POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DRF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.75
    Temperature 303.0
    Details 16% PEG6000, 0.5M NaCl, 25mM CaCl2, 5% methanol, 50mM HEPES, 50 mM Tris-HCl, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 303K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 59.67 α = 81.27
    b = 59.71 β = 87.67
    c = 101.54 γ = 88.39
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.9787
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.6
    Resolution(Low) 50
    Number Reflections(All) 34296
    Number Reflections(Observed) 41067
    Percent Possible(Observed) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 42.404
    Cut-off Sigma(F) 0.16
    Number of Reflections(all) 42680
    Number of Reflections(Observed) 33610
    Number of Reflections(R-Free) 1978
    Percent Reflections(Observed) 96.22
    R-Factor(Observed) 0.1874
    R-Work 0.1845
    R-Free 0.2446
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -5.8585
    Anisotropic B[1][2] -10.1317
    Anisotropic B[1][3] -2.3552
    Anisotropic B[2][2] -2.1152
    Anisotropic B[2][3] 1.1218
    Anisotropic B[3][3] 7.9737
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.661
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2449
    R-Factor(R-Work) 0.2735
    R-Factor(R-Free) 0.3934
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.661
    Shell Resolution(Low) 2.7329
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.2436
    R-Factor(R-Free) 0.3204
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7329
    Shell Resolution(Low) 2.8133
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2698
    R-Factor(R-Work) 0.2561
    R-Factor(R-Free) 0.3414
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8133
    Shell Resolution(Low) 2.9041
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.2114
    R-Factor(R-Free) 0.3524
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9041
    Shell Resolution(Low) 3.0079
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2822
    R-Factor(R-Work) 0.2247
    R-Factor(R-Free) 0.3044
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0079
    Shell Resolution(Low) 3.1283
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2807
    R-Factor(R-Work) 0.1941
    R-Factor(R-Free) 0.2904
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1283
    Shell Resolution(Low) 3.2706
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2816
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.299
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2706
    Shell Resolution(Low) 3.443
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2844
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.2772
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.443
    Shell Resolution(Low) 3.6586
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2881
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.2407
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6586
    Shell Resolution(Low) 3.9409
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2866
    R-Factor(R-Work) 0.1738
    R-Factor(R-Free) 0.2036
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9409
    Shell Resolution(Low) 4.3371
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2885
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.2198
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3371
    Shell Resolution(Low) 4.9638
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2906
    R-Factor(R-Work) 0.1342
    R-Factor(R-Free) 0.1991
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9638
    Shell Resolution(Low) 6.2507
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2871
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.1916
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2507
    Shell Resolution(Low) 42.4101
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2874
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.207
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.085
    f_dihedral_angle_d 16.23
    f_angle_d 1.284
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9886
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 154
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHRNIX
    Structure Refinement PHENIX
     
    Software
    refinement PHENIX
    model building PHRNIX
    data collection MAR345dtb