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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GUJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 300.0
    Details protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal incubated in and frozen from 2 M sodium shikimate, VAPOR DIFFUSION, SITTING DROP, temperature 300K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.62 α = 90
    b = 74.97 β = 100.49
    c = 63.04 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Details Beryllium lens
    Collection Date 2012-08-06
     
    Diffraction Radiation
    Monochromator diamond(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.5
    Resolution(Low) 30
    Number Reflections(All) 69175
    Number Reflections(Observed) 69175
    Percent Possible(Observed) 96.9
    R Merge I(Observed) 0.045
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.53
    Percent Possible(All) 94.5
    R Merge I(Observed) 0.367
    Mean I Over Sigma(Observed) 3.8
    Redundancy 3.9
    Number Unique Reflections(All) 3375
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 28.66
    Number of Reflections(all) 65443
    Number of Reflections(Observed) 65443
    Number of Reflections(R-Free) 3483
    Percent Reflections(Observed) 96.85
    R-Factor(All) 0.15674
    R-Factor(Observed) 0.15674
    R-Work 0.15534
    R-Free 0.18237
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.966
    Anisotropic B[1][1] -1.96
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.7
    Anisotropic B[2][2] -0.32
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.84
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.539
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4760
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 94.99
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.006
    r_chiral_restr 0.085
    r_dihedral_angle_4_deg 13.25
    r_dihedral_angle_3_deg 9.8
    r_dihedral_angle_2_deg 33.58
    r_dihedral_angle_1_deg 3.547
    r_angle_other_deg 0.737
    r_angle_refined_deg 1.421
    r_bond_other_d 0.001
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3818
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 420
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blu Max
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.7.0029
    model building PHASER
    data collection Blu version: Max