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X-RAY DIFFRACTION
Materials and Methods page
3VYI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.0
    Details 0.2M AmSO4, 0.1M Tris-HCl (pH 8.5), 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 83.27 α = 90
    b = 84.01 β = 90
    c = 88.39 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Collection Date 2011-07-22
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.35
    Observed Criterion Sigma(I) 31.07
    Resolution(High) 2.3
    Resolution(Low) 50
    Number Reflections(All) 27731
    Number Reflections(Observed) 27673
    Percent Possible(Observed) 99.1
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.34
    Percent Possible(All) 97.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.305
    Resolution(Low) 39.114
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 27731
    Number of Reflections(Observed) 27673
    Number of Reflections(R-Free) 1396
    Percent Reflections(Observed) 98.74
    R-Factor(Observed) 0.2356
    R-Work 0.2324
    R-Free 0.2948
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -6.6009
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.1526
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.7535
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3046
    Shell Resolution(Low) 2.3869
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2474
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.3369
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3869
    Shell Resolution(Low) 2.4825
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2576
    R-Factor(R-Work) 0.228
    R-Factor(R-Free) 0.272
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4825
    Shell Resolution(Low) 2.5954
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.2165
    R-Factor(R-Free) 0.3389
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5954
    Shell Resolution(Low) 2.7322
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.2303
    R-Factor(R-Free) 0.2888
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7322
    Shell Resolution(Low) 2.9034
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.2396
    R-Factor(R-Free) 0.3098
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9034
    Shell Resolution(Low) 3.1274
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2454
    R-Factor(R-Free) 0.3301
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1274
    Shell Resolution(Low) 3.442
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.2417
    R-Factor(R-Free) 0.2739
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.442
    Shell Resolution(Low) 3.9397
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.2144
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9397
    Shell Resolution(Low) 4.962
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.2029
    R-Factor(R-Free) 0.268
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.962
    Shell Resolution(Low) 39.1196
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.2725
    R-Factor(R-Free) 0.3254
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.069
    f_dihedral_angle_d 18.938
    f_angle_d 1.026
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4369
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 160
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP & PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building MOLREP version: & PHASER
    data collection HKL-2000