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X-RAY DIFFRACTION
Materials and Methods page
3VNS
  •   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 = 156.54 α = 90
    b = 156.54 β = 90
    c = 156.54 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 2006-11-22
     
    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
    Resolution(Low) 50
    Number Reflections(Observed) 43061
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.062
    Redundancy 22.6
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.03
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.461
    Mean I Over Sigma(Observed) 8.185
    R-Sym I(Observed) 0.461
    Redundancy 20.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.001
    Resolution(Low) 39.136
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 42998
    Number of Reflections(R-Free) 2175
    Percent Reflections(Observed) 99.94
    R-Factor(Observed) 0.1926
    R-Work 0.1914
    R-Free 0.2156
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.0518
    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) 2.0011
    Shell Resolution(Low) 2.0446
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2541
    R-Factor(R-Work) 0.2234
    R-Factor(R-Free) 0.2689
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0446
    Shell Resolution(Low) 2.0921
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2528
    R-Factor(R-Work) 0.2024
    R-Factor(R-Free) 0.2548
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0921
    Shell Resolution(Low) 2.1444
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2548
    R-Factor(R-Work) 0.1998
    R-Factor(R-Free) 0.246
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1444
    Shell Resolution(Low) 2.2024
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2522
    R-Factor(R-Work) 0.1928
    R-Factor(R-Free) 0.2274
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2024
    Shell Resolution(Low) 2.2672
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2527
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2505
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2672
    Shell Resolution(Low) 2.3404
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 2571
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.2548
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3404
    Shell Resolution(Low) 2.424
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2518
    R-Factor(R-Work) 0.1979
    R-Factor(R-Free) 0.2287
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.424
    Shell Resolution(Low) 2.5211
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2550
    R-Factor(R-Work) 0.2006
    R-Factor(R-Free) 0.2622
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5211
    Shell Resolution(Low) 2.6358
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2525
    R-Factor(R-Work) 0.2133
    R-Factor(R-Free) 0.2542
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6358
    Shell Resolution(Low) 2.7747
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7747
    Shell Resolution(Low) 2.9485
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.2051
    R-Factor(R-Free) 0.2306
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9485
    Shell Resolution(Low) 3.1761
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2527
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2242
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1761
    Shell Resolution(Low) 3.4955
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2552
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4955
    Shell Resolution(Low) 4.0009
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2546
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.1908
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0009
    Shell Resolution(Low) 5.039
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.1446
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.039
    Shell Resolution(Low) 39.1435
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.282
    f_plane_restr 0.004
    f_chiral_restr 0.068
    f_angle_d 1.012
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3805
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 278
     
     
  •   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
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement MOLREP
    data reduction HKL