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X-RAY DIFFRACTION
Materials and Methods page
4LF7
  •   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 = 402.45 α = 90
    b = 402.45 β = 90
    c = 176.92 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) 3.15
    Resolution(Low) 35
    Number Reflections(All) 243896
    Number Reflections(Observed) 243896
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.078
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 3.1484
    Resolution(Low) 3.26
    Percent Possible(All) 99.1
    R Merge I(Observed) 0.677
    Redundancy 3.3
    Number Unique Reflections(All) 24313
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.1484
    Resolution(Low) 34.615
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 243798
    Number of Reflections(Observed) 243798
    Number of Reflections(R-Free) 12361
    Percent Reflections(Observed) 98.24
    R-Factor(All) 0.1701
    R-Factor(Observed) 0.1701
    R-Work 0.1682
    R-Free 0.2054
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 105.725
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1484
    Shell Resolution(Low) 3.1841
    Number of Reflections(R-Free) 454
    Number of Reflections(R-Work) 7625
    R-Factor(R-Work) 0.3005
    R-Factor(R-Free) 0.3471
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1841
    Shell Resolution(Low) 3.2216
    Number of Reflections(R-Free) 428
    Number of Reflections(R-Work) 7660
    R-Factor(R-Work) 0.2854
    R-Factor(R-Free) 0.3134
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2216
    Shell Resolution(Low) 3.2608
    Number of Reflections(R-Free) 411
    Number of Reflections(R-Work) 7684
    R-Factor(R-Work) 0.2654
    R-Factor(R-Free) 0.2934
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2608
    Shell Resolution(Low) 3.3021
    Number of Reflections(R-Free) 431
    Number of Reflections(R-Work) 7689
    R-Factor(R-Work) 0.2588
    R-Factor(R-Free) 0.298
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3021
    Shell Resolution(Low) 3.3455
    Number of Reflections(R-Free) 415
    Number of Reflections(R-Work) 7717
    R-Factor(R-Work) 0.2416
    R-Factor(R-Free) 0.2601
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3455
    Shell Resolution(Low) 3.3913
    Number of Reflections(R-Free) 399
    Number of Reflections(R-Work) 7753
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.2709
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3913
    Shell Resolution(Low) 3.4397
    Number of Reflections(R-Free) 423
    Number of Reflections(R-Work) 7711
    R-Factor(R-Work) 0.223
    R-Factor(R-Free) 0.2595
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4397
    Shell Resolution(Low) 3.491
    Number of Reflections(R-Free) 438
    Number of Reflections(R-Work) 7694
    R-Factor(R-Work) 0.2186
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.491
    Shell Resolution(Low) 3.5455
    Number of Reflections(R-Free) 422
    Number of Reflections(R-Work) 7697
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.2422
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5455
    Shell Resolution(Low) 3.6036
    Number of Reflections(R-Free) 439
    Number of Reflections(R-Work) 7716
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2189
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6036
    Shell Resolution(Low) 3.6656
    Number of Reflections(R-Free) 397
    Number of Reflections(R-Work) 7760
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.217
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6656
    Shell Resolution(Low) 3.7322
    Number of Reflections(R-Free) 453
    Number of Reflections(R-Work) 7669
    R-Factor(R-Work) 0.1765
    R-Factor(R-Free) 0.2047
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7322
    Shell Resolution(Low) 3.8039
    Number of Reflections(R-Free) 403
    Number of Reflections(R-Work) 7737
    R-Factor(R-Work) 0.1661
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8039
    Shell Resolution(Low) 3.8815
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7775
    R-Factor(R-Work) 0.1588
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8815
    Shell Resolution(Low) 3.9657
    Number of Reflections(R-Free) 412
    Number of Reflections(R-Work) 7770
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9657
    Shell Resolution(Low) 4.0578
    Number of Reflections(R-Free) 418
    Number of Reflections(R-Work) 7746
    R-Factor(R-Work) 0.1508
    R-Factor(R-Free) 0.184
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0578
    Shell Resolution(Low) 4.1592
    Number of Reflections(R-Free) 424
    Number of Reflections(R-Work) 7730
    R-Factor(R-Work) 0.1452
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1592
    Shell Resolution(Low) 4.2714
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7786
    R-Factor(R-Work) 0.1396
    R-Factor(R-Free) 0.1869
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2714
    Shell Resolution(Low) 4.3969
    Number of Reflections(R-Free) 437
    Number of Reflections(R-Work) 7743
    R-Factor(R-Work) 0.1399
    R-Factor(R-Free) 0.1877
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3969
    Shell Resolution(Low) 4.5385
    Number of Reflections(R-Free) 431
    Number of Reflections(R-Work) 7734
    R-Factor(R-Work) 0.1367
    R-Factor(R-Free) 0.1677
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5385
    Shell Resolution(Low) 4.7003
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 7806
    R-Factor(R-Work) 0.1354
    R-Factor(R-Free) 0.1781
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7003
    Shell Resolution(Low) 4.888
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 7829
    R-Factor(R-Work) 0.1346
    R-Factor(R-Free) 0.1723
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.888
    Shell Resolution(Low) 5.1098
    Number of Reflections(R-Free) 427
    Number of Reflections(R-Work) 7737
    R-Factor(R-Work) 0.1282
    R-Factor(R-Free) 0.173
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1098
    Shell Resolution(Low) 5.3783
    Number of Reflections(R-Free) 391
    Number of Reflections(R-Work) 7769
    R-Factor(R-Work) 0.1307
    R-Factor(R-Free) 0.1717
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3783
    Shell Resolution(Low) 5.7139
    Number of Reflections(R-Free) 411
    Number of Reflections(R-Work) 7756
    R-Factor(R-Work) 0.1335
    R-Factor(R-Free) 0.1828
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7139
    Shell Resolution(Low) 6.1528
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 7759
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.1724
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1528
    Shell Resolution(Low) 6.7678
    Number of Reflections(R-Free) 402
    Number of Reflections(R-Work) 7740
    R-Factor(R-Work) 0.1421
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7678
    Shell Resolution(Low) 7.7375
    Number of Reflections(R-Free) 390
    Number of Reflections(R-Work) 7687
    R-Factor(R-Work) 0.1496
    R-Factor(R-Free) 0.1805
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7375
    Shell Resolution(Low) 9.7127
    Number of Reflections(R-Free) 413
    Number of Reflections(R-Work) 7578
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.1988
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.7127
    Shell Resolution(Low) 34.6167
    Number of Reflections(R-Free) 377
    Number of Reflections(R-Work) 7380
    R-Factor(R-Work) 0.218
    R-Factor(R-Free) 0.243
    Percent Reflections(Observed) 88.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.596
    f_plane_restr 0.004
    f_chiral_restr 0.049
    f_angle_d 0.816
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19134
    Nucleic Acid Atoms 32460
    Heterogen Atoms 602
    Solvent Atoms 24
     
     
  •   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