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X-RAY DIFFRACTION
Materials and Methods page
3RGD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.0
    Details 7 mg/mL frog M ferritin solution at pH 7.5 with TrisHCl. Precipitant: 2.1M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 210.74 α = 90
    b = 210.74 β = 90
    c = 322.04 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2010-12-10
     
    Diffraction Radiation
    Monochromator channel cut Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength List 1.740
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.89
    Resolution(Low) 50.01
    Number Reflections(All) 184115
    Number Reflections(Observed) 184115
    Percent Possible(Observed) 99.8
    B(Isotropic) From Wilson Plot 43.26
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 2.89
    Resolution(Low) 3.05
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.182
    Mean I Over Sigma(Observed) 3.8
    Redundancy 5.6
    Number Unique Reflections(All) 26736
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.89
    Resolution(Low) 48.537
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 184062
    Number of Reflections(R-Free) 9239
    Percent Reflections(Observed) 99.72
    R-Factor(Observed) 0.1751
    R-Work 0.1722
    R-Free 0.2286
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 0.0921
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0921
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.1841
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.89
    Shell Resolution(Low) 2.9933
    Number of Reflections(R-Free) 920
    Number of Reflections(R-Work) 17319
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.2915
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9933
    Shell Resolution(Low) 3.1131
    Number of Reflections(R-Free) 950
    Number of Reflections(R-Work) 17329
    R-Factor(R-Work) 0.2095
    R-Factor(R-Free) 0.2984
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1131
    Shell Resolution(Low) 3.2548
    Number of Reflections(R-Free) 883
    Number of Reflections(R-Work) 17370
    R-Factor(R-Work) 0.2066
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2548
    Shell Resolution(Low) 3.4263
    Number of Reflections(R-Free) 926
    Number of Reflections(R-Work) 17408
    R-Factor(R-Work) 0.1894
    R-Factor(R-Free) 0.2608
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4263
    Shell Resolution(Low) 3.6409
    Number of Reflections(R-Free) 934
    Number of Reflections(R-Work) 17429
    R-Factor(R-Work) 0.179
    R-Factor(R-Free) 0.2399
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6409
    Shell Resolution(Low) 3.9219
    Number of Reflections(R-Free) 936
    Number of Reflections(R-Work) 17463
    R-Factor(R-Work) 0.1635
    R-Factor(R-Free) 0.2189
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9219
    Shell Resolution(Low) 4.3164
    Number of Reflections(R-Free) 908
    Number of Reflections(R-Work) 17523
    R-Factor(R-Work) 0.1504
    R-Factor(R-Free) 0.2005
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3164
    Shell Resolution(Low) 4.9404
    Number of Reflections(R-Free) 877
    Number of Reflections(R-Work) 17503
    R-Factor(R-Work) 0.1473
    R-Factor(R-Free) 0.1961
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9404
    Shell Resolution(Low) 6.2224
    Number of Reflections(R-Free) 933
    Number of Reflections(R-Work) 17642
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2224
    Shell Resolution(Low) 48.5441
    Number of Reflections(R-Free) 972
    Number of Reflections(R-Work) 17837
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.1929
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.075
    f_dihedral_angle_d 17.648
    f_angle_d 1.097
    f_bond_d 0.008
     
    Coordinate Error
    Luzzati ESD(Observed) 0.39
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 33960
    Nucleic Acid Atoms 0
    Heterogen Atoms 62
    Solvent Atoms 919
     
     
  •   Software and Computing Hide
    Computing
    Data Collection rotation 0.1 slices
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building MOLREP
    data collection rotation version: 0.1 slices