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X-RAY DIFFRACTION
Materials and Methods page
4GPE
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 8.5
    Temperature 298.0
    Details 100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81.65 α = 90
    b = 95.76 β = 90
    c = 137.39 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2012-08-03
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-D
    Wavelength List 1.03
    Site APS
    Beamline 23-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.39
    Resolution(Low) 50
    Number Reflections(Observed) 107340
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.084
    Redundancy 9.5
     
    High Resolution Shell Details
    Resolution(High) 1.39
    Resolution(Low) 1.44
    Percent Possible(All) 98.1
    R Merge I(Observed) 0.718
    Redundancy 7.2
    Number Unique Reflections(All) 10486
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.39
    Resolution(Low) 47.882
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 107253
    Number of Reflections(R-Free) 5352
    Percent Reflections(Observed) 99.06
    R-Factor(Observed) 0.1322
    R-Work 0.1311
    R-Free 0.1529
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.6919
    Anisotropic B[1][1] 3.3109
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.4908
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.8201
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.39
    Shell Resolution(Low) 1.4047
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 3279
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4047
    Shell Resolution(Low) 1.4212
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 3312
    R-Factor(R-Work) 0.1725
    R-Factor(R-Free) 0.2059
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4212
    Shell Resolution(Low) 1.4385
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3335
    R-Factor(R-Work) 0.1528
    R-Factor(R-Free) 0.1858
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4385
    Shell Resolution(Low) 1.4567
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3366
    R-Factor(R-Work) 0.1477
    R-Factor(R-Free) 0.1759
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4567
    Shell Resolution(Low) 1.4759
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3303
    R-Factor(R-Work) 0.1408
    R-Factor(R-Free) 0.201
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4759
    Shell Resolution(Low) 1.4961
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3368
    R-Factor(R-Work) 0.1316
    R-Factor(R-Free) 0.1704
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4961
    Shell Resolution(Low) 1.5175
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 3307
    R-Factor(R-Work) 0.1268
    R-Factor(R-Free) 0.172
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5175
    Shell Resolution(Low) 1.5402
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3366
    R-Factor(R-Work) 0.1168
    R-Factor(R-Free) 0.1525
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5402
    Shell Resolution(Low) 1.5642
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3313
    R-Factor(R-Work) 0.1161
    R-Factor(R-Free) 0.155
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5642
    Shell Resolution(Low) 1.5899
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3354
    R-Factor(R-Work) 0.1085
    R-Factor(R-Free) 0.1439
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5899
    Shell Resolution(Low) 1.6173
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3360
    R-Factor(R-Work) 0.1075
    R-Factor(R-Free) 0.1438
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6173
    Shell Resolution(Low) 1.6467
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3387
    R-Factor(R-Work) 0.1113
    R-Factor(R-Free) 0.142
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6467
    Shell Resolution(Low) 1.6784
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3361
    R-Factor(R-Work) 0.1128
    R-Factor(R-Free) 0.1533
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6784
    Shell Resolution(Low) 1.7126
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3397
    R-Factor(R-Work) 0.113
    R-Factor(R-Free) 0.1646
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7126
    Shell Resolution(Low) 1.7499
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3395
    R-Factor(R-Work) 0.1154
    R-Factor(R-Free) 0.1612
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7499
    Shell Resolution(Low) 1.7906
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3405
    R-Factor(R-Work) 0.1105
    R-Factor(R-Free) 0.1573
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7906
    Shell Resolution(Low) 1.8354
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3366
    R-Factor(R-Work) 0.1084
    R-Factor(R-Free) 0.1494
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8354
    Shell Resolution(Low) 1.885
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3419
    R-Factor(R-Work) 0.1133
    R-Factor(R-Free) 0.1577
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.885
    Shell Resolution(Low) 1.9405
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3432
    R-Factor(R-Work) 0.1173
    R-Factor(R-Free) 0.1483
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9405
    Shell Resolution(Low) 2.0031
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3375
    R-Factor(R-Work) 0.1164
    R-Factor(R-Free) 0.1541
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0031
    Shell Resolution(Low) 2.0747
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3426
    R-Factor(R-Work) 0.1151
    R-Factor(R-Free) 0.1324
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0747
    Shell Resolution(Low) 2.1578
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3431
    R-Factor(R-Work) 0.1196
    R-Factor(R-Free) 0.1581
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1578
    Shell Resolution(Low) 2.256
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3415
    R-Factor(R-Work) 0.1184
    R-Factor(R-Free) 0.1492
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.256
    Shell Resolution(Low) 2.3749
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3440
    R-Factor(R-Work) 0.1209
    R-Factor(R-Free) 0.1539
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3749
    Shell Resolution(Low) 2.5237
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3452
    R-Factor(R-Work) 0.1276
    R-Factor(R-Free) 0.1297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5237
    Shell Resolution(Low) 2.7185
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3439
    R-Factor(R-Work) 0.1292
    R-Factor(R-Free) 0.1437
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7185
    Shell Resolution(Low) 2.9921
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3489
    R-Factor(R-Work) 0.1338
    R-Factor(R-Free) 0.1507
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9921
    Shell Resolution(Low) 3.4249
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3451
    R-Factor(R-Work) 0.139
    R-Factor(R-Free) 0.1661
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4249
    Shell Resolution(Low) 4.3146
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3508
    R-Factor(R-Work) 0.1379
    R-Factor(R-Free) 0.1262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3146
    Shell Resolution(Low) 47.882
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3650
    R-Factor(R-Work) 0.1663
    R-Factor(R-Free) 0.1714
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.496
    f_plane_restr 0.012
    f_chiral_restr 0.128
    f_angle_d 1.83
    f_bond_d 0.019
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3941
    Nucleic Acid Atoms 0
    Heterogen Atoms 42
    Solvent Atoms 432
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLUICE
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK