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X-RAY DIFFRACTION
Materials and Methods page
4GP9
  •   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 = 81.25 α = 90
    b = 95.55 β = 90
    c = 137.35 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 2011-07-07
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 1.03
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.07
    Resolution(Low) 50
    Number Reflections(Observed) 217292
    Percent Possible(Observed) 93.2
    R Merge I(Observed) 0.063
    Redundancy 7.6
     
    High Resolution Shell Details
    Resolution(High) 1.07
    Resolution(Low) 1.11
    Percent Possible(All) 57.6
    R Merge I(Observed) 0.572
    Redundancy 2.9
    Number Unique Reflections(All) 13317
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.07
    Resolution(Low) 45.978
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 217223
    Number of Reflections(R-Free) 10840
    Percent Reflections(Observed) 93.16
    R-Factor(Observed) 0.1379
    R-Work 0.1373
    R-Free 0.1503
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 12.628
    Anisotropic B[1][1] 2.6708
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.4524
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.2184
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.07
    Shell Resolution(Low) 1.0825
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3534
    R-Factor(R-Work) 0.2996
    R-Factor(R-Free) 0.3239
    Percent Reflections(Observed) 48.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0825
    Shell Resolution(Low) 1.0952
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4201
    R-Factor(R-Work) 0.2648
    R-Factor(R-Free) 0.2624
    Percent Reflections(Observed) 57.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0952
    Shell Resolution(Low) 1.1086
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4805
    R-Factor(R-Work) 0.2327
    R-Factor(R-Free) 0.2448
    Percent Reflections(Observed) 66.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1086
    Shell Resolution(Low) 1.1226
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5397
    R-Factor(R-Work) 0.2144
    R-Factor(R-Free) 0.2485
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1226
    Shell Resolution(Low) 1.1374
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 5877
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2133
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1374
    Shell Resolution(Low) 1.1529
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 6225
    R-Factor(R-Work) 0.1781
    R-Factor(R-Free) 0.2206
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1529
    Shell Resolution(Low) 1.1694
    Number of Reflections(R-Free) 332
    Number of Reflections(R-Work) 6613
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1694
    Shell Resolution(Low) 1.1869
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6916
    R-Factor(R-Work) 0.147
    R-Factor(R-Free) 0.1742
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1869
    Shell Resolution(Low) 1.2054
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 7355
    R-Factor(R-Work) 0.138
    R-Factor(R-Free) 0.1705
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2054
    Shell Resolution(Low) 1.2252
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 7368
    R-Factor(R-Work) 0.1308
    R-Factor(R-Free) 0.1753
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2252
    Shell Resolution(Low) 1.2463
    Number of Reflections(R-Free) 396
    Number of Reflections(R-Work) 7314
    R-Factor(R-Work) 0.1294
    R-Factor(R-Free) 0.1484
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2463
    Shell Resolution(Low) 1.269
    Number of Reflections(R-Free) 385
    Number of Reflections(R-Work) 7372
    R-Factor(R-Work) 0.1266
    R-Factor(R-Free) 0.1475
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.269
    Shell Resolution(Low) 1.2934
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 7375
    R-Factor(R-Work) 0.1236
    R-Factor(R-Free) 0.1471
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2934
    Shell Resolution(Low) 1.3198
    Number of Reflections(R-Free) 389
    Number of Reflections(R-Work) 7324
    R-Factor(R-Work) 0.1198
    R-Factor(R-Free) 0.1413
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3198
    Shell Resolution(Low) 1.3485
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 7390
    R-Factor(R-Work) 0.125
    R-Factor(R-Free) 0.1401
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3485
    Shell Resolution(Low) 1.3799
    Number of Reflections(R-Free) 358
    Number of Reflections(R-Work) 7374
    R-Factor(R-Work) 0.12
    R-Factor(R-Free) 0.1491
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3799
    Shell Resolution(Low) 1.4144
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 7329
    R-Factor(R-Work) 0.1187
    R-Factor(R-Free) 0.1448
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4144
    Shell Resolution(Low) 1.4526
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 7445
    R-Factor(R-Work) 0.12
    R-Factor(R-Free) 0.1386
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4526
    Shell Resolution(Low) 1.4954
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 7345
    R-Factor(R-Work) 0.1181
    R-Factor(R-Free) 0.1442
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4954
    Shell Resolution(Low) 1.5436
    Number of Reflections(R-Free) 399
    Number of Reflections(R-Work) 7337
    R-Factor(R-Work) 0.1154
    R-Factor(R-Free) 0.1266
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5436
    Shell Resolution(Low) 1.5988
    Number of Reflections(R-Free) 394
    Number of Reflections(R-Work) 7373
    R-Factor(R-Work) 0.1134
    R-Factor(R-Free) 0.1371
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5988
    Shell Resolution(Low) 1.6628
    Number of Reflections(R-Free) 402
    Number of Reflections(R-Work) 7402
    R-Factor(R-Work) 0.1147
    R-Factor(R-Free) 0.1334
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6628
    Shell Resolution(Low) 1.7385
    Number of Reflections(R-Free) 393
    Number of Reflections(R-Work) 7352
    R-Factor(R-Work) 0.1198
    R-Factor(R-Free) 0.1399
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7385
    Shell Resolution(Low) 1.8302
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 7432
    R-Factor(R-Work) 0.1207
    R-Factor(R-Free) 0.1405
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8302
    Shell Resolution(Low) 1.9448
    Number of Reflections(R-Free) 400
    Number of Reflections(R-Work) 7417
    R-Factor(R-Work) 0.131
    R-Factor(R-Free) 0.1265
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9448
    Shell Resolution(Low) 2.095
    Number of Reflections(R-Free) 407
    Number of Reflections(R-Work) 7381
    R-Factor(R-Work) 0.1303
    R-Factor(R-Free) 0.1367
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.095
    Shell Resolution(Low) 2.3058
    Number of Reflections(R-Free) 401
    Number of Reflections(R-Work) 7442
    R-Factor(R-Work) 0.1336
    R-Factor(R-Free) 0.145
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3058
    Shell Resolution(Low) 2.6394
    Number of Reflections(R-Free) 424
    Number of Reflections(R-Work) 7445
    R-Factor(R-Work) 0.1371
    R-Factor(R-Free) 0.1422
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6394
    Shell Resolution(Low) 3.3253
    Number of Reflections(R-Free) 404
    Number of Reflections(R-Work) 7538
    R-Factor(R-Work) 0.1465
    R-Factor(R-Free) 0.1554
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3253
    Shell Resolution(Low) 45.978
    Number of Reflections(R-Free) 443
    Number of Reflections(R-Work) 7705
    R-Factor(R-Work) 0.1505
    R-Factor(R-Free) 0.1525
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.489
    f_plane_restr 0.01
    f_chiral_restr 0.095
    f_angle_d 1.602
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3944
    Nucleic Acid Atoms 0
    Heterogen Atoms 42
    Solvent Atoms 609
     
     
  •   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