POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3W6J
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.2
    Temperature 293.0
    Details 0.49M NaH2PO4, 0.91M K2HPO4, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 90.86 α = 90
    b = 127.42 β = 113.84
    c = 97.22 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Details mirrors
    Collection Date 2009-07-14
     
    Diffraction Radiation
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL26B2
    Wavelength List 1.0000
    Site SPRING-8
    Beamline BL26B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.6
    Resolution(Low) 50
    Number Reflections(Observed) 61981
    Percent Possible(Observed) 98.5
    R Merge I(Observed) 0.063
    B(Isotropic) From Wilson Plot 66.659
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.69
    Percent Possible(All) 89.5
    R Merge I(Observed) 0.669
    Mean I Over Sigma(Observed) 1.625
    R-Sym I(Observed) 0.669
    Redundancy 3.6
    Number Unique Reflections(All) 5598
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.6
    Resolution(Low) 30.7
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 61972
    Number of Reflections(Observed) 61951
    Number of Reflections(R-Free) 3144
    Percent Reflections(Observed) 98.69
    R-Factor(Observed) 0.2267
    R-Work 0.2247
    R-Free 0.2641
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 14.6874
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 9.8465
    Anisotropic B[2][2] -16.2021
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.5148
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.633
    Number of Reflections(Observed) 2323
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2204
    R-Factor(R-Work) 0.3643
    R-Factor(R-Free) 0.4382
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.633
    Shell Resolution(Low) 2.6761
    Number of Reflections(Observed) 2775
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.3358
    R-Factor(R-Free) 0.3459
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6761
    Shell Resolution(Low) 2.7222
    Number of Reflections(Observed) 2807
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.3276
    R-Factor(R-Free) 0.4065
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7222
    Shell Resolution(Low) 2.7717
    Number of Reflections(Observed) 2847
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2681
    R-Factor(R-Work) 0.3132
    R-Factor(R-Free) 0.3714
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7717
    Shell Resolution(Low) 2.825
    Number of Reflections(Observed) 2808
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.3004
    R-Factor(R-Free) 0.337
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.825
    Shell Resolution(Low) 2.8826
    Number of Reflections(Observed) 2807
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.2778
    R-Factor(R-Free) 0.3159
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8826
    Shell Resolution(Low) 2.9452
    Number of Reflections(Observed) 2840
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.2866
    R-Factor(R-Free) 0.3546
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9452
    Shell Resolution(Low) 3.0137
    Number of Reflections(Observed) 2833
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.2773
    R-Factor(R-Free) 0.2965
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0137
    Shell Resolution(Low) 3.089
    Number of Reflections(Observed) 2806
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.2707
    R-Factor(R-Free) 0.2871
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.089
    Shell Resolution(Low) 3.1724
    Number of Reflections(Observed) 2842
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2698
    R-Factor(R-Work) 0.2645
    R-Factor(R-Free) 0.3175
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1724
    Shell Resolution(Low) 3.2657
    Number of Reflections(Observed) 2849
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.2654
    R-Factor(R-Free) 0.3433
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2657
    Shell Resolution(Low) 3.3709
    Number of Reflections(Observed) 2824
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.2377
    R-Factor(R-Free) 0.2789
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3709
    Shell Resolution(Low) 3.4913
    Number of Reflections(Observed) 2845
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.2322
    R-Factor(R-Free) 0.2816
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4913
    Shell Resolution(Low) 3.6308
    Number of Reflections(Observed) 2859
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.2178
    R-Factor(R-Free) 0.2408
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6308
    Shell Resolution(Low) 3.7958
    Number of Reflections(Observed) 2814
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.242
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7958
    Shell Resolution(Low) 3.9955
    Number of Reflections(Observed) 2847
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.1977
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9955
    Shell Resolution(Low) 4.2453
    Number of Reflections(Observed) 2862
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2731
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.2339
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2453
    Shell Resolution(Low) 4.5721
    Number of Reflections(Observed) 2861
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1772
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5721
    Shell Resolution(Low) 5.0304
    Number of Reflections(Observed) 2846
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.1914
    R-Factor(R-Free) 0.2166
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0304
    Shell Resolution(Low) 5.7541
    Number of Reflections(Observed) 2873
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.298
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7541
    Shell Resolution(Low) 7.2339
    Number of Reflections(Observed) 2865
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.2459
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.2339
    Shell Resolution(Low) 30.7026
    Number of Reflections(Observed) 2908
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2749
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.1939
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.072
    f_dihedral_angle_d 15.47
    f_angle_d 1.181
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7499
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 43
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX
     
    Software
    refinement PHENIX
    model building PHENIX
    data collection HKL-2000