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X-RAY DIFFRACTION
Materials and Methods page
4KHN
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 298.0
    Details 12% PEG 8000, 0.1 M MES, 0.2 Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 74.26 α = 90
    b = 119.35 β = 91.64
    c = 148.03 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2013-01-28
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.55
    Resolution(Low) 39.3
    Number Reflections(Observed) 84020
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.063
    Redundancy 4.9
     
    High Resolution Shell Details
    Resolution(High) 2.55
    Resolution(Low) 2.559
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.617
    Mean I Over Sigma(Observed) 2.5
    Redundancy 4.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.55
    Resolution(Low) 35.334
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 83990
    Number of Reflections(R-Free) 4149
    Percent Reflections(Observed) 99.85
    R-Factor(Observed) 0.1704
    R-Work 0.1682
    R-Free 0.2109
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.55
    Shell Resolution(Low) 2.579
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.2615
    R-Factor(R-Free) 0.3017
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.579
    Shell Resolution(Low) 2.6093
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.266
    R-Factor(R-Free) 0.3105
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6093
    Shell Resolution(Low) 2.6411
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.2574
    R-Factor(R-Free) 0.3434
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6411
    Shell Resolution(Low) 2.6745
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.2482
    R-Factor(R-Free) 0.2896
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6745
    Shell Resolution(Low) 2.7097
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2391
    R-Factor(R-Free) 0.2867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7097
    Shell Resolution(Low) 2.7468
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.2271
    R-Factor(R-Free) 0.2746
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7468
    Shell Resolution(Low) 2.7861
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.2183
    R-Factor(R-Free) 0.2969
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7861
    Shell Resolution(Low) 2.8276
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.2089
    R-Factor(R-Free) 0.2686
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8276
    Shell Resolution(Low) 2.8718
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2709
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.2614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8718
    Shell Resolution(Low) 2.9188
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2495
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9188
    Shell Resolution(Low) 2.9692
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.2031
    R-Factor(R-Free) 0.2468
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9692
    Shell Resolution(Low) 3.0231
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1964
    R-Factor(R-Free) 0.2541
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0231
    Shell Resolution(Low) 3.0812
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.2003
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0812
    Shell Resolution(Low) 3.1441
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.2507
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1441
    Shell Resolution(Low) 3.2124
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.2071
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2124
    Shell Resolution(Low) 3.2871
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.191
    R-Factor(R-Free) 0.2567
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2871
    Shell Resolution(Low) 3.3692
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.2479
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3692
    Shell Resolution(Low) 3.4602
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.1798
    R-Factor(R-Free) 0.2332
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4602
    Shell Resolution(Low) 3.562
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.2368
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.562
    Shell Resolution(Low) 3.6768
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.2228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6768
    Shell Resolution(Low) 3.8081
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.2249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8081
    Shell Resolution(Low) 3.9604
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1507
    R-Factor(R-Free) 0.1796
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9604
    Shell Resolution(Low) 4.1404
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1366
    R-Factor(R-Free) 0.1622
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1404
    Shell Resolution(Low) 4.3583
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.1375
    R-Factor(R-Free) 0.1699
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3583
    Shell Resolution(Low) 4.6308
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2690
    R-Factor(R-Work) 0.1273
    R-Factor(R-Free) 0.1764
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6308
    Shell Resolution(Low) 4.9874
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1325
    R-Factor(R-Free) 0.1701
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9874
    Shell Resolution(Low) 5.4876
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.1445
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4876
    Shell Resolution(Low) 6.2779
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2779
    Shell Resolution(Low) 7.8949
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1675
    R-Factor(R-Free) 0.2086
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8949
    Shell Resolution(Low) 35.3376
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.1478
    R-Factor(R-Free) 0.1563
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.081
    f_dihedral_angle_d 17.24
    f_angle_d 1.192
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13909
    Nucleic Acid Atoms 1256
    Heterogen Atoms 169
    Solvent Atoms 304
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_1363)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_1363)
    model building PHASER
    data collection CBASS