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X-RAY DIFFRACTION
Materials and Methods page
3VAS
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Temperature 293.0
    Details 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 58.97 α = 90
    b = 180.12 β = 90
    c = 79.27 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details Compound Refractive Lenses
    Collection Date 2011-09-25
     
    Diffraction Radiation
    Monochromator DCM
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04
    Wavelength List 0.96110
    Site DIAMOND
    Beamline I04
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.26
    Resolution(Low) 90.06
    Number Reflections(All) 40098
    Number Reflections(Observed) 40098
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.099
    B(Isotropic) From Wilson Plot 36.926
     
    High Resolution Shell Details
    Resolution(High) 2.26
    Resolution(Low) 2.32
    Percent Possible(All) 97.4
    R Merge I(Observed) 0.57
    Mean I Over Sigma(Observed) 1.63
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.26
    Resolution(Low) 90.06
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 40098
    Number of Reflections(Observed) 40098
    Number of Reflections(R-Free) 2011
    Percent Reflections(Observed) 99.17
    R-Factor(Observed) 0.1792
    R-Work 0.1771
    R-Free 0.2216
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.0587
    Anisotropic B[1][1] -7.6289
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 9.2205
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.19
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.26
    Shell Resolution(Low) 2.3165
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.2376
    R-Factor(R-Free) 0.2791
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3165
    Shell Resolution(Low) 2.3792
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.2219
    R-Factor(R-Free) 0.289
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3792
    Shell Resolution(Low) 2.4492
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2704
    R-Factor(R-Work) 0.2123
    R-Factor(R-Free) 0.2788
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4492
    Shell Resolution(Low) 2.5283
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.2406
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5283
    Shell Resolution(Low) 2.6186
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.1886
    R-Factor(R-Free) 0.2404
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6186
    Shell Resolution(Low) 2.7235
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.1833
    R-Factor(R-Free) 0.2256
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7235
    Shell Resolution(Low) 2.8474
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.1895
    R-Factor(R-Free) 0.2446
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8474
    Shell Resolution(Low) 2.9976
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.1956
    R-Factor(R-Free) 0.2675
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9976
    Shell Resolution(Low) 3.1854
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2728
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2717
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1854
    Shell Resolution(Low) 3.4313
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2405
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4313
    Shell Resolution(Low) 3.7766
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1921
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7766
    Shell Resolution(Low) 4.3231
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2751
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3231
    Shell Resolution(Low) 5.4466
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4466
    Shell Resolution(Low) 90.1315
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2933
    R-Factor(R-Work) 0.1834
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.058
    f_dihedral_angle_d 12.814
    f_angle_d 0.819
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5354
    Nucleic Acid Atoms 0
    Heterogen Atoms 40
    Solvent Atoms 278
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction Xscale