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X-RAY DIFFRACTION
Materials and Methods page
3RJ4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 289.0
    Details 0.2 M Lithium sulfate, 0.1 M TRIS pH 8.5, 16 % (w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 123.4 α = 90
    b = 71.84 β = 131.74
    c = 81.93 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details mirrors
    Collection Date 2010-07-26
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97921
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.72
    Resolution(Low) 50
    Number Reflections(All) 53457
    Number Reflections(Observed) 53457
    Percent Possible(Observed) 99.6
    B(Isotropic) From Wilson Plot 23.62
    Redundancy 4.9
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.78
    Percent Possible(All) 99.6
    Mean I Over Sigma(Observed) 8.2
    R-Sym I(Observed) 0.303
    Redundancy 4.5
    Number Unique Reflections(All) 2675
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.75
    Resolution(Low) 35.067
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 53353
    Number of Reflections(Observed) 53353
    Number of Reflections(R-Free) 2709
    Percent Reflections(Observed) 98.97
    R-Factor(All) 0.163
    R-Factor(Observed) 0.163
    R-Work 0.161
    R-Free 0.191
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model mixed
    Mean Isotropic B Value 28.9
    Anisotropic B[1][1] -3.0228
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.4596
    Anisotropic B[2][2] 2.5798
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.443
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7501
    Shell Resolution(Low) 1.7819
    Number of Reflections(Observed) 2552
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2416
    R-Factor(R-Work) 0.2074
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7819
    Shell Resolution(Low) 1.8162
    Number of Reflections(Observed) 2779
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.2022
    R-Factor(R-Free) 0.2337
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8162
    Shell Resolution(Low) 1.8533
    Number of Reflections(Observed) 2802
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8533
    Shell Resolution(Low) 1.8935
    Number of Reflections(Observed) 2805
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.2093
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8935
    Shell Resolution(Low) 1.9376
    Number of Reflections(Observed) 2842
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.2
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9376
    Shell Resolution(Low) 1.986
    Number of Reflections(Observed) 2799
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.986
    Shell Resolution(Low) 2.0397
    Number of Reflections(Observed) 2836
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2702
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.1855
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0397
    Shell Resolution(Low) 2.0997
    Number of Reflections(Observed) 2825
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1553
    R-Factor(R-Free) 0.2043
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0997
    Shell Resolution(Low) 2.1675
    Number of Reflections(Observed) 2823
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1675
    Shell Resolution(Low) 2.245
    Number of Reflections(Observed) 2795
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.2029
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.245
    Shell Resolution(Low) 2.3348
    Number of Reflections(Observed) 2821
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1959
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3348
    Shell Resolution(Low) 2.4411
    Number of Reflections(Observed) 2832
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1623
    R-Factor(R-Free) 0.2237
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4411
    Shell Resolution(Low) 2.5697
    Number of Reflections(Observed) 2847
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2716
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5697
    Shell Resolution(Low) 2.7307
    Number of Reflections(Observed) 2824
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1749
    R-Factor(R-Free) 0.2332
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7307
    Shell Resolution(Low) 2.9414
    Number of Reflections(Observed) 2837
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9414
    Shell Resolution(Low) 3.2372
    Number of Reflections(Observed) 2868
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.1806
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2372
    Shell Resolution(Low) 3.7052
    Number of Reflections(Observed) 2825
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1486
    R-Factor(R-Free) 0.1845
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7052
    Shell Resolution(Low) 4.6665
    Number of Reflections(Observed) 2851
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.1356
    R-Factor(R-Free) 0.1486
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6665
    Shell Resolution(Low) 35.0741
    Number of Reflections(Observed) 2790
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1841
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.105
    f_dihedral_angle_d 15.433
    f_angle_d 1.27
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4129
    Nucleic Acid Atoms 0
    Heterogen Atoms 13
    Solvent Atoms 447
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SBCCOLLECT, HKL3000
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution HKL3000, SHELXS,MLPHARE,BUCCANEER
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building BUCCANEER
    model building MLPHARE
    model building SHELXS
    model building HKL3000
    data collection HKL3000
    data collection SBCCOLLECT