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X-RAY DIFFRACTION
Materials and Methods page
4K8G
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 7.5
    Temperature 277.0
    Details Mother liqueur contained 28% PEG 400, 100 mM HEPES, NaOH, 200 mM Calcium chloride. Protein solution was at 20 mg/mL, 100 mM NaCl, 50 mM Tris, pH 7.5, vapor diffusion, sitting drop, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 125.77 α = 90
    b = 125.77 β = 90
    c = 119.74 γ = 90
     
    Space Group
    Space Group Name:    I 4 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-325
    Collection Date 2003-01-01
     
    Diffraction Radiation
    Monochromator C(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97857
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.25
    Resolution(Low) 29.9
    Number Reflections(All) 131226
    Number Reflections(Observed) 131204
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.093
    B(Isotropic) From Wilson Plot 15.263
     
    High Resolution Shell Details
    Resolution(High) 1.25
    Resolution(Low) 1.28
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.766
    Mean I Over Sigma(Observed) 3.84
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.25
    Resolution(Low) 29.9
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 131204
    Number of Reflections(Observed) 131191
    Number of Reflections(R-Free) 6560
    Percent Reflections(Observed) 99.98
    R-Factor(Observed) 0.1413
    R-Work 0.141
    R-Free 0.1482
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 12.2156
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.25
    Shell Resolution(Low) 1.2642
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4117
    R-Factor(R-Work) 0.1861
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2642
    Shell Resolution(Low) 1.2791
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4098
    R-Factor(R-Work) 0.1821
    R-Factor(R-Free) 0.1796
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2791
    Shell Resolution(Low) 1.2947
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4131
    R-Factor(R-Work) 0.1771
    R-Factor(R-Free) 0.2041
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2947
    Shell Resolution(Low) 1.311
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4095
    R-Factor(R-Work) 0.1681
    R-Factor(R-Free) 0.1713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.311
    Shell Resolution(Low) 1.3283
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4121
    R-Factor(R-Work) 0.1621
    R-Factor(R-Free) 0.1678
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3283
    Shell Resolution(Low) 1.3465
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4130
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.1724
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3465
    Shell Resolution(Low) 1.3657
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4104
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.1598
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3657
    Shell Resolution(Low) 1.3861
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4104
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.1639
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3861
    Shell Resolution(Low) 1.4078
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4124
    R-Factor(R-Work) 0.1488
    R-Factor(R-Free) 0.1582
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4078
    Shell Resolution(Low) 1.4309
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4129
    R-Factor(R-Work) 0.1475
    R-Factor(R-Free) 0.1614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4309
    Shell Resolution(Low) 1.4555
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4099
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.1452
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4555
    Shell Resolution(Low) 1.482
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4145
    R-Factor(R-Work) 0.1371
    R-Factor(R-Free) 0.1558
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.482
    Shell Resolution(Low) 1.5105
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4127
    R-Factor(R-Work) 0.1336
    R-Factor(R-Free) 0.1341
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5105
    Shell Resolution(Low) 1.5413
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4120
    R-Factor(R-Work) 0.1308
    R-Factor(R-Free) 0.1484
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5413
    Shell Resolution(Low) 1.5748
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.1318
    R-Factor(R-Free) 0.1479
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5748
    Shell Resolution(Low) 1.6115
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4110
    R-Factor(R-Work) 0.129
    R-Factor(R-Free) 0.1467
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6115
    Shell Resolution(Low) 1.6518
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4136
    R-Factor(R-Work) 0.1289
    R-Factor(R-Free) 0.1449
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6518
    Shell Resolution(Low) 1.6964
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4155
    R-Factor(R-Work) 0.1275
    R-Factor(R-Free) 0.1432
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6964
    Shell Resolution(Low) 1.7463
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4144
    R-Factor(R-Work) 0.132
    R-Factor(R-Free) 0.1391
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7463
    Shell Resolution(Low) 1.8027
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4133
    R-Factor(R-Work) 0.1326
    R-Factor(R-Free) 0.1475
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8027
    Shell Resolution(Low) 1.8671
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4159
    R-Factor(R-Work) 0.133
    R-Factor(R-Free) 0.1431
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8671
    Shell Resolution(Low) 1.9419
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4167
    R-Factor(R-Work) 0.1347
    R-Factor(R-Free) 0.1586
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9419
    Shell Resolution(Low) 2.0302
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4170
    R-Factor(R-Work) 0.1339
    R-Factor(R-Free) 0.1546
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0302
    Shell Resolution(Low) 2.1372
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4170
    R-Factor(R-Work) 0.1363
    R-Factor(R-Free) 0.1389
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1372
    Shell Resolution(Low) 2.2711
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.1314
    R-Factor(R-Free) 0.1512
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2711
    Shell Resolution(Low) 2.4464
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 4214
    R-Factor(R-Work) 0.1397
    R-Factor(R-Free) 0.1508
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4464
    Shell Resolution(Low) 2.6924
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4191
    R-Factor(R-Work) 0.1424
    R-Factor(R-Free) 0.1436
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6924
    Shell Resolution(Low) 3.0817
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 4231
    R-Factor(R-Work) 0.1448
    R-Factor(R-Free) 0.1426
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0817
    Shell Resolution(Low) 3.8813
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4264
    R-Factor(R-Work) 0.1372
    R-Factor(R-Free) 0.1389
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8813
    Shell Resolution(Low) 29.9436
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4445
    R-Factor(R-Work) 0.1456
    R-Factor(R-Free) 0.1358
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.55
    f_plane_restr 0.006
    f_chiral_restr 0.076
    f_angle_d 1.138
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3072
    Nucleic Acid Atoms 0
    Heterogen Atoms 7
    Solvent Atoms 534
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale