POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4H13
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.3
    Temperature 293.0
    Details pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 157.2 α = 90
    b = 157.2 β = 90
    c = 363.28 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2006-07-07
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.07
    Resolution(Low) 34.57
    Number Reflections(All) 50067
    Number Reflections(Observed) 50067
    B(Isotropic) From Wilson Plot 91.83
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.07
    Resolution(Low) 34.567
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 49966
    Number of Reflections(R-Free) 2544
    Percent Reflections(Observed) 99.07
    R-Factor(Observed) 0.2148
    R-Work 0.2136
    R-Free 0.238
     
    Temperature Factor Modeling
    Mean Isotropic B Value 115.821
    Anisotropic B[1][1] -0.03
    Anisotropic B[1][2] -0.03
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.03
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.11
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0682
    Shell Resolution(Low) 3.1272
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2452
    R-Factor(R-Work) 0.306
    R-Factor(R-Free) 0.3506
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1272
    Shell Resolution(Low) 3.191
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.2992
    R-Factor(R-Free) 0.3784
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.191
    Shell Resolution(Low) 3.2603
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.2824
    R-Factor(R-Free) 0.3224
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2603
    Shell Resolution(Low) 3.3361
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.2633
    R-Factor(R-Free) 0.2831
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3361
    Shell Resolution(Low) 3.4194
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.3029
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4194
    Shell Resolution(Low) 3.5118
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2589
    R-Factor(R-Work) 0.235
    R-Factor(R-Free) 0.2906
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5118
    Shell Resolution(Low) 3.615
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2378
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.615
    Shell Resolution(Low) 3.7316
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2206
    R-Factor(R-Free) 0.243
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7316
    Shell Resolution(Low) 3.8648
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2587
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8648
    Shell Resolution(Low) 4.0193
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.2046
    R-Factor(R-Free) 0.2501
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0193
    Shell Resolution(Low) 4.202
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.2059
    R-Factor(R-Free) 0.2233
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.202
    Shell Resolution(Low) 4.4231
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1913
    R-Factor(R-Free) 0.2217
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4231
    Shell Resolution(Low) 4.6996
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.1851
    R-Factor(R-Free) 0.2044
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6996
    Shell Resolution(Low) 5.0614
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.1885
    R-Factor(R-Free) 0.2322
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0614
    Shell Resolution(Low) 5.5688
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5688
    Shell Resolution(Low) 6.3703
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.2285
    R-Factor(R-Free) 0.2565
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3703
    Shell Resolution(Low) 8.0094
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2037
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0094
    Shell Resolution(Low) 34.5688
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.2144
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.168
    f_dihedral_angle_d 20.841
    f_angle_d 1.28
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7459
    Nucleic Acid Atoms 0
    Heterogen Atoms 644
    Solvent Atoms 24
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement REFMAC version: 5.7.0029
    data collection ADSC version: Quantum