POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4M30
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 70% (v/v) MPD in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81.1 α = 90
    b = 81.1 β = 90
    c = 223.96 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Details mirror
    Collection Date 2006-03-26
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 1.0
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.5
    Resolution(Low) 30
    Number Reflections(All) 28418
    Number Reflections(Observed) 28418
    Percent Possible(Observed) 93.2
    R Merge I(Observed) 0.072
    B(Isotropic) From Wilson Plot 74.45
    Redundancy 6.3
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.59
    Percent Possible(All) 66.8
    R Merge I(Observed) 0.298
    Mean I Over Sigma(Observed) 2.22
    Redundancy 2.1
    Number Unique Reflections(All) 1993
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.501
    Resolution(Low) 29.116
    Cut-off Sigma(F) 1.49
    Number of Reflections(all) 30431
    Number of Reflections(Observed) 28395
    Number of Reflections(R-Free) 988
    Percent Reflections(Observed) 93.31
    R-Factor(Observed) 0.2001
    R-Work 0.1979
    R-Free 0.2607
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 80.2303
    Anisotropic B[1][1] -0.1766
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.1766
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.3532
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5006
    Shell Resolution(Low) 2.6324
    Number of Reflections(Observed) 3050
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 3050
    R-Factor(R-Work) 0.2707
    R-Factor(R-Free) 0.3307
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6324
    Shell Resolution(Low) 2.7972
    Number of Reflections(Observed) 4045
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 4045
    R-Factor(R-Work) 0.2667
    R-Factor(R-Free) 0.315
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7972
    Shell Resolution(Low) 3.0129
    Number of Reflections(Observed) 4099
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 4099
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.328
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0129
    Shell Resolution(Low) 3.3158
    Number of Reflections(Observed) 4123
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 4123
    R-Factor(R-Work) 0.2194
    R-Factor(R-Free) 0.2956
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3158
    Shell Resolution(Low) 3.7947
    Number of Reflections(Observed) 4159
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 4159
    R-Factor(R-Work) 0.2026
    R-Factor(R-Free) 0.2685
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7947
    Shell Resolution(Low) 4.7775
    Number of Reflections(Observed) 4011
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 4011
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.2458
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7775
    Shell Resolution(Low) 29.1181
    Number of Reflections(Observed) 3920
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3920
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2322
    Percent Reflections(Observed) 89.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.275
    f_plane_restr 0.004
    f_chiral_restr 0.069
    f_angle_d 1.052
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3659
    Nucleic Acid Atoms 1152
    Heterogen Atoms 63
    Solvent Atoms 70
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SERGUI
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK