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X-RAY DIFFRACTION
Materials and Methods page
4E05
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.0
    Details 100 mM HEPES, pH 7.5, 1.4 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 120.18 α = 90
    b = 120.18 β = 90
    c = 77.81 γ = 120
     
    Space Group
    Space Group Name:    P 31 1 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-10-29
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.9792
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.3
    Resolution(Low) 104.08
    Number Reflections(All) 28423
    Number Reflections(Observed) 28423
    Percent Possible(Observed) 99.8
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 2.304
    Resolution(Low) 2.43
    Percent Possible(All) 99.0
    R Merge I(Observed) 0.683
    Mean I Over Sigma(Observed) 1.1
    R-Sym I(Observed) 0.683
    Redundancy 4.1
    Number Unique Reflections(All) 4113
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.304
    Resolution(Low) 32.658
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 28423
    Number of Reflections(Observed) 28396
    Number of Reflections(R-Free) 1438
    Percent Reflections(Observed) 99.74
    R-Factor(Observed) 0.1709
    R-Work 0.1693
    R-Free 0.2014
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 63.1407
    Anisotropic B[1][1] -12.4073
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -12.4073
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 24.8146
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.304
    Shell Resolution(Low) 2.3866
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.3174
    R-Factor(R-Free) 0.3479
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3866
    Shell Resolution(Low) 2.4821
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.2989
    R-Factor(R-Free) 0.3367
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4821
    Shell Resolution(Low) 2.5951
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.2563
    R-Factor(R-Free) 0.3075
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5951
    Shell Resolution(Low) 2.7318
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.2415
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7318
    Shell Resolution(Low) 2.9029
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9029
    Shell Resolution(Low) 3.1268
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.1855
    R-Factor(R-Free) 0.1976
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1268
    Shell Resolution(Low) 3.4412
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2296
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4412
    Shell Resolution(Low) 3.9384
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.1486
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9384
    Shell Resolution(Low) 4.9592
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.1249
    R-Factor(R-Free) 0.1474
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9592
    Shell Resolution(Low) 32.661
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2760
    R-Factor(R-Work) 0.1599
    R-Factor(R-Free) 0.1779
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.093
    f_plane_restr 0.004
    f_chiral_restr 0.073
    f_angle_d 1.059
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2509
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 87
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 3.3.16