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X-RAY DIFFRACTION
Materials and Methods page
4IXN
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 298.0
    Details 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 56.07 α = 90
    b = 68.44 β = 104.23
    c = 77.7 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 PIXEL
    Type PSI PILATUS 6M
    Collection Date 2012-07-15
     
    Diffraction Radiation
    Monochromator Si(111) cryo-cooled double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9795
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.05
    Resolution(Low) 75.3
    Number Reflections(All) 35715
    Number Reflections(Observed) 35715
    Percent Possible(Observed) 98.5
    Redundancy 6.5
     
    High Resolution Shell Details
    Resolution(High) 2.05
    Resolution(Low) 2.09
    Percent Possible(All) 98.8
    Mean I Over Sigma(Observed) 2.9
    R-Sym I(Observed) 0.59
    Redundancy 5.7
    Number Unique Reflections(All) 1784
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.05
    Resolution(Low) 75.3
    Cut-off Sigma(F) 1.38
    Number of Reflections(all) 35309
    Number of Reflections(Observed) 35309
    Number of Reflections(R-Free) 1747
    Percent Reflections(Observed) 98.31
    R-Factor(Observed) 0.2044
    R-Work 0.2027
    R-Free 0.2381
    R-Free Selection Details same as for Zn(II)-soaked WT YjiA between 30 and 2.57 A resolution, random for remainder
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic with TLS
    Mean Isotropic B Value 43.79
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.1103
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2790
    R-Factor(R-Work) 0.2556
    R-Factor(R-Free) 0.2964
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1103
    Shell Resolution(Low) 2.1785
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.2477
    R-Factor(R-Free) 0.3248
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1785
    Shell Resolution(Low) 2.2563
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2822
    R-Factor(R-Work) 0.2385
    R-Factor(R-Free) 0.2847
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2563
    Shell Resolution(Low) 2.3467
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2779
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.2684
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3467
    Shell Resolution(Low) 2.4535
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.2347
    R-Factor(R-Free) 0.2604
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4535
    Shell Resolution(Low) 2.5828
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2797
    R-Factor(R-Work) 0.2219
    R-Factor(R-Free) 0.2691
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5828
    Shell Resolution(Low) 2.7447
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2768
    R-Factor(R-Work) 0.2151
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7447
    Shell Resolution(Low) 2.9566
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2806
    R-Factor(R-Work) 0.2224
    R-Factor(R-Free) 0.2491
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9566
    Shell Resolution(Low) 3.2541
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2813
    R-Factor(R-Work) 0.209
    R-Factor(R-Free) 0.2422
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2541
    Shell Resolution(Low) 3.725
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2775
    R-Factor(R-Work) 0.1804
    R-Factor(R-Free) 0.2052
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.725
    Shell Resolution(Low) 4.693
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2835
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.693
    Shell Resolution(Low) 75.3651
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2803
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2214
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.049
    f_dihedral_angle_d 11.38
    f_angle_d 0.727
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4811
    Nucleic Acid Atoms 0
    Heterogen Atoms 13
    Solvent Atoms 256
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APS console
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHENIX
    data collection APS version: console