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X-RAY DIFFRACTION
Materials and Methods page
4NDI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 7.5
    Temperature 277.0
    Details 200 mM potassium acetate, 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.47 α = 90
    b = 115.49 β = 90
    c = 116.17 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 2012-12-16
     
    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) 1.9
    Resolution(Low) 50
    Number Reflections(All) 43956
    Number Reflections(Observed) 43868
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.102
    B(Isotropic) From Wilson Plot 18.75
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.551
    Mean I Over Sigma(Observed) 2.4
    Redundancy 3.9
    Number Unique Reflections(All) 4308
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 38.216
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 43956
    Number of Reflections(Observed) 43811
    Number of Reflections(R-Free) 2204
    Percent Reflections(Observed) 99.84
    R-Factor(Observed) 0.1558
    R-Work 0.1544
    R-Free 0.1817
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.7509
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.9416
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.2648
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9416
    Shell Resolution(Low) 1.9867
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2563
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9867
    Shell Resolution(Low) 2.0364
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2581
    R-Factor(R-Work) 0.1923
    R-Factor(R-Free) 0.2177
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0364
    Shell Resolution(Low) 2.0915
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2523
    R-Factor(R-Work) 0.1699
    R-Factor(R-Free) 0.2268
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0915
    Shell Resolution(Low) 2.153
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.1662
    R-Factor(R-Free) 0.1999
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.153
    Shell Resolution(Low) 2.2225
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2574
    R-Factor(R-Work) 0.1638
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2225
    Shell Resolution(Low) 2.3019
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.1598
    R-Factor(R-Free) 0.2196
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3019
    Shell Resolution(Low) 2.3941
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1679
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3941
    Shell Resolution(Low) 2.503
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2570
    R-Factor(R-Work) 0.1631
    R-Factor(R-Free) 0.2321
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.503
    Shell Resolution(Low) 2.6349
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2568
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.1786
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6349
    Shell Resolution(Low) 2.8
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.1615
    R-Factor(R-Free) 0.184
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 3.0161
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.1649
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0161
    Shell Resolution(Low) 3.3195
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.1399
    R-Factor(R-Free) 0.1812
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3195
    Shell Resolution(Low) 3.7994
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.1302
    R-Factor(R-Free) 0.1426
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7994
    Shell Resolution(Low) 4.7854
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.1249
    R-Factor(R-Free) 0.1485
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7854
    Shell Resolution(Low) 38.2235
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2779
    R-Factor(R-Work) 0.1571
    R-Factor(R-Free) 0.1566
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.12
    f_plane_restr 0.005
    f_chiral_restr 0.078
    f_angle_d 1.299
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2954
    Nucleic Acid Atoms 818
    Heterogen Atoms 65
    Solvent Atoms 698
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SER-gui
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: 1.8.1_1168)
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO