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X-RAY DIFFRACTION
Materials and Methods page
3W6K
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4
    Temperature 293.0
    Details 100mM Na malonate-HCl, 3.0-3.3M Na formate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 107.82 α = 90
    b = 88.92 β = 94.31
    c = 60.68 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2012-02-01
     
    Diffraction Radiation
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL26B2
    Wavelength List 1.0000
    Site SPRING-8
    Beamline BL26B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.37
    Resolution(Low) 50
    Number Reflections(Observed) 23087
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.051
    B(Isotropic) From Wilson Plot 40.586
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.374
    Resolution(Low) 2.42
    Percent Possible(All) 89.8
    R Merge I(Observed) 0.116
    Mean I Over Sigma(Observed) 11.464
    R-Sym I(Observed) 0.116
    Redundancy 3.6
    Number Unique Reflections(All) 1048
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.374
    Resolution(Low) 46.476
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 23191
    Number of Reflections(Observed) 23058
    Number of Reflections(R-Free) 1182
    Percent Reflections(Observed) 99.42
    R-Factor(Observed) 0.2383
    R-Work 0.2358
    R-Free 0.2846
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 6.7307
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.3997
    Anisotropic B[2][2] -4.2974
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.4333
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.374
    Shell Resolution(Low) 2.4818
    Number of Reflections(Observed) 2810
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.2869
    R-Factor(R-Free) 0.4116
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4818
    Shell Resolution(Low) 2.6127
    Number of Reflections(Observed) 2857
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.2542
    R-Factor(R-Free) 0.2962
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6127
    Shell Resolution(Low) 2.7763
    Number of Reflections(Observed) 2895
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2756
    R-Factor(R-Work) 0.2337
    R-Factor(R-Free) 0.2953
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7763
    Shell Resolution(Low) 2.9907
    Number of Reflections(Observed) 2885
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2735
    R-Factor(R-Work) 0.2475
    R-Factor(R-Free) 0.3009
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9907
    Shell Resolution(Low) 3.2915
    Number of Reflections(Observed) 2870
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.2504
    R-Factor(R-Free) 0.2767
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2915
    Shell Resolution(Low) 3.7677
    Number of Reflections(Observed) 2896
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2733
    R-Factor(R-Work) 0.2305
    R-Factor(R-Free) 0.2976
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7677
    Shell Resolution(Low) 4.7461
    Number of Reflections(Observed) 2906
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2755
    R-Factor(R-Work) 0.2081
    R-Factor(R-Free) 0.2877
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7461
    Shell Resolution(Low) 46.4847
    Number of Reflections(Observed) 2941
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2796
    R-Factor(R-Work) 0.2397
    R-Factor(R-Free) 0.2361
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.073
    f_dihedral_angle_d 15.578
    f_angle_d 1.296
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2759
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 101
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX
     
    Software
    refinement PHENIX
    model building PHENIX
    data collection HKL-2000