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X-RAY DIFFRACTION
Materials and Methods page
4DMI
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.4
    Details 20% w/v PEG 3350, 0.2M Potassium Formate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 100K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 57.57 α = 90
    b = 147.87 β = 112.05
    c = 57.85 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 AREA DETECTOR
    Type ADSC QUANTUM 315r
    Collection Date 2011-11-11
     
    Diffraction Radiation
    Monochromator SI(220) ASYMMETRIC CUT SINGLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.1
    Wavelength 0.97740
    Site ALS
    Beamline 5.0.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.5
    Resolution(Low) 43.41
    Number Reflections(Observed) 139069
    Percent Possible(Observed) 97.3
    R Merge I(Observed) 0.066
    B(Isotropic) From Wilson Plot 19.9
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.54
    Percent Possible(All) 93.1
    R Merge I(Observed) 0.413
    Mean I Over Sigma(Observed) 3.94
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 43.41
    Cut-off Sigma(F) 1.37
    Number of Reflections(all) 146018
    Number of Reflections(Observed) 139061
    Number of Reflections(R-Free) 6957
    Percent Reflections(Observed) 97.5
    R-Factor(Observed) 0.16
    R-Work 0.158
    R-Free 0.182
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.5171
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4139
    R-Factor(R-Work) 0.2433
    R-Factor(R-Free) 0.2844
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5171
    Shell Resolution(Low) 1.5349
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4197
    R-Factor(R-Work) 0.2135
    R-Factor(R-Free) 0.259
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5349
    Shell Resolution(Low) 1.5536
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4255
    R-Factor(R-Work) 0.2091
    R-Factor(R-Free) 0.239
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5536
    Shell Resolution(Low) 1.5733
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4309
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.2313
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5733
    Shell Resolution(Low) 1.594
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4278
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2262
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.594
    Shell Resolution(Low) 1.6158
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4362
    R-Factor(R-Work) 0.1878
    R-Factor(R-Free) 0.2139
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6158
    Shell Resolution(Low) 1.6389
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4335
    R-Factor(R-Work) 0.1819
    R-Factor(R-Free) 0.231
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6389
    Shell Resolution(Low) 1.6634
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4368
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.1958
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6634
    Shell Resolution(Low) 1.6894
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4409
    R-Factor(R-Work) 0.1695
    R-Factor(R-Free) 0.2142
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6894
    Shell Resolution(Low) 1.7171
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4339
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7171
    Shell Resolution(Low) 1.7467
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4439
    R-Factor(R-Work) 0.1648
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7467
    Shell Resolution(Low) 1.7784
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4357
    R-Factor(R-Work) 0.1632
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7784
    Shell Resolution(Low) 1.8126
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4406
    R-Factor(R-Work) 0.1504
    R-Factor(R-Free) 0.1857
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8126
    Shell Resolution(Low) 1.8496
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4438
    R-Factor(R-Work) 0.1502
    R-Factor(R-Free) 0.1718
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8496
    Shell Resolution(Low) 1.8899
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4381
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.157
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8899
    Shell Resolution(Low) 1.9338
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4452
    R-Factor(R-Work) 0.1574
    R-Factor(R-Free) 0.1663
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9338
    Shell Resolution(Low) 1.9822
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4428
    R-Factor(R-Work) 0.1515
    R-Factor(R-Free) 0.1681
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9822
    Shell Resolution(Low) 2.0358
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4416
    R-Factor(R-Work) 0.1515
    R-Factor(R-Free) 0.1554
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0358
    Shell Resolution(Low) 2.0957
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4415
    R-Factor(R-Work) 0.1561
    R-Factor(R-Free) 0.1752
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0957
    Shell Resolution(Low) 2.1633
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4448
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.1934
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1633
    Shell Resolution(Low) 2.2406
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4482
    R-Factor(R-Work) 0.1581
    R-Factor(R-Free) 0.1849
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2406
    Shell Resolution(Low) 2.3303
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4425
    R-Factor(R-Work) 0.1562
    R-Factor(R-Free) 0.1665
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3303
    Shell Resolution(Low) 2.4364
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4468
    R-Factor(R-Work) 0.1462
    R-Factor(R-Free) 0.163
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4364
    Shell Resolution(Low) 2.5648
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4478
    R-Factor(R-Work) 0.1532
    R-Factor(R-Free) 0.1754
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5648
    Shell Resolution(Low) 2.7255
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4506
    R-Factor(R-Work) 0.1605
    R-Factor(R-Free) 0.1737
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7255
    Shell Resolution(Low) 2.9359
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4495
    R-Factor(R-Work) 0.1527
    R-Factor(R-Free) 0.1778
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9359
    Shell Resolution(Low) 3.2313
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4502
    R-Factor(R-Work) 0.1516
    R-Factor(R-Free) 0.1786
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2313
    Shell Resolution(Low) 3.6986
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4488
    R-Factor(R-Work) 0.1475
    R-Factor(R-Free) 0.1756
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6986
    Shell Resolution(Low) 4.659
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 4545
    R-Factor(R-Work) 0.1376
    R-Factor(R-Free) 0.1735
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.659
    Shell Resolution(Low) 43.425
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4544
    R-Factor(R-Work) 0.1649
    R-Factor(R-Free) 0.1708
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.075
    f_dihedral_angle_d 11.24
    f_angle_d 1.102
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6128
    Nucleic Acid Atoms 0
    Heterogen Atoms 16
    Solvent Atoms 1145
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser version: 2.4.0
    data reduction Xscale