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X-RAY DIFFRACTION
Materials and Methods page
3VNQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.2
    Temperature 293.0
    Details 0.1M ammonium sulfate, 24-32% PEG5000 monomethyl ether, 1mM ATP, 100mM Hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 156.15 α = 90
    b = 156.15 β = 90
    c = 156.15 γ = 90
     
    Space Group
    Space Group Name:    I 2 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Details mirrors
    Collection Date 2006-12-14
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44B2
    Wavelength List 1.0
    Site SPRING-8
    Beamline BL44B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(Observed) 37003
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.066
    B(Isotropic) From Wilson Plot 27.52
    Redundancy 15.1
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.14
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.405
    Mean I Over Sigma(Observed) 7.878
    R-Sym I(Observed) 0.405
    Redundancy 15.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 34.915
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 36956
    Number of Reflections(R-Free) 1853
    Percent Reflections(Observed) 99.91
    R-Factor(Observed) 0.1858
    R-Work 0.184
    R-Free 0.221
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.1802
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1001
    Shell Resolution(Low) 2.1569
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1843
    R-Factor(R-Free) 0.2558
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1569
    Shell Resolution(Low) 2.2204
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2719
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.2292
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2204
    Shell Resolution(Low) 2.292
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.2117
    R-Factor(R-Free) 0.2715
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.292
    Shell Resolution(Low) 2.3739
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.1914
    R-Factor(R-Free) 0.2425
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3739
    Shell Resolution(Low) 2.4689
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.1815
    R-Factor(R-Free) 0.226
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4689
    Shell Resolution(Low) 2.5813
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5813
    Shell Resolution(Low) 2.7173
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.272
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7173
    Shell Resolution(Low) 2.8875
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.1962
    R-Factor(R-Free) 0.2651
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8875
    Shell Resolution(Low) 3.1103
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2692
    R-Factor(R-Work) 0.2047
    R-Factor(R-Free) 0.2246
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1103
    Shell Resolution(Low) 3.4231
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1999
    R-Factor(R-Free) 0.2481
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4231
    Shell Resolution(Low) 3.9178
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.1779
    R-Factor(R-Free) 0.1946
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9178
    Shell Resolution(Low) 4.9338
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.1489
    R-Factor(R-Free) 0.165
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9338
    Shell Resolution(Low) 34.9201
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2788
    R-Factor(R-Work) 0.1777
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.699
    f_plane_restr 0.006
    f_chiral_restr 0.083
    f_angle_d 1.3
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3805
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 281
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molrep
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building Molrep
    data collection BSS