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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JBK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 289.0
    Details 0.2M calcium acetate, 0.1M Tris-HCl, 20%(w/v) polyethylene glycol 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 106.3 α = 90
    b = 109.94 β = 120.03
    c = 106.14 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-01-12
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.1
    Wavelength List 0.98
    Site ALS
    Beamline 5.0.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.96
    Resolution(Low) 50
    Number Reflections(All) 22039
    Number Reflections(Observed) 21825
    Percent Possible(Observed) 99.0
    B(Isotropic) From Wilson Plot 57.95
     
    High Resolution Shell Details
    Resolution(High) 3.0
    Resolution(Low) 3.11
    Percent Possible(All) 99.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.963
    Resolution(Low) 47.173
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 22039
    Number of Reflections(Observed) 21825
    Number of Reflections(R-Free) 1990
    Percent Reflections(Observed) 99.03
    R-Factor(All) 0.2219
    R-Factor(Observed) 0.2234
    R-Work 0.2203
    R-Free 0.2532
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 77.3168
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9633
    Shell Resolution(Low) 3.0374
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1319
    R-Factor(R-Work) 0.3445
    R-Factor(R-Free) 0.3876
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0374
    Shell Resolution(Low) 3.1195
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1445
    R-Factor(R-Work) 0.2991
    R-Factor(R-Free) 0.355
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1195
    Shell Resolution(Low) 3.2113
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1412
    R-Factor(R-Work) 0.2753
    R-Factor(R-Free) 0.3732
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2113
    Shell Resolution(Low) 3.3149
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1374
    R-Factor(R-Work) 0.2723
    R-Factor(R-Free) 0.313
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3149
    Shell Resolution(Low) 3.4333
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1408
    R-Factor(R-Work) 0.2522
    R-Factor(R-Free) 0.3297
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4333
    Shell Resolution(Low) 3.5708
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1414
    R-Factor(R-Work) 0.2401
    R-Factor(R-Free) 0.2762
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5708
    Shell Resolution(Low) 3.7332
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1410
    R-Factor(R-Work) 0.2302
    R-Factor(R-Free) 0.2836
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7332
    Shell Resolution(Low) 3.9299
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1442
    R-Factor(R-Work) 0.2223
    R-Factor(R-Free) 0.295
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9299
    Shell Resolution(Low) 4.176
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1429
    R-Factor(R-Work) 0.2137
    R-Factor(R-Free) 0.2418
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.176
    Shell Resolution(Low) 4.4982
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1440
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2476
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4982
    Shell Resolution(Low) 4.9505
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1416
    R-Factor(R-Work) 0.1772
    R-Factor(R-Free) 0.1962
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9505
    Shell Resolution(Low) 5.6658
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1430
    R-Factor(R-Work) 0.1951
    R-Factor(R-Free) 0.2125
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6658
    Shell Resolution(Low) 7.1343
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1455
    R-Factor(R-Work) 0.214
    R-Factor(R-Free) 0.2362
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1343
    Shell Resolution(Low) 47.1794
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1441
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.1924
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.526
    f_plane_restr 0.005
    f_chiral_restr 0.088
    f_angle_d 1.315
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6087
    Nucleic Acid Atoms 1148
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHASES
    data collection HKL-2000