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X-RAY DIFFRACTION
Materials and Methods page
4GUI
  •   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 5 M sodium quinate, VAPOR DIFFUSION, SITTING DROP, temperature 300K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.67 α = 90
    b = 74.43 β = 100.57
    c = 63.13 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 300 mm CCD
    Details Beryllium lens
    Collection Date 2012-07-20
     
    Diffraction Radiation
    Monochromator diamond(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97857
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.78
    Resolution(Low) 30
    Number Reflections(All) 41378
    Number Reflections(Observed) 41378
    Percent Possible(Observed) 97.2
    R Merge I(Observed) 0.056
    Redundancy 3.0
     
    High Resolution Shell Details
    Resolution(High) 1.78
    Resolution(Low) 1.81
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.314
    Mean I Over Sigma(Observed) 2.4
    Redundancy 2.3
    Number Unique Reflections(All) 2109
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.78
    Resolution(Low) 28.66
    Number of Reflections(all) 39202
    Number of Reflections(Observed) 39202
    Number of Reflections(R-Free) 2100
    Percent Reflections(Observed) 97.22
    R-Factor(All) 0.16079
    R-Factor(Observed) 0.16079
    R-Work 0.15927
    R-Free 0.18801
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.88
    Anisotropic B[1][1] 0.08
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 3.42
    Anisotropic B[2][2] -0.35
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.35
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.78
    Shell Resolution(Low) 1.826
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2917
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 99.29
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.005
    r_chiral_restr 0.082
    r_dihedral_angle_4_deg 12.821
    r_dihedral_angle_3_deg 9.917
    r_dihedral_angle_2_deg 33.743
    r_dihedral_angle_1_deg 3.128
    r_angle_other_deg 0.727
    r_angle_refined_deg 1.351
    r_bond_other_d 0.001
    r_bond_refined_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3818
    Nucleic Acid Atoms 0
    Heterogen Atoms 32
    Solvent Atoms 239
     
     
  •   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