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X-RAY DIFFRACTION
Materials and Methods page
4HG4
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 7.5
    Temperature 295.7
    Details 10% PEG6000, 0.1 M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 295.7K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 126.84 α = 90
    b = 133.14 β = 90
    c = 812.99 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Details Shutterless data collection; Fine phi slicing experiments
    Collection Date 2012-01-11
     
    Diffraction Radiation
    Monochromator Liquid nitrogen-cooled double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 0.97950
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.15
    Resolution(Low) 50
    Number Reflections(Observed) 234983
    Percent Possible(Observed) 98.7
    R Merge I(Observed) 0.133
    Redundancy 6.6
     
    High Resolution Shell Details
    Resolution(High) 3.15
    Resolution(Low) 3.26
    Percent Possible(All) 95.6
    R Merge I(Observed) 0.819
    Redundancy 5.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.2
    Resolution(Low) 48.13
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 205778
    Number of Reflections(R-Free) 10333
    Percent Reflections(Observed) 90.25
    R-Factor(Observed) 0.2517
    R-Work 0.249
    R-Free 0.3019
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -4.7199
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.6156
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -7.4957
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2
    Shell Resolution(Low) 3.2364
    Number of Reflections(R-Free) 57
    Number of Reflections(R-Work) 1077
    R-Factor(R-Work) 0.3615
    R-Factor(R-Free) 0.3956
    Percent Reflections(Observed) 15.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2364
    Shell Resolution(Low) 3.2744
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 1915
    R-Factor(R-Work) 0.3521
    R-Factor(R-Free) 0.4125
    Percent Reflections(Observed) 27.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2744
    Shell Resolution(Low) 3.3144
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2975
    R-Factor(R-Work) 0.333
    R-Factor(R-Free) 0.3835
    Percent Reflections(Observed) 42.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3144
    Shell Resolution(Low) 3.3563
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4554
    R-Factor(R-Work) 0.3313
    R-Factor(R-Free) 0.3823
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3563
    Shell Resolution(Low) 3.4004
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 6048
    R-Factor(R-Work) 0.3262
    R-Factor(R-Free) 0.4054
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4004
    Shell Resolution(Low) 3.447
    Number of Reflections(R-Free) 368
    Number of Reflections(R-Work) 6962
    R-Factor(R-Work) 0.3248
    R-Factor(R-Free) 0.3747
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.447
    Shell Resolution(Low) 3.4962
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7122
    R-Factor(R-Work) 0.3158
    R-Factor(R-Free) 0.3404
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4962
    Shell Resolution(Low) 3.5484
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 7116
    R-Factor(R-Work) 0.3117
    R-Factor(R-Free) 0.3513
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5484
    Shell Resolution(Low) 3.6038
    Number of Reflections(R-Free) 358
    Number of Reflections(R-Work) 7203
    R-Factor(R-Work) 0.2986
    R-Factor(R-Free) 0.37
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6038
    Shell Resolution(Low) 3.6629
    Number of Reflections(R-Free) 390
    Number of Reflections(R-Work) 7032
    R-Factor(R-Work) 0.2925
    R-Factor(R-Free) 0.3695
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6629
    Shell Resolution(Low) 3.7261
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6831
    R-Factor(R-Work) 0.2796
    R-Factor(R-Free) 0.3411
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7261
    Shell Resolution(Low) 3.7938
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 7024
    R-Factor(R-Work) 0.274
    R-Factor(R-Free) 0.3449
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7938
    Shell Resolution(Low) 3.8667
    Number of Reflections(R-Free) 392
    Number of Reflections(R-Work) 7143
    R-Factor(R-Work) 0.2685
    R-Factor(R-Free) 0.3256
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8667
    Shell Resolution(Low) 3.9456
    Number of Reflections(R-Free) 375
    Number of Reflections(R-Work) 7161
    R-Factor(R-Work) 0.2712
    R-Factor(R-Free) 0.3244
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9456
    Shell Resolution(Low) 4.0314
    Number of Reflections(R-Free) 402
    Number of Reflections(R-Work) 7155
    R-Factor(R-Work) 0.2344
    R-Factor(R-Free) 0.3204
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0314
    Shell Resolution(Low) 4.1251
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 7165
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.2843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1251
    Shell Resolution(Low) 4.2282
    Number of Reflections(R-Free) 389
    Number of Reflections(R-Work) 7204
    R-Factor(R-Work) 0.2268
    R-Factor(R-Free) 0.2677
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2282
    Shell Resolution(Low) 4.3424
    Number of Reflections(R-Free) 420
    Number of Reflections(R-Work) 7130
    R-Factor(R-Work) 0.2193
    R-Factor(R-Free) 0.2638
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3424
    Shell Resolution(Low) 4.4701
    Number of Reflections(R-Free) 386
    Number of Reflections(R-Work) 7177
    R-Factor(R-Work) 0.2067
    R-Factor(R-Free) 0.2511
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4701
    Shell Resolution(Low) 4.6143
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 6884
    R-Factor(R-Work) 0.2095
    R-Factor(R-Free) 0.261
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6143
    Shell Resolution(Low) 4.7791
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 7147
    R-Factor(R-Work) 0.2053
    R-Factor(R-Free) 0.2871
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7791
    Shell Resolution(Low) 4.9702
    Number of Reflections(R-Free) 430
    Number of Reflections(R-Work) 7194
    R-Factor(R-Work) 0.201
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9702
    Shell Resolution(Low) 5.1962
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 7202
    R-Factor(R-Work) 0.2047
    R-Factor(R-Free) 0.2621
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1962
    Shell Resolution(Low) 5.4698
    Number of Reflections(R-Free) 389
    Number of Reflections(R-Work) 7235
    R-Factor(R-Work) 0.2211
    R-Factor(R-Free) 0.2488
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4698
    Shell Resolution(Low) 5.812
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 7293
    R-Factor(R-Work) 0.2386
    R-Factor(R-Free) 0.297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.812
    Shell Resolution(Low) 6.2598
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 7042
    R-Factor(R-Work) 0.2442
    R-Factor(R-Free) 0.3292
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2598
    Shell Resolution(Low) 6.8881
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7295
    R-Factor(R-Work) 0.2323
    R-Factor(R-Free) 0.2896
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8881
    Shell Resolution(Low) 7.8811
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 7397
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.2741
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8811
    Shell Resolution(Low) 9.9151
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 7252
    R-Factor(R-Work) 0.2026
    R-Factor(R-Free) 0.2472
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.9151
    Shell Resolution(Low) 48.1353
    Number of Reflections(R-Free) 396
    Number of Reflections(R-Work) 7510
    R-Factor(R-Work) 0.2884
    R-Factor(R-Free) 0.3232
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.088
    f_dihedral_angle_d 20.838
    f_angle_d 1.366
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 58356
    Nucleic Acid Atoms 0
    Heterogen Atoms 386
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Bluice
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) HKL2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL
    data collection DENZO