POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3VT0
  •   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 = 107.69 α = 90
    b = 122.38 β = 90
    c = 404.66 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 2012-03-04
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.979150
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(All) 117324
    Number Reflections(Observed) 117324
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.138
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.703
    Redundancy 7.2
    Number Unique Reflections(All) 11557
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.913
    Resolution(Low) 49.287
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 117178
    Number of Reflections(R-Free) 2115
    Percent Reflections(Observed) 99.57
    R-Factor(Observed) 0.2531
    R-Work 0.2528
    R-Free 0.2685
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 76.8921
    Anisotropic B[1][1] 18.747
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.2561
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -15.491
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9134
    Shell Resolution(Low) 2.9812
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 7104
    R-Factor(R-Work) 0.3843
    R-Factor(R-Free) 0.3732
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9812
    Shell Resolution(Low) 3.0557
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 7592
    R-Factor(R-Work) 0.3633
    R-Factor(R-Free) 0.384
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0557
    Shell Resolution(Low) 3.1383
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 7630
    R-Factor(R-Work) 0.3477
    R-Factor(R-Free) 0.3447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1383
    Shell Resolution(Low) 3.2307
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 7604
    R-Factor(R-Work) 0.3356
    R-Factor(R-Free) 0.369
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2307
    Shell Resolution(Low) 3.3349
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 7624
    R-Factor(R-Work) 0.3101
    R-Factor(R-Free) 0.3518
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3349
    Shell Resolution(Low) 3.4541
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7640
    R-Factor(R-Work) 0.2949
    R-Factor(R-Free) 0.2997
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4541
    Shell Resolution(Low) 3.5924
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7675
    R-Factor(R-Work) 0.2827
    R-Factor(R-Free) 0.31
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5924
    Shell Resolution(Low) 3.7558
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 7630
    R-Factor(R-Work) 0.2621
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7558
    Shell Resolution(Low) 3.9537
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 7692
    R-Factor(R-Work) 0.2493
    R-Factor(R-Free) 0.2362
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9537
    Shell Resolution(Low) 4.2013
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 7663
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2013
    Shell Resolution(Low) 4.5255
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 7743
    R-Factor(R-Work) 0.2096
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5255
    Shell Resolution(Low) 4.9805
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 7709
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2043
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9805
    Shell Resolution(Low) 5.7003
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 7788
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.2733
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7003
    Shell Resolution(Low) 7.1782
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 7860
    R-Factor(R-Work) 0.2367
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1782
    Shell Resolution(Low) 49.2938
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 8109
    R-Factor(R-Work) 0.2298
    R-Factor(R-Free) 0.2455
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 9.495
    f_plane_restr 0.001
    f_chiral_restr 0.033
    f_angle_d 0.463
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22127
    Nucleic Acid Atoms 0
    Heterogen Atoms 156
    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