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An Information Portal to 107049 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IJ8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 7.5
    Temperature 291.0
    Details 1.2 M sodium citrate, 0.1 M HEPES, 10-fold excess SAM, pH 7.5, VAPOR DIFFUSION, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 101.44 α = 90
    b = 101.44 β = 90
    c = 140.8 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-300
    Collection Date 2012-01-25
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.97949
    Site CLSI
    Beamline 08ID-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2
    Resolution(Low) 87.85
    Number Reflections(All) 29619
    Number Reflections(Observed) 29619
    Percent Possible(Observed) 100.0
    Redundancy 21.6
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.11
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.942
    Mean I Over Sigma(Observed) 0.8
    R-Sym I(Observed) 0.942
    Redundancy 22.0
    Number Unique Reflections(All) 4231
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 43.96
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 29561
    Number of Reflections(R-Free) 1516
    Percent Reflections(Observed) 99.97
    R-Factor(Observed) 0.1769
    R-Work 0.1757
    R-Free 0.1985
    R-Free Selection Details THIN SHELLS (SFTOOLS)
     
    Temperature Factor Modeling
    Mean Isotropic B Value 37.7619
    Anisotropic B[1][1] -0.14
    Anisotropic B[1][2] -0.14
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.14
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.44
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.052
    Number of Reflections(R-Free) 2
    Number of Reflections(R-Work) 2116
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.321
    Percent Reflections(Observed) 99.95
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_mcangle_it 2.38
    r_mcbond_other 1.645
    r_bond_refined_d 0.015
    r_bond_other_d 0.002
    r_angle_refined_deg 1.481
    r_angle_other_deg 0.72
    r_dihedral_angle_1_deg 6.144
    r_dihedral_angle_2_deg 30.14
    r_dihedral_angle_3_deg 11.84
    r_dihedral_angle_4_deg 18.086
    r_chiral_restr 0.086
    r_gen_planes_refined 0.005
    r_gen_planes_other 0.001
    r_mcbond_it 1.645
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2440
    Nucleic Acid Atoms 0
    Heterogen Atoms 76
    Solvent Atoms 130
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) xds
    Data Reduction (data scaling) SCALA
    Structure Solution phaser
    Structure Refinement REFMAC 5.7.0032
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.7.0032
    molecular replacement Phaser
    data reduction SCALA version: 3.3.20