POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4B2L
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.2
    Details 10-15% PEG-1000, 50 MM NAKPHOSPHATE PH 6.2
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 37.62 α = 90
    b = 78.77 β = 118.06
    c = 39.63 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Collection Date 2008-12-10
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04
    Wavelength 0.972800
    Site DIAMOND
    Beamline I04
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.5
    Resolution(Low) 32.09
    Number Reflections(Observed) 31779
    Percent Possible(Observed) 96.7
    R Merge I(Observed) 0.04
    B(Isotropic) From Wilson Plot 23.63
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.59
    Percent Possible(All) 94.6
    R Merge I(Observed) 0.47
    Mean I Over Sigma(Observed) 3.78
    Redundancy 3.78
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 39.31
    Cut-off Sigma(F) 2.0
    Number of Reflections(Observed) 31773
    Number of Reflections(R-Free) 1636
    Percent Reflections(Observed) 97.07
    R-Factor(Observed) 0.1881
    R-Work 0.1862
    R-Free 0.223
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 0.8674
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 2.8925
    Anisotropic B[2][2] -0.233
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.6344
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4994
    Shell Resolution(Low) 1.5435
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2398
    R-Factor(R-Work) 0.2564
    R-Factor(R-Free) 0.2989
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5435
    Shell Resolution(Low) 1.5933
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2466
    R-Factor(R-Work) 0.2397
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5933
    Shell Resolution(Low) 1.6503
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2497
    R-Factor(R-Work) 0.2276
    R-Factor(R-Free) 0.2645
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6503
    Shell Resolution(Low) 1.7163
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2491
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7163
    Shell Resolution(Low) 1.7944
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2520
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.244
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7944
    Shell Resolution(Low) 1.889
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2491
    R-Factor(R-Work) 0.2018
    R-Factor(R-Free) 0.2499
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.889
    Shell Resolution(Low) 2.0074
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2535
    R-Factor(R-Work) 0.1955
    R-Factor(R-Free) 0.2338
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0074
    Shell Resolution(Low) 2.1623
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2481
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2405
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1623
    Shell Resolution(Low) 2.3799
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2574
    R-Factor(R-Work) 0.1837
    R-Factor(R-Free) 0.2312
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3799
    Shell Resolution(Low) 2.7241
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2536
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.2051
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7241
    Shell Resolution(Low) 3.4315
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.1751
    R-Factor(R-Free) 0.1985
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4315
    Shell Resolution(Low) 32.097
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2585
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1883
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.144
    f_dihedral_angle_d 17.008
    f_angle_d 1.545
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1714
    Nucleic Acid Atoms 0
    Heterogen Atoms 21
    Solvent Atoms 279
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution AMORE
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building AMORE