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X-RAY DIFFRACTION
Materials and Methods page
4HNK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.6
    Temperature 293.0
    Details 0.25 M CaAcetate, pH 8.6, 7.5% PEG20K and 7.5% PEG MME500, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 178.79 α = 90
    b = 105.85 β = 118.1
    c = 186.4 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2007-04-11
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CHESS BEAMLINE A1
    Wavelength List 0.979
    Site CHESS
    Beamline A1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(Observed) 66514
    Percent Possible(Observed) 96.7
    R Merge I(Observed) 0.075
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 2.95
    Percent Possible(All) 87.8
    R Merge I(Observed) 0.764
    Redundancy 3.0
    Number Unique Reflections(All) 2987
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 45.542
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 66514
    Number of Reflections(R-Free) 3633
    Percent Reflections(Observed) 88.58
    R-Factor(Observed) 0.203
    R-Work 0.2017
    R-Free 0.2431
     
    Temperature Factor Modeling
    Mean Isotropic B Value 87.7514
    Anisotropic B[1][1] 4.9747
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -4.9814
    Anisotropic B[2][2] -3.6998
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.2749
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9
    Shell Resolution(Low) 2.9147
    Number of Reflections(R-Free) 80
    Number of Reflections(R-Work) 2482
    R-Factor(R-Work) 0.3946
    R-Factor(R-Free) 0.4719
    Percent Reflections(Observed) 49.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9147
    Shell Resolution(Low) 2.9546
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 4048
    R-Factor(R-Work) 0.345
    R-Factor(R-Free) 0.3573
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9546
    Shell Resolution(Low) 2.9968
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 4124
    R-Factor(R-Work) 0.3293
    R-Factor(R-Free) 0.4225
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9968
    Shell Resolution(Low) 3.0415
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 4162
    R-Factor(R-Work) 0.3117
    R-Factor(R-Free) 0.3888
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0415
    Shell Resolution(Low) 3.089
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 4196
    R-Factor(R-Work) 0.3024
    R-Factor(R-Free) 0.3421
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.089
    Shell Resolution(Low) 3.1397
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 4272
    R-Factor(R-Work) 0.2845
    R-Factor(R-Free) 0.3074
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1397
    Shell Resolution(Low) 3.1938
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 4235
    R-Factor(R-Work) 0.2714
    R-Factor(R-Free) 0.3425
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1938
    Shell Resolution(Low) 3.2518
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 4443
    R-Factor(R-Work) 0.263
    R-Factor(R-Free) 0.3192
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2518
    Shell Resolution(Low) 3.3144
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 4435
    R-Factor(R-Work) 0.2585
    R-Factor(R-Free) 0.3421
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3144
    Shell Resolution(Low) 3.382
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4473
    R-Factor(R-Work) 0.2465
    R-Factor(R-Free) 0.3218
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.382
    Shell Resolution(Low) 3.4555
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4623
    R-Factor(R-Work) 0.2341
    R-Factor(R-Free) 0.2661
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4555
    Shell Resolution(Low) 3.5359
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 4564
    R-Factor(R-Work) 0.2301
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5359
    Shell Resolution(Low) 3.6243
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4677
    R-Factor(R-Work) 0.2388
    R-Factor(R-Free) 0.2705
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6243
    Shell Resolution(Low) 3.7222
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4729
    R-Factor(R-Work) 0.2401
    R-Factor(R-Free) 0.2719
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7222
    Shell Resolution(Low) 3.8317
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 4753
    R-Factor(R-Work) 0.2081
    R-Factor(R-Free) 0.2967
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8317
    Shell Resolution(Low) 3.9553
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 4831
    R-Factor(R-Work) 0.2057
    R-Factor(R-Free) 0.2418
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9553
    Shell Resolution(Low) 4.0966
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 4833
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2794
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0966
    Shell Resolution(Low) 4.2605
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 4882
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.2167
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2605
    Shell Resolution(Low) 4.4542
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4884
    R-Factor(R-Work) 0.1502
    R-Factor(R-Free) 0.1854
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4542
    Shell Resolution(Low) 4.6888
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 4922
    R-Factor(R-Work) 0.1322
    R-Factor(R-Free) 0.1579
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6888
    Shell Resolution(Low) 4.9823
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 4925
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1596
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9823
    Shell Resolution(Low) 5.3664
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 4909
    R-Factor(R-Work) 0.1693
    R-Factor(R-Free) 0.2016
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3664
    Shell Resolution(Low) 5.9054
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 4895
    R-Factor(R-Work) 0.2027
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9054
    Shell Resolution(Low) 6.7575
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 4907
    R-Factor(R-Work) 0.2247
    R-Factor(R-Free) 0.2894
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7575
    Shell Resolution(Low) 8.5047
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 4831
    R-Factor(R-Work) 0.1815
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.5047
    Shell Resolution(Low) 45.542
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 4520
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.2395
    Percent Reflections(Observed) 89.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.297
    f_plane_restr 0.006
    f_chiral_restr 0.088
    f_angle_d 1.126
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 18850
    Nucleic Acid Atoms 0
    Heterogen Atoms 12
    Solvent Atoms 70
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALEPACK