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X-RAY DIFFRACTION
Materials and Methods page
4L6J
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 289.0
    Details Mix complex 1:1 with solution containing 4% PEG 20000, 8% MPD, 0.2M KSCN, 0.1M Tris-HCl , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 211.53 α = 90
    b = 454.44 β = 90
    c = 620.87 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2012-08-08
     
    Diffraction Radiation
    Monochromator Si-111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.4
    Resolution(Low) 50
    Number Reflections(All) 810608
    Number Reflections(Observed) 810608
    Percent Possible(Observed) 100.0
     
    High Resolution Shell Details
    Resolution(High) 3.4
    Resolution(Low) 50.0
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.4
    Resolution(Low) 49.981
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 810608
    Number of Reflections(Observed) 810607
    Number of Reflections(R-Free) 16210
    Percent Reflections(Observed) 99.83
    R-Factor(Observed) 0.2321
    R-Work 0.2314
    R-Free 0.268
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 3.1655
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.2449
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0795
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4
    Shell Resolution(Low) 3.4386
    Number of Reflections(R-Free) 512
    Number of Reflections(R-Work) 25397
    R-Factor(R-Work) 0.3528
    R-Factor(R-Free) 0.3959
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4386
    Shell Resolution(Low) 3.4791
    Number of Reflections(R-Free) 539
    Number of Reflections(R-Work) 26334
    R-Factor(R-Work) 0.3386
    R-Factor(R-Free) 0.3584
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4791
    Shell Resolution(Low) 3.5215
    Number of Reflections(R-Free) 545
    Number of Reflections(R-Work) 26363
    R-Factor(R-Work) 0.3253
    R-Factor(R-Free) 0.3452
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5215
    Shell Resolution(Low) 3.5661
    Number of Reflections(R-Free) 539
    Number of Reflections(R-Work) 26291
    R-Factor(R-Work) 0.3298
    R-Factor(R-Free) 0.3712
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5661
    Shell Resolution(Low) 3.613
    Number of Reflections(R-Free) 534
    Number of Reflections(R-Work) 26367
    R-Factor(R-Work) 0.329
    R-Factor(R-Free) 0.3749
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.613
    Shell Resolution(Low) 3.6624
    Number of Reflections(R-Free) 545
    Number of Reflections(R-Work) 26339
    R-Factor(R-Work) 0.3322
    R-Factor(R-Free) 0.3576
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6624
    Shell Resolution(Low) 3.7148
    Number of Reflections(R-Free) 528
    Number of Reflections(R-Work) 26381
    R-Factor(R-Work) 0.3093
    R-Factor(R-Free) 0.331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7148
    Shell Resolution(Low) 3.7702
    Number of Reflections(R-Free) 536
    Number of Reflections(R-Work) 26344
    R-Factor(R-Work) 0.2852
    R-Factor(R-Free) 0.3232
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7702
    Shell Resolution(Low) 3.8291
    Number of Reflections(R-Free) 542
    Number of Reflections(R-Work) 26361
    R-Factor(R-Work) 0.2835
    R-Factor(R-Free) 0.3082
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8291
    Shell Resolution(Low) 3.8918
    Number of Reflections(R-Free) 544
    Number of Reflections(R-Work) 26335
    R-Factor(R-Work) 0.3099
    R-Factor(R-Free) 0.3462
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8918
    Shell Resolution(Low) 3.9589
    Number of Reflections(R-Free) 523
    Number of Reflections(R-Work) 26339
    R-Factor(R-Work) 0.2941
    R-Factor(R-Free) 0.3195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9589
    Shell Resolution(Low) 4.0309
    Number of Reflections(R-Free) 551
    Number of Reflections(R-Work) 26387
    R-Factor(R-Work) 0.2488
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0309
    Shell Resolution(Low) 4.1084
    Number of Reflections(R-Free) 530
    Number of Reflections(R-Work) 26449
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.3023
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1084
    Shell Resolution(Low) 4.1922
    Number of Reflections(R-Free) 547
    Number of Reflections(R-Work) 26374
    R-Factor(R-Work) 0.2344
    R-Factor(R-Free) 0.2751
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1922
    Shell Resolution(Low) 4.2833
    Number of Reflections(R-Free) 538
    Number of Reflections(R-Work) 26458
    R-Factor(R-Work) 0.2261
    R-Factor(R-Free) 0.2732
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2833
    Shell Resolution(Low) 4.3829
    Number of Reflections(R-Free) 533
    Number of Reflections(R-Work) 26419
    R-Factor(R-Work) 0.2165
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3829
    Shell Resolution(Low) 4.4924
    Number of Reflections(R-Free) 544
    Number of Reflections(R-Work) 26492
    R-Factor(R-Work) 0.2148
    R-Factor(R-Free) 0.2496
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4924
    Shell Resolution(Low) 4.6138
    Number of Reflections(R-Free) 543
    Number of Reflections(R-Work) 26433
    R-Factor(R-Work) 0.2081
    R-Factor(R-Free) 0.257
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6138
    Shell Resolution(Low) 4.7494
    Number of Reflections(R-Free) 538
    Number of Reflections(R-Work) 26491
    R-Factor(R-Work) 0.2065
    R-Factor(R-Free) 0.2745
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7494
    Shell Resolution(Low) 4.9026
    Number of Reflections(R-Free) 540
    Number of Reflections(R-Work) 26487
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2543
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9026
    Shell Resolution(Low) 5.0777
    Number of Reflections(R-Free) 541
    Number of Reflections(R-Work) 26466
    R-Factor(R-Work) 0.1912
    R-Factor(R-Free) 0.2303
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0777
    Shell Resolution(Low) 5.2808
    Number of Reflections(R-Free) 541
    Number of Reflections(R-Work) 26598
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.2244
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2808
    Shell Resolution(Low) 5.5208
    Number of Reflections(R-Free) 538
    Number of Reflections(R-Work) 26489
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.2165
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5208
    Shell Resolution(Low) 5.8115
    Number of Reflections(R-Free) 549
    Number of Reflections(R-Work) 26612
    R-Factor(R-Work) 0.1728
    R-Factor(R-Free) 0.2203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8115
    Shell Resolution(Low) 6.175
    Number of Reflections(R-Free) 539
    Number of Reflections(R-Work) 26621
    R-Factor(R-Work) 0.1763
    R-Factor(R-Free) 0.2171
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.175
    Shell Resolution(Low) 6.6507
    Number of Reflections(R-Free) 541
    Number of Reflections(R-Work) 26673
    R-Factor(R-Work) 0.1783
    R-Factor(R-Free) 0.2369
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6507
    Shell Resolution(Low) 7.3182
    Number of Reflections(R-Free) 547
    Number of Reflections(R-Work) 26752
    R-Factor(R-Work) 0.1709
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3182
    Shell Resolution(Low) 8.3728
    Number of Reflections(R-Free) 550
    Number of Reflections(R-Work) 26809
    R-Factor(R-Work) 0.1844
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.3728
    Shell Resolution(Low) 10.5327
    Number of Reflections(R-Free) 550
    Number of Reflections(R-Work) 26996
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2381
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.5327
    Shell Resolution(Low) 49.9867
    Number of Reflections(R-Free) 563
    Number of Reflections(R-Work) 27540
    R-Factor(R-Work) 0.2536
    R-Factor(R-Free) 0.2671
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.054
    f_dihedral_angle_d 18.973
    f_angle_d 0.613
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 26017
    Nucleic Acid Atoms 63546
    Heterogen Atoms 4393
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution CNS
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building CNS
    data collection CBASS