POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4BAC
  •   Crystallization Hide
    Crystallization Experiments
    Details CRYSTALS WERE GROWN THROUGH REVERSE VAPOR DIFFUSION IN HANGING DROPS AT 23 C BY MIXING 1 UL IN-DNA COMPLEX SOLUTION (20 MM HEPES, PH 7.5, 500 MM NACL, 5 MM MGCL2, 2 MM TCEP AND 8% (W/V) GLYCEROL) WITH 1 UL RESERVOIR SOLUTION (50 MM NA CACODYLATE, PH 6.5, 100 MM MGCL2, 1 MM COCL3 AND 6% (V/V) ETHANOL).
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 160.62 α = 90
    b = 160.62 β = 90
    c = 125.09 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD (MAR225)
    Type MARRESEARCH
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTAL - SI (220)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength 1
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 3.26
    Resolution(Low) 30
    Number Reflections(Observed) 25740
    Percent Possible(Observed) 98.8
    B(Isotropic) From Wilson Plot 75.3
    Redundancy 6.3
     
    High Resolution Shell Details
    Resolution(High) 3.26
    Resolution(Low) 3.32
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 2.0
    R-Sym I(Observed) 0.62
    Redundancy 6.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.263
    Resolution(Low) 29.141
    Cut-off Sigma(F) 0.13
    Number of Reflections(Observed) 24101
    Number of Reflections(R-Free) 1223
    Percent Reflections(Observed) 92.66
    R-Factor(Observed) 0.1868
    R-Work 0.1847
    R-Free 0.2263
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 9.9139
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 9.9139
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -19.8278
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2626
    Shell Resolution(Low) 3.393
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2306
    R-Factor(R-Work) 0.2935
    R-Factor(R-Free) 0.3555
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.393
    Shell Resolution(Low) 3.5472
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 2365
    R-Factor(R-Work) 0.2427
    R-Factor(R-Free) 0.2809
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5472
    Shell Resolution(Low) 3.7339
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2447
    R-Factor(R-Work) 0.2149
    R-Factor(R-Free) 0.2817
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7339
    Shell Resolution(Low) 3.9673
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2477
    R-Factor(R-Work) 0.1991
    R-Factor(R-Free) 0.2672
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9673
    Shell Resolution(Low) 4.2727
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.1637
    R-Factor(R-Free) 0.1865
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2727
    Shell Resolution(Low) 4.7011
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1383
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7011
    Shell Resolution(Low) 5.3776
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.1477
    R-Factor(R-Free) 0.1771
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3776
    Shell Resolution(Low) 6.7613
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.1655
    R-Factor(R-Free) 0.1993
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7613
    Shell Resolution(Low) 29.1426
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2771
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.2089
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.073
    f_dihedral_angle_d 21.72
    f_angle_d 1.313
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4378
    Nucleic Acid Atoms 1305
    Heterogen Atoms 3
    Solvent Atoms 3
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building MOLREP