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X-RAY DIFFRACTION
Materials and Methods page
4LF9
  •   Crystallization Hide
    Crystallization Experiments
    Method hanging drop
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, hanging drop, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402.04 α = 90
    b = 402.04 β = 90
    c = 176.39 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-11-07
     
    Diffraction Radiation
    Monochromator KOHZU HLD8-24
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.98
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.28
    Resolution(Low) 35
    Number Reflections(All) 216436
    Number Reflections(Observed) 216436
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.093
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 3.28
    Resolution(Low) 3.4
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.911
    Redundancy 4.0
    Number Unique Reflections(All) 21443
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.2811
    Resolution(Low) 34.475
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 216354
    Number of Reflections(Observed) 216354
    Number of Reflections(R-Free) 10916
    Percent Reflections(Observed) 99.06
    R-Factor(All) 0.1704
    R-Factor(Observed) 0.1704
    R-Work 0.1688
    R-Free 0.2012
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 117.537
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2811
    Shell Resolution(Low) 3.3183
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6623
    R-Factor(R-Work) 0.2825
    R-Factor(R-Free) 0.3113
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3183
    Shell Resolution(Low) 3.3573
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 6772
    R-Factor(R-Work) 0.2663
    R-Factor(R-Free) 0.2887
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3573
    Shell Resolution(Low) 3.3983
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 6800
    R-Factor(R-Work) 0.2525
    R-Factor(R-Free) 0.2817
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3983
    Shell Resolution(Low) 3.4412
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6829
    R-Factor(R-Work) 0.2455
    R-Factor(R-Free) 0.2721
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4412
    Shell Resolution(Low) 3.4865
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 6754
    R-Factor(R-Work) 0.241
    R-Factor(R-Free) 0.2694
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4865
    Shell Resolution(Low) 3.5342
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 6770
    R-Factor(R-Work) 0.2302
    R-Factor(R-Free) 0.2661
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5342
    Shell Resolution(Low) 3.5846
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 6808
    R-Factor(R-Work) 0.2186
    R-Factor(R-Free) 0.2388
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5846
    Shell Resolution(Low) 3.6381
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6807
    R-Factor(R-Work) 0.1988
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6381
    Shell Resolution(Low) 3.6949
    Number of Reflections(R-Free) 370
    Number of Reflections(R-Work) 6818
    R-Factor(R-Work) 0.1901
    R-Factor(R-Free) 0.2066
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6949
    Shell Resolution(Low) 3.7554
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 6807
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7554
    Shell Resolution(Low) 3.82
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 6863
    R-Factor(R-Work) 0.1738
    R-Factor(R-Free) 0.2128
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.82
    Shell Resolution(Low) 3.8894
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6832
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8894
    Shell Resolution(Low) 3.9641
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6820
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.2005
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9641
    Shell Resolution(Low) 4.0449
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6816
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.1837
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0449
    Shell Resolution(Low) 4.1327
    Number of Reflections(R-Free) 400
    Number of Reflections(R-Work) 6818
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1327
    Shell Resolution(Low) 4.2287
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6869
    R-Factor(R-Work) 0.1441
    R-Factor(R-Free) 0.1754
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2287
    Shell Resolution(Low) 4.3342
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6853
    R-Factor(R-Work) 0.1454
    R-Factor(R-Free) 0.1961
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3342
    Shell Resolution(Low) 4.4512
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 6850
    R-Factor(R-Work) 0.1453
    R-Factor(R-Free) 0.1863
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4512
    Shell Resolution(Low) 4.5819
    Number of Reflections(R-Free) 386
    Number of Reflections(R-Work) 6869
    R-Factor(R-Work) 0.1436
    R-Factor(R-Free) 0.1864
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5819
    Shell Resolution(Low) 4.7294
    Number of Reflections(R-Free) 334
    Number of Reflections(R-Work) 6897
    R-Factor(R-Work) 0.1433
    R-Factor(R-Free) 0.1868
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7294
    Shell Resolution(Low) 4.898
    Number of Reflections(R-Free) 343
    Number of Reflections(R-Work) 6943
    R-Factor(R-Work) 0.1425
    R-Factor(R-Free) 0.1826
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.898
    Shell Resolution(Low) 5.0935
    Number of Reflections(R-Free) 375
    Number of Reflections(R-Work) 6873
    R-Factor(R-Work) 0.1369
    R-Factor(R-Free) 0.1895
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0935
    Shell Resolution(Low) 5.3245
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6930
    R-Factor(R-Work) 0.1391
    R-Factor(R-Free) 0.1673
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3245
    Shell Resolution(Low) 5.6041
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 6899
    R-Factor(R-Work) 0.1369
    R-Factor(R-Free) 0.1884
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6041
    Shell Resolution(Low) 5.9536
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6954
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.1669
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9536
    Shell Resolution(Low) 6.4106
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6970
    R-Factor(R-Work) 0.1545
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4106
    Shell Resolution(Low) 7.0507
    Number of Reflections(R-Free) 367
    Number of Reflections(R-Work) 7017
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.1855
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0507
    Shell Resolution(Low) 8.0596
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6988
    R-Factor(R-Work) 0.151
    R-Factor(R-Free) 0.1777
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0596
    Shell Resolution(Low) 10.1115
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 6996
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.1904
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.1115
    Shell Resolution(Low) 34.4767
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 6593
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2313
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.836
    f_plane_restr 0.004
    f_chiral_restr 0.046
    f_angle_d 0.771
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19153
    Nucleic Acid Atoms 32504
    Heterogen Atoms 184
    Solvent Atoms 42
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: dev_1119)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO