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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DZW
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 291.0
    Details 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 57.97 α = 90
    b = 57.97 β = 90
    c = 395.03 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 ADSC QUANTUM 210
    Collection Date 2011-11-11
     
    Diffraction Radiation
    Monochromator Si(111) channel cut
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X6A
    Wavelength List 0.979
    Site NSLS
    Beamline X6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.05
    Resolution(Low) 65.84
    Number Reflections(Observed) 7407
    Percent Possible(Observed) 87.8
    R Merge I(Observed) 0.069
    Redundancy 10.8
     
    High Resolution Shell Details
    Resolution(High) 3.05
    Resolution(Low) 3.1
    Percent Possible(All) 90.3
    R Merge I(Observed) 0.143
    Redundancy 11.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.05
    Resolution(Low) 65.838
    Number of Reflections(Observed) 6850
    Number of Reflections(R-Free) 327
    Percent Reflections(Observed) 85.97
    R-Factor(Observed) 0.23046
    R-Work 0.22732
    R-Free 0.29661
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 45.336
    Anisotropic B[1][1] 2.87
    Anisotropic B[1][2] 1.43
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.87
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.3
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.05
    Shell Resolution(Low) 3.219
    Number of Reflections(R-Free) 50
    Number of Reflections(R-Work) 935
    R-Factor(R-Work) 0.245
    R-Factor(R-Free) 0.328
    Percent Reflections(Observed) 84.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.048
    r_scbond_it 0.608
    r_mcangle_it 0.525
    r_mcbond_it 0.278
    r_gen_planes_refined 0.004
    r_chiral_restr 0.067
    r_dihedral_angle_4_deg 14.987
    r_dihedral_angle_3_deg 16.854
    r_dihedral_angle_2_deg 39.334
    r_dihedral_angle_1_deg 4.451
    r_angle_refined_deg 0.974
    r_bond_refined_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2875
    Nucleic Acid Atoms 0
    Heterogen Atoms 43
    Solvent Atoms 3
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    data reduction SCALEPACK