 114.58 β = 90
    c = 124.66 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 MARMOSAIC 300 mm CCD
    Collection Date 2013-02-02
     
    Diffraction Radiation
    Monochromator Rosenbaum-Rock double-crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 1.000
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.54
    Resolution(Low) 50
    Number Reflections(All) 19773
    Number Reflections(Observed) 19635
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.079
    B(Isotropic) From Wilson Plot 61.87
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.541
    Resolution(Low) 2.64
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.582
    Redundancy 4.1
    Number Unique Reflections(All) 1921
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.541
    Resolution(Low) 39.063
    Cut-off Sigma(F) 1.37
    Number of Reflections(all) 19773
    Number of Reflections(Observed) 19503
    Number of Reflections(R-Free) 1002
    Percent Reflections(Observed) 98.62
    R-Factor(Observed) 0.211
    R-Work 0.2084
    R-Free 0.2599
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 88.5488
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.541
    Shell Resolution(Low) 2.6745
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2581
    R-Factor(R-Work) 0.3442
    R-Factor(R-Free) 0.4316
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6745
    Shell Resolution(Low) 2.8421
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.314
    R-Factor(R-Free) 0.3337
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8421
    Shell Resolution(Low) 3.0614
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.2882
    R-Factor(R-Free) 0.3541
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0614
    Shell Resolution(Low) 3.3693
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2645
    R-Factor(R-Work) 0.2184
    R-Factor(R-Free) 0.2726
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3693
    Shell Resolution(Low) 3.8565
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.2155
    R-Factor(R-Free) 0.2837
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8565
    Shell Resolution(Low) 4.8574
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1784
    R-Factor(R-Free) 0.2294
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8574
    Shell Resolution(Low) 39.0679
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2744
    R-Factor(R-Work) 0.1717
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.484
    f_plane_restr 0.007
    f_chiral_restr 0.048
    f_angle_d 1.223
    f_bond_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2921
    Nucleic Acid Atoms 818
    Heterogen Atoms 46
    Solvent Atoms 25
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SER-gui
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: 1.8.2_1309)
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO