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X-RAY DIFFRACTION
Materials and Methods page
4NDH
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 8.5
    Temperature 277.0
    Details 100 mM Tris, 20% w/v PEG10000, pH 8.5, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.4 α = 90
    b = 117.08 β = 90
    c = 118.2 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 2012-11-20
     
    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) 1.85
    Resolution(Low) 50
    Number Reflections(All) 49053
    Number Reflections(Observed) 48759
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.063
    B(Isotropic) From Wilson Plot 25.07
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.848
    Resolution(Low) 1.92
    Percent Possible(All) 98.5
    R Merge I(Observed) 0.436
    Redundancy 3.3
    Number Unique Reflections(All) 4747
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.848
    Resolution(Low) 32.687
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 49053
    Number of Reflections(Observed) 48675
    Number of Reflections(R-Free) 2457
    Percent Reflections(Observed) 99.37
    R-Factor(Observed) 0.1642
    R-Work 0.1625
    R-Free 0.1964
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.3702
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.848
    Shell Resolution(Low) 1.884
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2475
    R-Factor(R-Work) 0.2194
    R-Factor(R-Free) 0.2597
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.884
    Shell Resolution(Low) 1.9224
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.2066
    R-Factor(R-Free) 0.2381
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9224
    Shell Resolution(Low) 1.9642
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2484
    R-Factor(R-Work) 0.1994
    R-Factor(R-Free) 0.2444
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9642
    Shell Resolution(Low) 2.0099
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2542
    R-Factor(R-Work) 0.1843
    R-Factor(R-Free) 0.2365
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0099
    Shell Resolution(Low) 2.0602
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2526
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0602
    Shell Resolution(Low) 2.1159
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.1701
    R-Factor(R-Free) 0.2192
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1159
    Shell Resolution(Low) 2.1781
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.1685
    R-Factor(R-Free) 0.1944
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1781
    Shell Resolution(Low) 2.2484
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.1685
    R-Factor(R-Free) 0.2247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2484
    Shell Resolution(Low) 2.3287
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2510
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.2134
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3287
    Shell Resolution(Low) 2.422
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2578
    R-Factor(R-Work) 0.1747
    R-Factor(R-Free) 0.2605
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.422
    Shell Resolution(Low) 2.5321
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2568
    R-Factor(R-Work) 0.1732
    R-Factor(R-Free) 0.2142
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5321
    Shell Resolution(Low) 2.6656
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2548
    R-Factor(R-Work) 0.1789
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6656
    Shell Resolution(Low) 2.8325
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.1779
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8325
    Shell Resolution(Low) 3.0511
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.1803
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0511
    Shell Resolution(Low) 3.3578
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.1519
    R-Factor(R-Free) 0.165
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3578
    Shell Resolution(Low) 3.8431
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.1384
    R-Factor(R-Free) 0.1799
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8431
    Shell Resolution(Low) 4.8393
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2617
    R-Factor(R-Work) 0.1277
    R-Factor(R-Free) 0.1532
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8393
    Shell Resolution(Low) 32.6919
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2761
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1771
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.889
    f_plane_restr 0.004
    f_chiral_restr 0.066
    f_angle_d 1.099
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2944
    Nucleic Acid Atoms 824
    Heterogen Atoms 48
    Solvent Atoms 501
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SER-gui
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    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