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X-RAY DIFFRACTION
Materials and Methods page
3VT1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 289.0
    Details 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 106.64 α = 90
    b = 122.53 β = 90
    c = 403.48 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-02-17
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.979305
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.19
    Resolution(Low) 50
    Number Reflections(All) 88841
    Number Reflections(Observed) 88841
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.175
    Redundancy 7.3
     
    High Resolution Shell Details
    Resolution(High) 3.2
    Resolution(Low) 3.31
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.557
    Redundancy 7.5
    Number Unique Reflections(All) 8740
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.187
    Resolution(Low) 48.796
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 88617
    Number of Reflections(R-Free) 1592
    Percent Reflections(Observed) 99.27
    R-Factor(Observed) 0.2361
    R-Work 0.2355
    R-Free 0.2697
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 84.4398
    Anisotropic B[1][1] 26.0357
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.5667
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -26.6024
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.187
    Shell Resolution(Low) 3.2899
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 7678
    R-Factor(R-Work) 0.316
    R-Factor(R-Free) 0.3604
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2899
    Shell Resolution(Low) 3.4074
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 7811
    R-Factor(R-Work) 0.285
    R-Factor(R-Free) 0.3087
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4074
    Shell Resolution(Low) 3.5438
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 7827
    R-Factor(R-Work) 0.2718
    R-Factor(R-Free) 0.3203
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5438
    Shell Resolution(Low) 3.7051
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 7858
    R-Factor(R-Work) 0.2557
    R-Factor(R-Free) 0.3062
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7051
    Shell Resolution(Low) 3.9003
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 7858
    R-Factor(R-Work) 0.2411
    R-Factor(R-Free) 0.2977
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9003
    Shell Resolution(Low) 4.1446
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 7871
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1446
    Shell Resolution(Low) 4.4644
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 7884
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.2312
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4644
    Shell Resolution(Low) 4.9133
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 7960
    R-Factor(R-Work) 0.1977
    R-Factor(R-Free) 0.2035
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9133
    Shell Resolution(Low) 5.6233
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 7983
    R-Factor(R-Work) 0.2227
    R-Factor(R-Free) 0.2636
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6233
    Shell Resolution(Low) 7.0813
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 8055
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0813
    Shell Resolution(Low) 48.8021
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 8240
    R-Factor(R-Work) 0.241
    R-Factor(R-Free) 0.2817
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 9.734
    f_plane_restr 0.002
    f_chiral_restr 0.035
    f_angle_d 0.532
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22127
    Nucleic Acid Atoms 0
    Heterogen Atoms 84
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK