POP-OUT | CLOSE

An Information Portal to 111558 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2YNO
  •   Crystallization Hide
    Crystallization Experiments
    Details 12% PEG1500
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 171.56 α = 90
    b = 50.51 β = 103.99
    c = 74.47 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector CCD
    Collection Date 2009-05-25
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I02
    Wavelength 1.0
    Site DIAMOND
    Beamline I02
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.8
    Resolution(Low) 49
    Number Reflections(Observed) 55618
    Percent Possible(Observed) 96.6
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 13.09
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 81.6
    R Merge I(Observed) 0.1
    Mean I Over Sigma(Observed) 10.2
    Redundancy 4.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SIRAS
    reflnsShellList 1.8
    Resolution(Low) 49.015
    Cut-off Sigma(F) 1.36
    Number of Reflections(Observed) 55618
    Number of Reflections(R-Free) 2824
    Percent Reflections(Observed) 96.37
    R-Factor(Observed) 0.1898
    R-Work 0.188
    R-Free 0.2233
     
    Temperature Factor Modeling
    Mean Isotropic B Value 13.1
    Anisotropic B[1][1] -3.207
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.2424
    Anisotropic B[2][2] -3.1393
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.3462
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8311
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 1989
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2582
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8311
    Shell Resolution(Low) 1.8644
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2261
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2541
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8644
    Shell Resolution(Low) 1.9002
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2349
    R-Factor(R-Work) 0.1955
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9002
    Shell Resolution(Low) 1.939
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2507
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9812
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.2077
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9812
    Shell Resolution(Low) 2.0273
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2725
    R-Factor(R-Work) 0.2048
    R-Factor(R-Free) 0.2817
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0273
    Shell Resolution(Low) 2.078
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2761
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.2278
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.078
    Shell Resolution(Low) 2.1342
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2716
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.2505
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1342
    Shell Resolution(Low) 2.197
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2732
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2584
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.197
    Shell Resolution(Low) 2.2679
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2505
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2679
    Shell Resolution(Low) 2.3489
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3489
    Shell Resolution(Low) 2.443
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.1889
    R-Factor(R-Free) 0.2073
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.443
    Shell Resolution(Low) 2.5541
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2750
    R-Factor(R-Work) 0.1956
    R-Factor(R-Free) 0.2387
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5541
    Shell Resolution(Low) 2.6888
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2712
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.216
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6888
    Shell Resolution(Low) 2.8572
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.2073
    R-Factor(R-Free) 0.2368
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8572
    Shell Resolution(Low) 3.0778
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2746
    R-Factor(R-Work) 0.2099
    R-Factor(R-Free) 0.2456
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0778
    Shell Resolution(Low) 3.3875
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.202
    R-Factor(R-Free) 0.2181
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3875
    Shell Resolution(Low) 3.8775
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2750
    R-Factor(R-Work) 0.174
    R-Factor(R-Free) 0.1819
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8775
    Shell Resolution(Low) 4.8845
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2730
    R-Factor(R-Work) 0.1471
    R-Factor(R-Free) 0.1672
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8845
    Shell Resolution(Low) 49.0333
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2808
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2007
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.088
    f_dihedral_angle_d 12.476
    f_angle_d 1.22
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5039
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 403
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) IMOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution SHARP
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building SHARP