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X-RAY DIFFRACTION
Materials and Methods page
4IXM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.9
    Temperature 298.0
    Details 1.5 uL of 13.2 mg/mL YjiA in 0.1 M NaCl, 25 mM HEPES, pH 7.6, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.55 M ammonium sulfate, 0.1 M , VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 56.29 α = 90
    b = 68.87 β = 104.09
    c = 77.83 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 325 mm CCD
    Collection Date 2007-07-21
     
    Diffraction Radiation
    Monochromator Si(111) Double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength List 1.1808
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.57
    Resolution(Low) 30
    Number Reflections(All) 35529
    Number Reflections(Observed) 35529
    Percent Possible(Observed) 97.0
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.57
    Resolution(Low) 2.61
    Percent Possible(All) 84.6
    Mean I Over Sigma(Observed) 3.3
    R-Sym I(Observed) 0.412
    Redundancy 3.6
    Number Unique Reflections(All) 1535
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.57
    Resolution(Low) 29.126
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 35283
    Number of Reflections(Observed) 35283
    Number of Reflections(R-Free) 940
    Percent Reflections(Observed) 97.46
    R-Factor(Observed) 0.2221
    R-Work 0.2199
    R-Free 0.2623
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic with TLS
    Mean Isotropic B Value 71.69
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.57
    Shell Resolution(Low) 2.6395
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.3142
    R-Factor(R-Free) 0.3748
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6395
    Shell Resolution(Low) 2.7171
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.2796
    R-Factor(R-Free) 0.3002
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7171
    Shell Resolution(Low) 2.8047
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2689
    R-Factor(R-Free) 0.3238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8047
    Shell Resolution(Low) 2.9049
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.2748
    R-Factor(R-Free) 0.3134
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9049
    Shell Resolution(Low) 3.0211
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.2626
    R-Factor(R-Free) 0.2971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0211
    Shell Resolution(Low) 3.1584
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.263
    R-Factor(R-Free) 0.3299
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1584
    Shell Resolution(Low) 3.3247
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.2456
    R-Factor(R-Free) 0.3111
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3247
    Shell Resolution(Low) 3.5327
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.2329
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5327
    Shell Resolution(Low) 3.8049
    Number of Reflections(R-Free) 106
    Number of Reflections(R-Work) 1836
    R-Factor(R-Work) 0.2437
    R-Factor(R-Free) 0.3045
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8049
    Shell Resolution(Low) 4.1868
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2603
    R-Factor(R-Work) 0.2008
    R-Factor(R-Free) 0.2608
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1868
    Shell Resolution(Low) 4.7903
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.2252
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7903
    Shell Resolution(Low) 6.0265
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.1966
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0265
    Shell Resolution(Low) 29.128
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2544
    R-Factor(R-Work) 0.1956
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.002
    f_chiral_restr 0.039
    f_dihedral_angle_d 9.79
    f_angle_d 0.56
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4821
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 43
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blu-ice
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building Phaser
    data collection Blu-ice