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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2YNF
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Details 100MM HEPES PH7.5, 10MM SPERMIDINE, 1.1M SODIUM POTASSIUM TARTRATE
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 119.58 α = 90
    b = 154.51 β = 90
    c = 157.03 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details BERYLLIUM LENSES
    Collection Date 2008-10-03
     
    Diffraction Radiation
    Monochromator DIAMOND LAUE MONOCHROMATORS SUPPLIED BY JJ X-RAY
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength 0.97872
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.35
    Resolution(Low) 50
    Number Reflections(Observed) 59250
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.06
    Redundancy 5.3
     
    High Resolution Shell Details
    Resolution(High) 2.35
    Resolution(Low) 2.39
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.45
    Mean I Over Sigma(Observed) 4.15
    Redundancy 5.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.36
    Resolution(Low) 47.57
    Number of Reflections(Observed) 57009
    Number of Reflections(R-Free) 1783
    Percent Reflections(Observed) 98.41
    R-Factor(Observed) 0.1984
    R-Work 0.19722
    R-Free 0.23631
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.099
    Anisotropic B[1][1] -0.27
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.31
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.364
    Shell Resolution(Low) 2.425
    Number of Reflections(R-Free) 105
    Number of Reflections(R-Work) 3302
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.312
    Percent Reflections(Observed) 80.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.006
    r_chiral_restr 0.072
    r_dihedral_angle_4_deg 19.948
    r_dihedral_angle_3_deg 15.108
    r_dihedral_angle_2_deg 37.772
    r_dihedral_angle_1_deg 5.924
    r_angle_other_deg 0.85
    r_angle_refined_deg 1.354
    r_bond_other_d 0.001
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7728
    Nucleic Acid Atoms 0
    Heterogen Atoms 42
    Solvent Atoms 434
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building PHASER