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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4K98
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5
    Temperature 293.0
    Details 0.1 M NaAc, 10% MPD, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 85.38 α = 90
    b = 97.88 β = 90
    c = 133.46 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 200
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2013-02-21
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.9792
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.94
    Resolution(Low) 50
    Number Reflections(All) 41683
    Number Reflections(Observed) 41225
    Percent Possible(Observed) 98.9
     
    High Resolution Shell Details
    Resolution(High) 1.94
    Resolution(Low) 2.04
    Percent Possible(All) 93.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.94
    Resolution(Low) 39.453
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 41683
    Number of Reflections(Observed) 41225
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 98.82
    R-Factor(Observed) 0.1593
    R-Work 0.1572
    R-Free 0.1992
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.94
    Shell Resolution(Low) 1.988
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2441
    R-Factor(R-Work) 0.2913
    R-Factor(R-Free) 0.3341
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.988
    Shell Resolution(Low) 2.0417
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.2254
    R-Factor(R-Free) 0.2545
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0417
    Shell Resolution(Low) 2.1018
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2794
    R-Factor(R-Work) 0.1935
    R-Factor(R-Free) 0.2705
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1018
    Shell Resolution(Low) 2.1696
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2836
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.2423
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1696
    Shell Resolution(Low) 2.2472
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2784
    R-Factor(R-Work) 0.1665
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2472
    Shell Resolution(Low) 2.3371
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2813
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.206
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3371
    Shell Resolution(Low) 2.4435
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2825
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.2166
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4435
    Shell Resolution(Low) 2.5723
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2814
    R-Factor(R-Work) 0.1643
    R-Factor(R-Free) 0.2188
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5723
    Shell Resolution(Low) 2.7334
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2841
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.2305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7334
    Shell Resolution(Low) 2.9444
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2810
    R-Factor(R-Work) 0.1656
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9444
    Shell Resolution(Low) 3.2406
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2845
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.2044
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2406
    Shell Resolution(Low) 3.7092
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2873
    R-Factor(R-Work) 0.1409
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7092
    Shell Resolution(Low) 4.672
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2888
    R-Factor(R-Work) 0.1306
    R-Factor(R-Free) 0.1576
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.672
    Shell Resolution(Low) 39.4613
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2928
    R-Factor(R-Work) 0.1506
    R-Factor(R-Free) 0.1874
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.191
    f_dihedral_angle_d 21.132
    f_angle_d 2.183
    f_bond_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2924
    Nucleic Acid Atoms 592
    Heterogen Atoms 58
    Solvent Atoms 361
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHASER
    data collection ADSC version: Quantum