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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DMZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 298.0
    Details 11.5% PEG 8000, 0.1M Tris-HCl, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.51 α = 90
    b = 113.35 β = 90
    c = 61.85 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2011-06-16
     
    Diffraction Radiation
    Monochromator Si 111 channel
    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) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(Observed) 36951
    Percent Possible(Observed) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.102
    Resolution(Low) 47.728
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 36980
    Number of Reflections(Observed) 36951
    Number of Reflections(R-Free) 2000
    Percent Reflections(Observed) 99.92
    R-Factor(Observed) 0.1979
    R-Work 0.1956
    R-Free 0.2378
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 5.5518
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -8.0278
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.476
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.102
    Shell Resolution(Low) 2.1544
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2476
    R-Factor(R-Work) 0.2463
    R-Factor(R-Free) 0.2995
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1544
    Shell Resolution(Low) 2.2127
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2458
    R-Factor(R-Work) 0.2275
    R-Factor(R-Free) 0.3228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2127
    Shell Resolution(Low) 2.2778
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2422
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2778
    Shell Resolution(Low) 2.3513
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2469
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.2739
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3513
    Shell Resolution(Low) 2.4353
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2459
    R-Factor(R-Work) 0.2121
    R-Factor(R-Free) 0.2628
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4353
    Shell Resolution(Low) 2.5328
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2492
    R-Factor(R-Work) 0.2162
    R-Factor(R-Free) 0.2972
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5328
    Shell Resolution(Low) 2.6481
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2452
    R-Factor(R-Work) 0.2163
    R-Factor(R-Free) 0.2878
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6481
    Shell Resolution(Low) 2.7877
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2487
    R-Factor(R-Work) 0.2192
    R-Factor(R-Free) 0.2585
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7877
    Shell Resolution(Low) 2.9623
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2492
    R-Factor(R-Work) 0.2269
    R-Factor(R-Free) 0.3406
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9623
    Shell Resolution(Low) 3.191
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2484
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.3016
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.191
    Shell Resolution(Low) 3.5121
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2507
    R-Factor(R-Work) 0.199
    R-Factor(R-Free) 0.2381
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5121
    Shell Resolution(Low) 4.02
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2531
    R-Factor(R-Work) 0.1717
    R-Factor(R-Free) 0.2254
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.02
    Shell Resolution(Low) 5.0639
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.1509
    R-Factor(R-Free) 0.1682
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0639
    Shell Resolution(Low) 47.74
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.2083
    R-Factor(R-Free) 0.2131
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.061
    f_dihedral_angle_d 13.123
    f_angle_d 0.993
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4175
    Nucleic Acid Atoms 0
    Heterogen Atoms 40
    Solvent Atoms 129
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building SOLVE
    data collection HKL-2000