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X-RAY DIFFRACTION
Materials and Methods page
3W1H
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.0
    Details 120mM Tris-HCl, 11% PEG 4000, 200mM MgCl2, 90mM NiCl2, 50mM Na2S2O3, 50mM L-serine, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 167.03 α = 90
    b = 167.03 β = 90
    c = 211.11 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details mirrors
    Collection Date 2007-12-03
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.00000
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -2.0
    Resolution(High) 3.89
    Resolution(Low) 50
    Number Reflections(All) 28051
    Number Reflections(Observed) 26396
    Percent Possible(Observed) 94.1
    R Merge I(Observed) 0.103
    B(Isotropic) From Wilson Plot 130.32
    Redundancy 9.1
     
    High Resolution Shell Details
    Resolution(High) 3.9
    Resolution(Low) 4.04
    Percent Possible(All) 86.8
    R Merge I(Observed) 0.736
    Mean I Over Sigma(Observed) 2.02
    R-Sym I(Observed) 0.736
    Redundancy 8.1
    Number Unique Reflections(All) 2717
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.893
    Resolution(Low) 49.247
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 28003
    Number of Reflections(Observed) 26354
    Number of Reflections(R-Free) 1345
    Percent Reflections(Observed) 94.11
    R-Factor(Observed) 0.2235
    R-Work 0.2203
    R-Free 0.2822
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 209.76
    Anisotropic B[1][1] -46.8339
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -46.8339
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 93.6677
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8931
    Shell Resolution(Low) 4.0322
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2244
    R-Factor(R-Work) 0.3686
    R-Factor(R-Free) 0.4
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0322
    Shell Resolution(Low) 4.1935
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 2340
    R-Factor(R-Work) 0.3127
    R-Factor(R-Free) 0.3535
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1935
    Shell Resolution(Low) 4.3843
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2400
    R-Factor(R-Work) 0.2728
    R-Factor(R-Free) 0.2989
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3843
    Shell Resolution(Low) 4.6152
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2388
    R-Factor(R-Work) 0.2183
    R-Factor(R-Free) 0.2916
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6152
    Shell Resolution(Low) 4.9042
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2485
    R-Factor(R-Work) 0.1957
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9042
    Shell Resolution(Low) 5.2824
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2544
    R-Factor(R-Work) 0.1932
    R-Factor(R-Free) 0.287
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2824
    Shell Resolution(Low) 5.8132
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.2289
    R-Factor(R-Free) 0.2681
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8132
    Shell Resolution(Low) 6.6527
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.2501
    R-Factor(R-Free) 0.3266
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6527
    Shell Resolution(Low) 8.375
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.2661
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.375
    Shell Resolution(Low) 49.2505
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2750
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.55
    f_plane_restr 0.004
    f_chiral_restr 0.07
    f_angle_d 1.222
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16913
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser