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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DEL
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.8
    Temperature 293.0
    Details 26% PEG 300, 0.1 M sodium acetate, 2mM phosphoglycolohydroxamate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 61.8 α = 90
    b = 119.61 β = 90
    c = 164.1 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2009-06-02
     
    Diffraction Radiation
    Monochromator Si 220
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 1
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.58
    Resolution(Low) 93.9
    Number Reflections(All) 79039
    Number Reflections(Observed) 78320
    Percent Possible(Observed) 94.0
     
    High Resolution Shell Details
    Resolution(High) 1.58
    Resolution(Low) 1.64
    Percent Possible(All) 77.5
    R Merge I(Observed) 0.279
    Mean I Over Sigma(Observed) 4.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.58
    Resolution(Low) 49.74
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 79039
    Number of Reflections(Observed) 78207
    Number of Reflections(R-Free) 3910
    Percent Reflections(Observed) 93.9
    R-Factor(Observed) 0.1893
    R-Work 0.1885
    R-Free 0.2054
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.0601
    Anisotropic B[1][1] 2.52
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.55
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.97
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.58
    Shell Resolution(Low) 1.622
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4359
    R-Factor(R-Work) 0.266
    R-Factor(R-Free) 0.278
    Percent Reflections(Observed) 76.26
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.835
    r_scbond_it 1.699
    r_mcangle_it 1.018
    r_mcbond_it 0.564
    r_symmetry_metal_ion_refined 0.027
    r_symmetry_hbond_refined 0.143
    r_symmetry_vdw_refined 0.198
    r_bond_refined_d 0.01
    r_angle_refined_deg 1.194
    r_dihedral_angle_1_deg 18.029
    r_dihedral_angle_2_deg 36.994
    r_dihedral_angle_3_deg 12.342
    r_dihedral_angle_4_deg 18.847
    r_chiral_restr 0.094
    r_gen_planes_refined 0.005
    r_nbd_refined 0.211
    r_nbtor_refined 0.302
    r_xyhbond_nbd_refined 0.112
    r_metal_ion_refined 0.473
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2583
    Nucleic Acid Atoms 0
    Heterogen Atoms 36
    Solvent Atoms 513
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL2000
    Data Reduction (data scaling) HKL-2000
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5