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X-RAY DIFFRACTION
Materials and Methods page
4M9J
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7.5
    Temperature 291.0
    Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.58 α = 90
    b = 79.13 β = 105.95
    c = 54.98 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 104
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details mirrors
    Collection Date 2013-07-10
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.04
    Resolution(Low) 14
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.089
    B(Isotropic) From Wilson Plot 31.15
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 2.04
    Resolution(Low) 2.11
    Percent Possible(All) 92.4
    R Merge I(Observed) 0.593
    Redundancy 4.4
    Number Unique Reflections(All) 2633
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method Isomorphous replacement
    reflnsShellList 2.038
    Resolution(Low) 13.984
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 55412
    Number of Reflections(R-Free) 5574
    Percent Reflections(Observed) 98.41
    R-Factor(Observed) 0.1909
    R-Work 0.1864
    R-Free 0.2299
     
    Temperature Factor Modeling
    Mean Isotropic B Value 37.336
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0379
    Shell Resolution(Low) 2.061
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1168
    R-Factor(R-Work) 0.4278
    R-Factor(R-Free) 0.4869
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.061
    Shell Resolution(Low) 2.0851
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 1548
    R-Factor(R-Work) 0.2987
    R-Factor(R-Free) 0.3551
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0851
    Shell Resolution(Low) 2.1105
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 1574
    R-Factor(R-Work) 0.2674
    R-Factor(R-Free) 0.2945
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1105
    Shell Resolution(Low) 2.1371
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1659
    R-Factor(R-Work) 0.266
    R-Factor(R-Free) 0.284
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1371
    Shell Resolution(Low) 2.1651
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 1603
    R-Factor(R-Work) 0.2702
    R-Factor(R-Free) 0.3355
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1651
    Shell Resolution(Low) 2.1947
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 1730
    R-Factor(R-Work) 0.2545
    R-Factor(R-Free) 0.2908
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1947
    Shell Resolution(Low) 2.2259
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 1635
    R-Factor(R-Work) 0.2328
    R-Factor(R-Free) 0.3249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2259
    Shell Resolution(Low) 2.259
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 1736
    R-Factor(R-Work) 0.2316
    R-Factor(R-Free) 0.2892
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.259
    Shell Resolution(Low) 2.2941
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 1697
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2452
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2941
    Shell Resolution(Low) 2.3316
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1648
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2503
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3316
    Shell Resolution(Low) 2.3716
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 1686
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.2827
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3716
    Shell Resolution(Low) 2.4145
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1734
    R-Factor(R-Work) 0.2106
    R-Factor(R-Free) 0.28
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4145
    Shell Resolution(Low) 2.4607
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1715
    R-Factor(R-Work) 0.2096
    R-Factor(R-Free) 0.2597
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4607
    Shell Resolution(Low) 2.5107
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 1697
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2895
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5107
    Shell Resolution(Low) 2.5649
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 1684
    R-Factor(R-Work) 0.2003
    R-Factor(R-Free) 0.2375
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5649
    Shell Resolution(Low) 2.6242
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 1676
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2877
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6242
    Shell Resolution(Low) 2.6894
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1674
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.2749
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6894
    Shell Resolution(Low) 2.7616
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 1683
    R-Factor(R-Work) 0.2023
    R-Factor(R-Free) 0.2874
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7616
    Shell Resolution(Low) 2.8422
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 1680
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.326
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8422
    Shell Resolution(Low) 2.9331
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1719
    R-Factor(R-Work) 0.2006
    R-Factor(R-Free) 0.2346
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9331
    Shell Resolution(Low) 3.0369
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 1732
    R-Factor(R-Work) 0.2084
    R-Factor(R-Free) 0.2597
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0369
    Shell Resolution(Low) 3.1571
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 1636
    R-Factor(R-Work) 0.1978
    R-Factor(R-Free) 0.2644
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1571
    Shell Resolution(Low) 3.299
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 1700
    R-Factor(R-Work) 0.1789
    R-Factor(R-Free) 0.2531
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.299
    Shell Resolution(Low) 3.4705
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1724
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.1931
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4705
    Shell Resolution(Low) 3.6842
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 1702
    R-Factor(R-Work) 0.1522
    R-Factor(R-Free) 0.1709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6842
    Shell Resolution(Low) 3.9626
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 1657
    R-Factor(R-Work) 0.1501
    R-Factor(R-Free) 0.1717
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9626
    Shell Resolution(Low) 4.3505
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 1686
    R-Factor(R-Work) 0.1452
    R-Factor(R-Free) 0.1646
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3505
    Shell Resolution(Low) 4.9553
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1711
    R-Factor(R-Work) 0.1482
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9553
    Shell Resolution(Low) 6.1533
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 1699
    R-Factor(R-Work) 0.1695
    R-Factor(R-Free) 0.1935
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1533
    Shell Resolution(Low) 13.9843
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 1645
    R-Factor(R-Work) 0.1703
    R-Factor(R-Free) 0.1924
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.319
    f_plane_restr 0.002
    f_chiral_restr 0.042
    f_angle_d 0.707
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2404
    Nucleic Acid Atoms 627
    Heterogen Atoms 33
    Solvent Atoms 339
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO