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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4EED
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 298.0
    Details PEG 400, MgCl2, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 121.7 α = 90
    b = 132.5 β = 90
    c = 179.1 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC CCD300
    Collection Date 2010-01-27
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.97949
    Site CLSI
    Beamline 08ID-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.92
    Resolution(Low) 48.8
    Number Reflections(All) 21818
    Number Reflections(Observed) 21818
    Percent Possible(Observed) 81.8
    Redundancy 7.4
     
    High Resolution Shell Details
    Resolution(High) 3.92
    Resolution(Low) 4.02
    Percent Possible(All) 24.9
    Mean I Over Sigma(Observed) 2.2
    Redundancy 7.5
    Number Unique Reflections(All) 466
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.92
    Resolution(Low) 48.79
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 21818
    Number of Reflections(Observed) 21818
    Number of Reflections(R-Free) 1096
    Percent Reflections(Observed) 82.07
    R-Factor(All) 0.2996
    R-Factor(Observed) 0.2996
    R-Work 0.2971
    R-Free 0.3512
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 145.236
    Anisotropic B[1][1] 0.01
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.922
    Shell Resolution(Low) 4.023
    Number of Reflections(Observed) 466
    Number of Reflections(R-Free) 20
    Number of Reflections(R-Work) 459
    R-Factor(R-Work) 0.411
    R-Factor(R-Free) 0.411
    Percent Reflections(Observed) 24.95
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.027
    r_scbond_it 2.034
    r_mcangle_it 2.216
    r_mcbond_other 0.102
    r_bond_refined_d 0.011
    r_bond_other_d 0.002
    r_angle_refined_deg 1.235
    r_angle_other_deg 0.834
    r_dihedral_angle_1_deg 6.364
    r_dihedral_angle_2_deg 38.315
    r_dihedral_angle_3_deg 18.431
    r_dihedral_angle_4_deg 12.729
    r_chiral_restr 0.061
    r_gen_planes_refined 0.005
    r_gen_planes_other 0.001
    r_mcbond_it 1.172
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12965
    Nucleic Acid Atoms 0
    Heterogen Atoms 14
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MxDC
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0102
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser
    data reduction HKL