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X-RAY DIFFRACTION
Materials and Methods page
4HD7
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.5
    Temperature 293.0
    Details PEG 8000, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.9 α = 90
    b = 78.67 β = 105.91
    c = 85.77 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Collection Date 2011-02-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.976300
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.1
    Resolution(Low) 82.48
    Number Reflections(All) 34263
    Number Reflections(Observed) 34263
    Percent Possible(Observed) 95.9
    Redundancy 2.4
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.21
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.181
    Mean I Over Sigma(Observed) 3.5
    R-Sym I(Observed) 0.181
    Redundancy 2.4
    Number Unique Reflections(All) 5092
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 36.214
    Cut-off Sigma(F) 1.37
    Number of Reflections(all) 34263
    Number of Reflections(Observed) 34184
    Number of Reflections(R-Free) 3427
    Percent Reflections(Observed) 95.38
    R-Factor(Observed) 0.2566
    R-Work 0.2537
    R-Free 0.2821
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.3701
    Anisotropic B[1][1] 5.716
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -9.4238
    Anisotropic B[2][2] -9.0141
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.2982
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.13
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1296
    R-Factor(R-Work) 0.2863
    R-Factor(R-Free) 0.3416
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.13
    Shell Resolution(Low) 2.1618
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1320
    R-Factor(R-Work) 0.2712
    R-Factor(R-Free) 0.3172
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1618
    Shell Resolution(Low) 2.1956
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1334
    R-Factor(R-Work) 0.2765
    R-Factor(R-Free) 0.3589
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1956
    Shell Resolution(Low) 2.2316
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1288
    R-Factor(R-Work) 0.3025
    R-Factor(R-Free) 0.3212
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2316
    Shell Resolution(Low) 2.27
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1231
    R-Factor(R-Work) 0.5095
    R-Factor(R-Free) 0.5446
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.27
    Shell Resolution(Low) 2.3113
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1301
    R-Factor(R-Work) 0.306
    R-Factor(R-Free) 0.3687
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3113
    Shell Resolution(Low) 2.3558
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1308
    R-Factor(R-Work) 0.2714
    R-Factor(R-Free) 0.3297
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3558
    Shell Resolution(Low) 2.4038
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1310
    R-Factor(R-Work) 0.2472
    R-Factor(R-Free) 0.3181
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4038
    Shell Resolution(Low) 2.4561
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1319
    R-Factor(R-Work) 0.2608
    R-Factor(R-Free) 0.292
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4561
    Shell Resolution(Low) 2.5132
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1288
    R-Factor(R-Work) 0.2462
    R-Factor(R-Free) 0.3523
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5132
    Shell Resolution(Low) 2.576
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1286
    R-Factor(R-Work) 0.2704
    R-Factor(R-Free) 0.2924
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.576
    Shell Resolution(Low) 2.6457
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 1331
    R-Factor(R-Work) 0.2786
    R-Factor(R-Free) 0.3074
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6457
    Shell Resolution(Low) 2.7235
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1255
    R-Factor(R-Work) 0.3515
    R-Factor(R-Free) 0.3785
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7235
    Shell Resolution(Low) 2.8114
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1332
    R-Factor(R-Work) 0.2729
    R-Factor(R-Free) 0.2998
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8114
    Shell Resolution(Low) 2.9118
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1275
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.2964
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9118
    Shell Resolution(Low) 3.0283
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1271
    R-Factor(R-Work) 0.2326
    R-Factor(R-Free) 0.2593
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0283
    Shell Resolution(Low) 3.1661
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1286
    R-Factor(R-Work) 0.2349
    R-Factor(R-Free) 0.2862
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1661
    Shell Resolution(Low) 3.3329
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1265
    R-Factor(R-Work) 0.2385
    R-Factor(R-Free) 0.2585
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3329
    Shell Resolution(Low) 3.5416
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1270
    R-Factor(R-Work) 0.2871
    R-Factor(R-Free) 0.287
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5416
    Shell Resolution(Low) 3.8147
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1235
    R-Factor(R-Work) 0.2288
    R-Factor(R-Free) 0.2339
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8147
    Shell Resolution(Low) 4.1981
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1255
    R-Factor(R-Work) 0.2038
    R-Factor(R-Free) 0.2248
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1981
    Shell Resolution(Low) 4.8044
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8044
    Shell Resolution(Low) 6.0484
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1255
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.2058
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0484
    Shell Resolution(Low) 36.2191
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1189
    R-Factor(R-Work) 0.2043
    R-Factor(R-Free) 0.2283
    Percent Reflections(Observed) 86.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.897
    f_plane_restr 0.006
    f_chiral_restr 0.09
    f_angle_d 1.214
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4686
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 214
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 3.3.16
    data collection Mosflm