POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IRE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 3.9
    Temperature 277.0
    Details 10-12% PEG 4000, 225 mM ammonium sulfate, 50 mM sodium acetate buffer (pH 3.9 - 4.1), VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 182.03 α = 90
    b = 133.62 β = 102.57
    c = 161.43 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 DECTRIS PILATUS 6M
    Details K-B focusing mirrors
    Collection Date 2011-03-25
     
    Diffraction Radiation
    Monochromator Liquid nitrogen-cooled double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 0.9795
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.19
    Resolution(Low) 30
    Number Reflections(All) 63002
    Number Reflections(Observed) 61417
    Percent Possible(Observed) 97.5
    R Merge I(Observed) 0.068
    B(Isotropic) From Wilson Plot 88.969
     
    High Resolution Shell Details
    Resolution(High) 3.19
    Resolution(Low) 3.38
    Percent Possible(All) 92.9
    R Merge I(Observed) 0.707
    Mean I Over Sigma(Observed) 1.83
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.19
    Resolution(Low) 29.857
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 61291
    Number of Reflections(R-Free) 999
    Percent Reflections(Observed) 97.54
    R-Factor(Observed) 0.2045
    R-Work 0.2039
    R-Free 0.243
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 88.5796
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1904
    Shell Resolution(Low) 3.3584
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 8122
    R-Factor(R-Work) 0.3038
    R-Factor(R-Free) 0.3157
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3584
    Shell Resolution(Low) 3.5685
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 8533
    R-Factor(R-Work) 0.2393
    R-Factor(R-Free) 0.2566
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5685
    Shell Resolution(Low) 3.8435
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 8759
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2378
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8435
    Shell Resolution(Low) 4.2293
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 8714
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.2188
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2293
    Shell Resolution(Low) 4.8391
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 8625
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.1953
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8391
    Shell Resolution(Low) 6.0882
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 8768
    R-Factor(R-Work) 0.2015
    R-Factor(R-Free) 0.1987
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0882
    Shell Resolution(Low) 29.858
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 8771
    R-Factor(R-Work) 0.2403
    R-Factor(R-Free) 0.299
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.494
    f_plane_restr 0.008
    f_chiral_restr 0.08
    f_angle_d 1.3
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12661
    Nucleic Acid Atoms 0
    Heterogen Atoms 698
    Solvent Atoms 56
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BlueIce
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale