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X-RAY DIFFRACTION
Materials and Methods page
4H4O
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 277.0
    Details 20% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine-HCl, 50 mM HEPES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 225.45 α = 90
    b = 69.57 β = 106.21
    c = 104.4 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details Monochromator
    Collection Date 2012-06-13
     
    Diffraction Radiation
    Monochromator Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.5
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.9
    Resolution(Low) 41.72
    Number Reflections(All) 34778
    Number Reflections(Observed) 34778
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.072
    B(Isotropic) From Wilson Plot 79.02
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 2.95
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.596
    Mean I Over Sigma(Observed) 2.6
    R-Sym I(Observed) 0.47
    Redundancy 3.7
    Number Unique Reflections(All) 1693
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 41.722
    Cut-off Sigma(I) 1.89
    Cut-off Sigma(F) 1.89
    Number of Reflections(all) 35694
    Number of Reflections(Observed) 34760
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 99.75
    R-Factor(All) 0.2343
    R-Factor(Observed) 0.2324
    R-Work 0.2324
    R-Free 0.265
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 164.087
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8982
    Shell Resolution(Low) 2.9706
    Number of Reflections(Observed) 2252
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2252
    R-Factor(R-Work) 0.3317
    R-Factor(R-Free) 0.364
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9706
    Shell Resolution(Low) 3.0509
    Number of Reflections(Observed) 2339
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2339
    R-Factor(R-Work) 0.3176
    R-Factor(R-Free) 0.354
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0509
    Shell Resolution(Low) 3.1407
    Number of Reflections(Observed) 2334
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2334
    R-Factor(R-Work) 0.2984
    R-Factor(R-Free) 0.3737
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1407
    Shell Resolution(Low) 3.242
    Number of Reflections(Observed) 2294
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2294
    R-Factor(R-Work) 0.2726
    R-Factor(R-Free) 0.3666
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.242
    Shell Resolution(Low) 3.3578
    Number of Reflections(Observed) 2342
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2342
    R-Factor(R-Work) 0.2804
    R-Factor(R-Free) 0.2848
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3578
    Shell Resolution(Low) 3.4922
    Number of Reflections(Observed) 2354
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2354
    R-Factor(R-Work) 0.2611
    R-Factor(R-Free) 0.3116
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4922
    Shell Resolution(Low) 3.651
    Number of Reflections(Observed) 2329
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2329
    R-Factor(R-Work) 0.2636
    R-Factor(R-Free) 0.2941
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.651
    Shell Resolution(Low) 3.8434
    Number of Reflections(Observed) 2339
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2339
    R-Factor(R-Work) 0.2515
    R-Factor(R-Free) 0.2856
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8434
    Shell Resolution(Low) 4.084
    Number of Reflections(Observed) 2338
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2338
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.2912
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.084
    Shell Resolution(Low) 4.399
    Number of Reflections(Observed) 2339
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2339
    R-Factor(R-Work) 0.206
    R-Factor(R-Free) 0.2302
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.399
    Shell Resolution(Low) 4.8411
    Number of Reflections(Observed) 2349
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2349
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2396
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8411
    Shell Resolution(Low) 5.5403
    Number of Reflections(Observed) 2359
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2359
    R-Factor(R-Work) 0.2121
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5403
    Shell Resolution(Low) 6.9749
    Number of Reflections(Observed) 2393
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2393
    R-Factor(R-Work) 0.2424
    R-Factor(R-Free) 0.2629
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9749
    Shell Resolution(Low) 41.7264
    Number of Reflections(Observed) 2400
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2400
    R-Factor(R-Work) 0.2004
    R-Factor(R-Free) 0.2094
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.534
    f_plane_restr 0.004
    f_chiral_restr 0.065
    f_angle_d 0.876
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8003
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 49
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL