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X-RAY DIFFRACTION
Materials and Methods page
3NGB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details 10% PEG 4000, 9% Isopropanol, 0.1M Ammonium Sulfate, 0.1M Tris/Cl-, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 108.63 α = 90
    b = 98.28 β = 99.68
    c = 205.26 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 CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2009-10-31
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 0.82656
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Resolution(High) 2.68
    Resolution(Low) 50
    Number Reflections(Observed) 97150
    Percent Possible(Observed) 94.8
    Redundancy 3.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.68
    Resolution(Low) 49.733
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 97150
    Number of Reflections(R-Free) 4867
    Percent Reflections(Observed) 94.8
    R-Factor(Observed) 0.1997
    R-Work 0.1967
    R-Free 0.2563
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Overall
    Mean Isotropic B Value 57.3
    Anisotropic B[1][1] 2.981
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 5.7775
    Anisotropic B[2][2] 2.2145
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.1954
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.68
    Shell Resolution(Low) 2.7134
    Number of Reflections(R-Free) 11
    Number of Reflections(R-Work) 270
    R-Factor(R-Work) 0.3116
    R-Factor(R-Free) 0.3373
    Percent Reflections(Observed) 7.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7134
    Shell Resolution(Low) 2.7453
    Number of Reflections(R-Free) 19
    Number of Reflections(R-Work) 530
    R-Factor(R-Work) 0.3339
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 14.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7453
    Shell Resolution(Low) 2.7788
    Number of Reflections(R-Free) 40
    Number of Reflections(R-Work) 803
    R-Factor(R-Work) 0.3578
    R-Factor(R-Free) 0.4039
    Percent Reflections(Observed) 21.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7788
    Shell Resolution(Low) 2.814
    Number of Reflections(R-Free) 63
    Number of Reflections(R-Work) 1127
    R-Factor(R-Work) 0.3438
    R-Factor(R-Free) 0.4475
    Percent Reflections(Observed) 30.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.814
    Shell Resolution(Low) 2.851
    Number of Reflections(R-Free) 66
    Number of Reflections(R-Work) 1551
    R-Factor(R-Work) 0.3606
    R-Factor(R-Free) 0.4184
    Percent Reflections(Observed) 41.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.851
    Shell Resolution(Low) 2.8901
    Number of Reflections(R-Free) 96
    Number of Reflections(R-Work) 1957
    R-Factor(R-Work) 0.3315
    R-Factor(R-Free) 0.3776
    Percent Reflections(Observed) 52.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8901
    Shell Resolution(Low) 2.9313
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 2367
    R-Factor(R-Work) 0.3397
    R-Factor(R-Free) 0.4131
    Percent Reflections(Observed) 62.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9313
    Shell Resolution(Low) 2.9751
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.3244
    R-Factor(R-Free) 0.3673
    Percent Reflections(Observed) 72.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9751
    Shell Resolution(Low) 3.0216
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2937
    R-Factor(R-Work) 0.3049
    R-Factor(R-Free) 0.3733
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0216
    Shell Resolution(Low) 3.0711
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3246
    R-Factor(R-Work) 0.2988
    R-Factor(R-Free) 0.3464
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0711
    Shell Resolution(Low) 3.1241
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3422
    R-Factor(R-Work) 0.2868
    R-Factor(R-Free) 0.3572
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1241
    Shell Resolution(Low) 3.1809
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3579
    R-Factor(R-Work) 0.2827
    R-Factor(R-Free) 0.3684
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1809
    Shell Resolution(Low) 3.242
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3642
    R-Factor(R-Work) 0.2704
    R-Factor(R-Free) 0.3367
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.242
    Shell Resolution(Low) 3.3082
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3714
    R-Factor(R-Work) 0.2601
    R-Factor(R-Free) 0.3175
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3082
    Shell Resolution(Low) 3.3801
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3755
    R-Factor(R-Work) 0.2385
    R-Factor(R-Free) 0.3194
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3801
    Shell Resolution(Low) 3.4587
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3745
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.2961
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4587
    Shell Resolution(Low) 3.5452
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3776
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5452
    Shell Resolution(Low) 3.641
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3786
    R-Factor(R-Work) 0.1941
    R-Factor(R-Free) 0.2751
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.641
    Shell Resolution(Low) 3.7481
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3795
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2617
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7481
    Shell Resolution(Low) 3.869
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 3745
    R-Factor(R-Work) 0.1817
    R-Factor(R-Free) 0.2312
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.869
    Shell Resolution(Low) 4.0073
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 3744
    R-Factor(R-Work) 0.1693
    R-Factor(R-Free) 0.2492
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0073
    Shell Resolution(Low) 4.1676
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3750
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.245
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1676
    Shell Resolution(Low) 4.3572
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3793
    R-Factor(R-Work) 0.1453
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3572
    Shell Resolution(Low) 4.5868
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3799
    R-Factor(R-Work) 0.1435
    R-Factor(R-Free) 0.2037
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5868
    Shell Resolution(Low) 4.8739
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 3773
    R-Factor(R-Work) 0.1372
    R-Factor(R-Free) 0.2053
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8739
    Shell Resolution(Low) 5.2499
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3765
    R-Factor(R-Work) 0.131
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2499
    Shell Resolution(Low) 5.7775
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3830
    R-Factor(R-Work) 0.1464
    R-Factor(R-Free) 0.2113
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7775
    Shell Resolution(Low) 6.6118
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 3785
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.2336
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6118
    Shell Resolution(Low) 8.3239
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 3817
    R-Factor(R-Work) 0.1715
    R-Factor(R-Free) 0.2409
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.3239
    Shell Resolution(Low) 49.7412
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 3825
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.2226
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.034
    f_dihedral_angle_d 14.653
    f_angle_d 0.534
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 24218
    Nucleic Acid Atoms 0
    Heterogen Atoms 1067
    Solvent Atoms 523
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APS SER-CAT MARCCD
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.5_2)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.5_2)
    model building Phaser
    data collection APS version: SER-CAT MARCCD