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X-RAY DIFFRACTION
Materials and Methods page
4NDF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 8.5
    Temperature 277.0
    Details 200 mM potassium sodium tartrate, 20% w/v PEG3350, pH 8.5, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.43 α = 90
    b = 116.21 β = 90
    c = 117.14 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 2012-12-10
     
    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) 1.94
    Resolution(Low) 50
    Number Reflections(All) 41560
    Number Reflections(Observed) 41518
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.078
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 1.944
    Resolution(Low) 2.02
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.588
    Redundancy 3.9
    Number Unique Reflections(All) 4096
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.944
    Resolution(Low) 32.409
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 41560
    Number of Reflections(Observed) 41440
    Number of Reflections(R-Free) 2082
    Percent Reflections(Observed) 99.69
    R-Factor(Observed) 0.1729
    R-Work 0.1712
    R-Free 0.2047
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.6341
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.944
    Shell Resolution(Low) 1.9894
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2505
    R-Factor(R-Work) 0.2448
    R-Factor(R-Free) 0.317
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9894
    Shell Resolution(Low) 2.0391
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2603
    R-Factor(R-Work) 0.2279
    R-Factor(R-Free) 0.2697
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0391
    Shell Resolution(Low) 2.0943
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.2172
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0943
    Shell Resolution(Low) 2.1559
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2595
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2493
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1559
    Shell Resolution(Low) 2.2254
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.1895
    R-Factor(R-Free) 0.2317
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2254
    Shell Resolution(Low) 2.305
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.305
    Shell Resolution(Low) 2.3972
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2617
    R-Factor(R-Work) 0.1861
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3972
    Shell Resolution(Low) 2.5063
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.1878
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5063
    Shell Resolution(Low) 2.6384
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.2386
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6384
    Shell Resolution(Low) 2.8036
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.2474
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8036
    Shell Resolution(Low) 3.0199
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1843
    R-Factor(R-Free) 0.2261
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0199
    Shell Resolution(Low) 3.3235
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.1954
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3235
    Shell Resolution(Low) 3.8038
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.1462
    R-Factor(R-Free) 0.1636
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8038
    Shell Resolution(Low) 4.7899
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.1361
    R-Factor(R-Free) 0.1602
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7899
    Shell Resolution(Low) 32.4135
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2822
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.1726
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.704
    f_plane_restr 0.004
    f_chiral_restr 0.066
    f_angle_d 1.154
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2954
    Nucleic Acid Atoms 818
    Heterogen Atoms 58
    Solvent Atoms 556
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SER-gui
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution phenix.refine
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK