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X-RAY DIFFRACTION
Materials and Methods page
4H2H
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Temperature 298.0
    Details Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 10% glycerol, 50 mM MgCl2, 5 mM EDTA, 2 mM NiCl2; Reservoir (0.1 M HEPES:NaOH pH 7.5 70% (v/v) MPD); Soak 2 minutes in (Reservoir + 50 mM MgCl2, 200 mM 4-OH Proline Betaine ) Cryoprotection (Soaking solution), sitting drop vapor diffuction, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 91.04 α = 90
    b = 152.82 β = 105.2
    c = 113.03 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 CCD
    Type RAYONIX MX225HE
    Details MIRRORS
    Collection Date 2012-04-14
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 31-ID
    Wavelength 0.9793
    Site APS
    Beamline 31-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.7
    Resolution(Low) 109.07
    Number Reflections(Observed) 325934
    Percent Possible(Observed) 99.9
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.79
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.577
    Mean I Over Sigma(Observed) 1.3
    R-Sym I(Observed) 0.577
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 25.68
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 325787
    Number of Reflections(Observed) 325787
    Number of Reflections(R-Free) 16434
    Percent Reflections(Observed) 99.9
    R-Factor(Observed) 0.16
    R-Work 0.159
    R-Free 0.192
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.53
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.7193
    Number of Reflections(R-Free) 522
    Number of Reflections(R-Work) 10371
    R-Factor(R-Work) 0.2359
    R-Factor(R-Free) 0.2683
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7193
    Shell Resolution(Low) 1.7395
    Number of Reflections(R-Free) 568
    Number of Reflections(R-Work) 10272
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.269
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7395
    Shell Resolution(Low) 1.7607
    Number of Reflections(R-Free) 535
    Number of Reflections(R-Work) 10326
    R-Factor(R-Work) 0.2263
    R-Factor(R-Free) 0.2591
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7607
    Shell Resolution(Low) 1.783
    Number of Reflections(R-Free) 559
    Number of Reflections(R-Work) 10190
    R-Factor(R-Work) 0.2272
    R-Factor(R-Free) 0.2583
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.783
    Shell Resolution(Low) 1.8065
    Number of Reflections(R-Free) 573
    Number of Reflections(R-Work) 10257
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.2581
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8065
    Shell Resolution(Low) 1.8312
    Number of Reflections(R-Free) 558
    Number of Reflections(R-Work) 10341
    R-Factor(R-Work) 0.2059
    R-Factor(R-Free) 0.2387
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8312
    Shell Resolution(Low) 1.8574
    Number of Reflections(R-Free) 562
    Number of Reflections(R-Work) 10284
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8574
    Shell Resolution(Low) 1.8851
    Number of Reflections(R-Free) 541
    Number of Reflections(R-Work) 10284
    R-Factor(R-Work) 0.1848
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8851
    Shell Resolution(Low) 1.9145
    Number of Reflections(R-Free) 540
    Number of Reflections(R-Work) 10309
    R-Factor(R-Work) 0.1737
    R-Factor(R-Free) 0.2103
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9145
    Shell Resolution(Low) 1.9459
    Number of Reflections(R-Free) 555
    Number of Reflections(R-Work) 10285
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9459
    Shell Resolution(Low) 1.9795
    Number of Reflections(R-Free) 528
    Number of Reflections(R-Work) 10380
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.2218
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9795
    Shell Resolution(Low) 2.0154
    Number of Reflections(R-Free) 564
    Number of Reflections(R-Work) 10250
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.2127
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0154
    Shell Resolution(Low) 2.0542
    Number of Reflections(R-Free) 532
    Number of Reflections(R-Work) 10289
    R-Factor(R-Work) 0.1608
    R-Factor(R-Free) 0.2054
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0542
    Shell Resolution(Low) 2.0961
    Number of Reflections(R-Free) 529
    Number of Reflections(R-Work) 10303
    R-Factor(R-Work) 0.1502
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0961
    Shell Resolution(Low) 2.1417
    Number of Reflections(R-Free) 511
    Number of Reflections(R-Work) 10363
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1995
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1417
    Shell Resolution(Low) 2.1915
    Number of Reflections(R-Free) 546
    Number of Reflections(R-Work) 10272
    R-Factor(R-Work) 0.153
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1915
    Shell Resolution(Low) 2.2462
    Number of Reflections(R-Free) 569
    Number of Reflections(R-Work) 10313
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2462
    Shell Resolution(Low) 2.3069
    Number of Reflections(R-Free) 544
    Number of Reflections(R-Work) 10304
    R-Factor(R-Work) 0.1488
    R-Factor(R-Free) 0.193
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3069
    Shell Resolution(Low) 2.3748
    Number of Reflections(R-Free) 526
    Number of Reflections(R-Work) 10359
    R-Factor(R-Work) 0.1527
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3748
    Shell Resolution(Low) 2.4514
    Number of Reflections(R-Free) 530
    Number of Reflections(R-Work) 10325
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.1887
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4514
    Shell Resolution(Low) 2.5389
    Number of Reflections(R-Free) 545
    Number of Reflections(R-Work) 10338
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1934
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5389
    Shell Resolution(Low) 2.6404
    Number of Reflections(R-Free) 582
    Number of Reflections(R-Work) 10264
    R-Factor(R-Work) 0.1551
    R-Factor(R-Free) 0.1904
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6404
    Shell Resolution(Low) 2.7605
    Number of Reflections(R-Free) 539
    Number of Reflections(R-Work) 10372
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.1961
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7605
    Shell Resolution(Low) 2.9058
    Number of Reflections(R-Free) 563
    Number of Reflections(R-Work) 10300
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.191
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9058
    Shell Resolution(Low) 3.0876
    Number of Reflections(R-Free) 562
    Number of Reflections(R-Work) 10309
    R-Factor(R-Work) 0.1576
    R-Factor(R-Free) 0.2033
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0876
    Shell Resolution(Low) 3.3256
    Number of Reflections(R-Free) 578
    Number of Reflections(R-Work) 10310
    R-Factor(R-Work) 0.1423
    R-Factor(R-Free) 0.1648
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3256
    Shell Resolution(Low) 3.6594
    Number of Reflections(R-Free) 528
    Number of Reflections(R-Work) 10393
    R-Factor(R-Work) 0.1378
    R-Factor(R-Free) 0.1707
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6594
    Shell Resolution(Low) 4.1869
    Number of Reflections(R-Free) 535
    Number of Reflections(R-Work) 10373
    R-Factor(R-Work) 0.1257
    R-Factor(R-Free) 0.1476
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1869
    Shell Resolution(Low) 5.2676
    Number of Reflections(R-Free) 521
    Number of Reflections(R-Work) 10408
    R-Factor(R-Work) 0.1347
    R-Factor(R-Free) 0.1616
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2676
    Shell Resolution(Low) 25.6847
    Number of Reflections(R-Free) 589
    Number of Reflections(R-Work) 10209
    R-Factor(R-Work) 0.1737
    R-Factor(R-Free) 0.1974
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.074
    f_dihedral_angle_d 12.802
    f_angle_d 1.109
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22160
    Nucleic Acid Atoms 0
    Heterogen Atoms 183
    Solvent Atoms 2066
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHENIX
    Structure Refinement PHENIX (PHENIX.REFINE: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALA version: 3.3.16