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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3L4K
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 291.0
    Details 20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 86.06 α = 90
    b = 91.85 β = 90
    c = 115.94 γ = 90
     
    Space Group
    Space Group Name:    P 21 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2009-10-18
     
    Diffraction Radiation
    Monochromator DOUBLE FLAT CRYSTAL, SI (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.2823
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.98
    Resolution(Low) 50
    Number Reflections(All) 19750
    Number Reflections(Observed) 18071
    Percent Possible(Observed) 91.4
    R Merge I(Observed) 0.102
    B(Isotropic) From Wilson Plot 72.6
    Redundancy 4.3
     
    High Resolution Shell Details
    Resolution(High) 2.98
    Resolution(Low) 3.07
    Percent Possible(All) 94.0
    R Merge I(Observed) 0.538
    Mean I Over Sigma(Observed) 2.1
    Redundancy 4.4
    Number Unique Reflections(All) 1827
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.98
    Resolution(Low) 49.023
    Cut-off Sigma(F) 1.9
    Number of Reflections(Observed) 17619
    Number of Reflections(R-Free) 1549
    Percent Reflections(Observed) 86.23
    R-Factor(Observed) 0.2408
    R-Work 0.2391
    R-Free 0.2733
    R-Free Selection Details IMPORTED FROM PDB ENTRY 3L4J
     
    Temperature Factor Modeling
    Mean Isotropic B Value 89.9
    Anisotropic B[1][1] -8.8659
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 14.0089
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.143
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.98
    Shell Resolution(Low) 3.0795
    Number of Reflections(Observed) 2849
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.3373
    R-Factor(R-Free) 0.3943
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0795
    Shell Resolution(Low) 3.1895
    Number of Reflections(Observed) 2869
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2740
    R-Factor(R-Work) 0.3301
    R-Factor(R-Free) 0.365
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1895
    Shell Resolution(Low) 3.3172
    Number of Reflections(Observed) 2863
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.3276
    R-Factor(R-Free) 0.398
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3172
    Shell Resolution(Low) 3.4682
    Number of Reflections(Observed) 2876
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.299
    R-Factor(R-Free) 0.3261
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4682
    Shell Resolution(Low) 3.651
    Number of Reflections(Observed) 2849
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.2725
    R-Factor(R-Free) 0.347
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.651
    Shell Resolution(Low) 3.8796
    Number of Reflections(Observed) 2873
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2716
    R-Factor(R-Work) 0.2549
    R-Factor(R-Free) 0.2904
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8796
    Shell Resolution(Low) 4.179
    Number of Reflections(Observed) 2824
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2687
    R-Factor(R-Work) 0.2291
    R-Factor(R-Free) 0.2826
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.179
    Shell Resolution(Low) 4.5993
    Number of Reflections(Observed) 2799
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2457
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5993
    Shell Resolution(Low) 5.2641
    Number of Reflections(Observed) 2791
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2641
    Shell Resolution(Low) 6.6297
    Number of Reflections(Observed) 2796
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.2677
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6297
    Shell Resolution(Low) 49.0292
    Number of Reflections(Observed) 2791
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.1935
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 85.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.103
    f_dihedral_angle_d 18.072
    f_angle_d 1.25
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5941
    Nucleic Acid Atoms 1039
    Heterogen Atoms 28
    Solvent Atoms 20
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.5_2)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.5_2)
    model building PHASER
    data collection BLU-ICE