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X-RAY DIFFRACTION
Materials and Methods page
4KZY
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 8.5
    Temperature 292.0
    Details 0.1M Ammonium acetate, 0.05M Tris-HCl pH 8.5, 2.5% PEG-20K, 4-6% MPD, 5.0mM Mg acetate, 2.0mM TCEP, vapor diffusion, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 296.9 α = 90
    b = 296.9 β = 90
    c = 478.3 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2012-06-18
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9789
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 7.01
    Resolution(Low) 120
    Number Reflections(All) 39111
    Number Reflections(Observed) 38929
    Percent Possible(Observed) 99.7
    B(Isotropic) From Wilson Plot 464.07
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 7.01
    Resolution(Low) 113.236
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 39111
    Number of Reflections(Observed) 38188
    Number of Reflections(R-Free) 1921
    Percent Reflections(Observed) 98.03
    R-Factor(All) 0.3653
    R-Factor(Observed) 0.3653
    R-Work 0.3662
    R-Free 0.3478
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 235.354
    Anisotropic B[1][1] 582.563
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 582.563
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 371.495
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0103
    Shell Resolution(Low) 7.1856
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2133
    R-Factor(R-Work) 0.507
    R-Factor(R-Free) 0.4781
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1856
    Shell Resolution(Low) 7.3799
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2548
    R-Factor(R-Work) 0.4689
    R-Factor(R-Free) 0.4718
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3799
    Shell Resolution(Low) 7.597
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2564
    R-Factor(R-Work) 0.4393
    R-Factor(R-Free) 0.4291
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.597
    Shell Resolution(Low) 7.8421
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.4321
    R-Factor(R-Free) 0.4002
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8421
    Shell Resolution(Low) 8.1223
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2576
    R-Factor(R-Work) 0.4205
    R-Factor(R-Free) 0.4436
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.1223
    Shell Resolution(Low) 8.4474
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.4195
    R-Factor(R-Free) 0.3579
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.4474
    Shell Resolution(Low) 8.8318
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.4075
    R-Factor(R-Free) 0.4208
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.8318
    Shell Resolution(Low) 9.2972
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.4235
    R-Factor(R-Free) 0.3822
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.2972
    Shell Resolution(Low) 9.8794
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.4153
    R-Factor(R-Free) 0.4026
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.8794
    Shell Resolution(Low) 10.6416
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.3909
    R-Factor(R-Free) 0.4058
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.6416
    Shell Resolution(Low) 11.7116
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.387
    R-Factor(R-Free) 0.3724
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.7116
    Shell Resolution(Low) 13.4039
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.372
    R-Factor(R-Free) 0.3348
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 13.4039
    Shell Resolution(Low) 16.8785
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.388
    R-Factor(R-Free) 0.3766
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 16.8785
    Shell Resolution(Low) 113.251
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2788
    R-Factor(R-Work) 0.308
    R-Factor(R-Free) 0.2842
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.723
    f_plane_restr 0.022
    f_chiral_restr 0.24
    f_angle_d 2.784
    f_bond_d 0.026
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 40341
    Nucleic Acid Atoms 38071
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) xds
    Data Reduction (data scaling) xds
    Structure Solution phaser
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix