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X-RAY DIFFRACTION
Materials and Methods page
4DLD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 279.0
    Details 17 % PEG4000, 0.1M cacodylic acid, 0.3M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 69.32 α = 90
    b = 69.32 β = 90
    c = 234.97 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2010-03-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type MAX II BEAMLINE I911-2
    Wavelength List 1.0380
    Site MAX II
    Beamline I911-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2
    Resolution(Low) 25.88
    Number Reflections(All) 39813
    Number Reflections(Observed) 39813
    Percent Possible(Observed) 99.9
    B(Isotropic) From Wilson Plot 21.09
    Redundancy 7.9
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.11
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.318
    Mean I Over Sigma(Observed) 1.8
    R-Sym I(Observed) 0.318
    Redundancy 8.0
    Number Unique Reflections(All) 5696
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 25.877
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 39768
    Number of Reflections(R-Free) 1997
    Percent Reflections(Observed) 99.83
    R-Factor(Observed) 0.1894
    R-Work 0.1864
    R-Free 0.246
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Restrained
    Mean Isotropic B Value 24.6097
    Anisotropic B[1][1] 2.019
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.019
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.038
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.05
    Number of Reflections(Observed) 2656
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.2213
    R-Factor(R-Free) 0.2943
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.1054
    Number of Reflections(Observed) 2622
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.2016
    R-Factor(R-Free) 0.279
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1054
    Shell Resolution(Low) 2.1674
    Number of Reflections(Observed) 2662
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1953
    R-Factor(R-Free) 0.2654
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1674
    Shell Resolution(Low) 2.2373
    Number of Reflections(Observed) 2671
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1804
    R-Factor(R-Free) 0.2427
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2373
    Shell Resolution(Low) 2.3172
    Number of Reflections(Observed) 2671
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.2561
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3172
    Shell Resolution(Low) 2.4099
    Number of Reflections(Observed) 2639
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.1952
    R-Factor(R-Free) 0.275
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4099
    Shell Resolution(Low) 2.5195
    Number of Reflections(Observed) 2646
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.1995
    R-Factor(R-Free) 0.2806
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5195
    Shell Resolution(Low) 2.6522
    Number of Reflections(Observed) 2684
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2801
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6522
    Shell Resolution(Low) 2.8182
    Number of Reflections(Observed) 2685
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2661
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8182
    Shell Resolution(Low) 3.0355
    Number of Reflections(Observed) 2723
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0355
    Shell Resolution(Low) 3.3404
    Number of Reflections(Observed) 2700
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1878
    R-Factor(R-Free) 0.2369
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3404
    Shell Resolution(Low) 3.8224
    Number of Reflections(Observed) 2726
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.1774
    R-Factor(R-Free) 0.2503
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8224
    Shell Resolution(Low) 4.8108
    Number of Reflections(Observed) 2757
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2757
    R-Factor(R-Work) 0.1507
    R-Factor(R-Free) 0.202
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8108
    Shell Resolution(Low) 25.8796
    Number of Reflections(Observed) 2929
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2929
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.22
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.384
    f_plane_restr 0.005
    f_chiral_restr 0.069
    f_angle_d 1.035
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4058
    Nucleic Acid Atoms 0
    Heterogen Atoms 54
    Solvent Atoms 501
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 3.3.9
    data collection Mosflm