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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IHT
  •   Crystallization Hide
    Crystallization Experiments
    Method MICROBATCH UNDER OIL
    pH 6.5
    Temperature 288.0
    Details Equal volumes of precipitant, protein solution and DNA. Precipitant: Optimized index screen 79- 25 mM bis-tris, 25% PEG 3000, 50 mM ammonium acetate. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 58.96 α = 90
    b = 300.3 β = 90
    c = 46 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2009-04-10
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97934
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(Observed) 17712
    Percent Possible(Observed) 92.7
    R Merge I(Observed) 0.065
    B(Isotropic) From Wilson Plot 99.4
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 2.95
    Percent Possible(All) 92.9
    R Merge I(Observed) 0.503
    Redundancy 3.3
    Number Unique Reflections(All) 875
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.0
    Resolution(Low) 31.66
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 15998
    Number of Reflections(R-Free) 820
    Percent Reflections(Observed) 92.52
    R-Factor(Observed) 0.1877
    R-Work 0.1845
    R-Free 0.2452
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 95.0928
    Anisotropic B[1][1] 8.54
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.54
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0
    Shell Resolution(Low) 3.078
    Number of Reflections(R-Free) 61
    Number of Reflections(R-Work) 1039
    R-Factor(R-Work) 0.272
    R-Factor(R-Free) 0.374
    Percent Reflections(Observed) 96.32
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.006
    r_chiral_restr 0.069
    r_dihedral_angle_4_deg 16.114
    r_dihedral_angle_3_deg 17.601
    r_dihedral_angle_2_deg 33.475
    r_dihedral_angle_1_deg 5.289
    r_angle_other_deg 0.842
    r_angle_refined_deg 1.143
    r_bond_other_d 0.001
    r_bond_refined_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2872
    Nucleic Acid Atoms 2038
    Heterogen Atoms 0
    Solvent Atoms 3
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molecular Replacement
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.6.0117
    data reduction SCALEPACK
    data collection DENZO