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X-RAY DIFFRACTION
Materials and Methods page
4MDX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 293.0
    Details 0.2 M sodium iodide, 20% w/v PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.79 α = 90
    b = 69.89 β = 90
    c = 79.21 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 ADSC QUANTUM 315
    Collection Date 2012-12-07
     
    Diffraction Radiation
    Monochromator Si(220)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.9792
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.5
    Resolution(Low) 25
    Number Reflections(Observed) 60026
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.082
    B(Isotropic) From Wilson Plot 13.5
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.55
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.531
    Redundancy 4.7
    Number Unique Reflections(All) 5947
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 24.554
    Cut-off Sigma(F) 1.36
    Number of Reflections(Observed) 59959
    Number of Reflections(R-Free) 1998
    Percent Reflections(Observed) 99.9
    R-Factor(Observed) 0.1648
    R-Work 0.1644
    R-Free 0.1776
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.2771
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5001
    Shell Resolution(Low) 1.5376
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 4082
    R-Factor(R-Work) 0.2332
    R-Factor(R-Free) 0.2945
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5376
    Shell Resolution(Low) 1.5792
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4084
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.2085
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5792
    Shell Resolution(Low) 1.6257
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 4110
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2384
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6257
    Shell Resolution(Low) 1.6781
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4073
    R-Factor(R-Work) 0.1845
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6781
    Shell Resolution(Low) 1.7381
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4094
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.2003
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7381
    Shell Resolution(Low) 1.8077
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4105
    R-Factor(R-Work) 0.1649
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8077
    Shell Resolution(Low) 1.8899
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 4141
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.1807
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8899
    Shell Resolution(Low) 1.9895
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 4103
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.1711
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9895
    Shell Resolution(Low) 2.1141
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 4120
    R-Factor(R-Work) 0.1546
    R-Factor(R-Free) 0.1986
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1141
    Shell Resolution(Low) 2.2772
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 4130
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.172
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2772
    Shell Resolution(Low) 2.5062
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4162
    R-Factor(R-Work) 0.1652
    R-Factor(R-Free) 0.1785
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5062
    Shell Resolution(Low) 2.8683
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 4178
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.1624
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8683
    Shell Resolution(Low) 3.612
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 4195
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.147
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.612
    Shell Resolution(Low) 24.5575
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 4384
    R-Factor(R-Work) 0.1517
    R-Factor(R-Free) 0.1729
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.722
    f_plane_restr 0.005
    f_chiral_restr 0.071
    f_angle_d 1.088
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1796
    Nucleic Acid Atoms 184
    Heterogen Atoms 7
    Solvent Atoms 354
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser version: 2.3.0
    data reduction HKL