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X-RAY DIFFRACTION
Materials and Methods page
4HKJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.55
    Temperature 293.0
    Details 10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.31 α = 76.18
    b = 88.25 β = 69.29
    c = 106.42 γ = 66.69
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type NOIR-1
    Collection Date 2010-09-10
     
    Diffraction Radiation
    Monochromator Rosenbaum-Rock monochromator 1: high-resolution double crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength List 0.97909
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3
    Resolution(Low) 50
    Number Reflections(All) 47950
    Number Reflections(Observed) 47882
    Percent Possible(Observed) 87.9
    R Merge I(Observed) 0.164
    B(Isotropic) From Wilson Plot 70.46
    Redundancy 4.1
     
    High Resolution Shell Details
    Resolution(High) 3.0
    Resolution(Low) 3.19
    Percent Possible(All) 84.9
    R Merge I(Observed) 0.622
    Mean I Over Sigma(Observed) 2.55
    Redundancy 4.2
    Number Unique Reflections(All) 7714
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD, MOLECULAR REPLACEMENT
    reflnsShellList 3.0
    Resolution(Low) 49.36
    Cut-off Sigma(I) 1.96
    Cut-off Sigma(F) 1.96
    Number of Reflections(all) 47950
    Number of Reflections(Observed) 47882
    Number of Reflections(R-Free) 2394
    Percent Reflections(Observed) 87.16
    R-Factor(Observed) 0.2307
    R-Work 0.2295
    R-Free 0.253
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 83.3211
    Anisotropic B[1][1] -3.3931
    Anisotropic B[1][2] 1.0886
    Anisotropic B[1][3] 4.4702
    Anisotropic B[2][2] -3.7601
    Anisotropic B[2][3] 4.2764
    Anisotropic B[3][3] 7.1532
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0
    Shell Resolution(Low) 3.0613
    Number of Reflections(Observed) 2244
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2244
    R-Factor(R-Work) 0.3506
    R-Factor(R-Free) 0.3887
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0613
    Shell Resolution(Low) 3.1279
    Number of Reflections(Observed) 2613
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.3198
    R-Factor(R-Free) 0.3255
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1279
    Shell Resolution(Low) 3.2006
    Number of Reflections(Observed) 2631
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.2895
    R-Factor(R-Free) 0.3703
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2006
    Shell Resolution(Low) 3.2806
    Number of Reflections(Observed) 2607
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.2817
    R-Factor(R-Free) 0.3207
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2806
    Shell Resolution(Low) 3.3693
    Number of Reflections(Observed) 2531
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2531
    R-Factor(R-Work) 0.2681
    R-Factor(R-Free) 0.2884
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3693
    Shell Resolution(Low) 3.4685
    Number of Reflections(Observed) 2552
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2552
    R-Factor(R-Work) 0.2877
    R-Factor(R-Free) 0.3478
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4685
    Shell Resolution(Low) 3.5804
    Number of Reflections(Observed) 2568
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2568
    R-Factor(R-Work) 0.2725
    R-Factor(R-Free) 0.28
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5804
    Shell Resolution(Low) 3.7083
    Number of Reflections(Observed) 2540
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.2963
    R-Factor(R-Free) 0.2798
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7083
    Shell Resolution(Low) 3.8567
    Number of Reflections(Observed) 2526
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2526
    R-Factor(R-Work) 0.2497
    R-Factor(R-Free) 0.2901
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8567
    Shell Resolution(Low) 4.0322
    Number of Reflections(Observed) 2518
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2518
    R-Factor(R-Work) 0.2573
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0322
    Shell Resolution(Low) 4.2446
    Number of Reflections(Observed) 2586
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2586
    R-Factor(R-Work) 0.2139
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2446
    Shell Resolution(Low) 4.5104
    Number of Reflections(Observed) 2638
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.2189
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5104
    Shell Resolution(Low) 4.8584
    Number of Reflections(Observed) 2810
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2810
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8584
    Shell Resolution(Low) 5.3468
    Number of Reflections(Observed) 2955
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2955
    R-Factor(R-Work) 0.1944
    R-Factor(R-Free) 0.2236
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3468
    Shell Resolution(Low) 6.1192
    Number of Reflections(Observed) 3049
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3049
    R-Factor(R-Work) 0.2095
    R-Factor(R-Free) 0.2417
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1192
    Shell Resolution(Low) 7.7049
    Number of Reflections(Observed) 3054
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3054
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.2519
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7049
    Shell Resolution(Low) 49.3669
    Number of Reflections(Observed) 3066
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3066
    R-Factor(R-Work) 0.1968
    R-Factor(R-Free) 0.2051
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 9.662
    f_plane_restr 0.002
    f_chiral_restr 0.041
    f_angle_d 0.538
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 18588
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 72
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLUE ICE
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE, PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    density modification RESOLVE
    phasing SOLVE
    molecular replacement Phaser
    data reduction HKL