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X-RAY DIFFRACTION
Materials and Methods page
4M9G
  •   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 = 54.42 α = 90
    b = 79.42 β = 105.25
    c = 54.81 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 2013-05-03
     
    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) 2.01
    Resolution(Low) 14
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.081
    B(Isotropic) From Wilson Plot 27.53
    Redundancy 6.8
     
    High Resolution Shell Details
    Resolution(High) 2.01
    Resolution(Low) 2.08
    Percent Possible(All) 94.1
    R Merge I(Observed) 0.674
    Redundancy 4.5
    Number Unique Reflections(All) 2772
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method Isomorphous replacement
    reflnsShellList 2.01
    Resolution(Low) 13.701
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 56743
    Number of Reflections(R-Free) 5711
    Percent Reflections(Observed) 96.59
    R-Factor(Observed) 0.1897
    R-Work 0.1858
    R-Free 0.2237
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.4245
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0098
    Shell Resolution(Low) 2.0326
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 1451
    R-Factor(R-Work) 0.314
    R-Factor(R-Free) 0.3687
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0326
    Shell Resolution(Low) 2.0564
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1523
    R-Factor(R-Work) 0.2911
    R-Factor(R-Free) 0.2714
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0564
    Shell Resolution(Low) 2.0814
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 1665
    R-Factor(R-Work) 0.2801
    R-Factor(R-Free) 0.3097
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0814
    Shell Resolution(Low) 2.1077
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 1639
    R-Factor(R-Work) 0.2598
    R-Factor(R-Free) 0.285
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1077
    Shell Resolution(Low) 2.1353
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1637
    R-Factor(R-Work) 0.2602
    R-Factor(R-Free) 0.2961
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1353
    Shell Resolution(Low) 2.1644
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 1685
    R-Factor(R-Work) 0.2479
    R-Factor(R-Free) 0.3055
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1644
    Shell Resolution(Low) 2.1952
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 1688
    R-Factor(R-Work) 0.2398
    R-Factor(R-Free) 0.2749
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1952
    Shell Resolution(Low) 2.2279
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 1654
    R-Factor(R-Work) 0.2341
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2279
    Shell Resolution(Low) 2.2625
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1722
    R-Factor(R-Work) 0.2158
    R-Factor(R-Free) 0.2534
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2625
    Shell Resolution(Low) 2.2995
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 1705
    R-Factor(R-Work) 0.2174
    R-Factor(R-Free) 0.2629
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2995
    Shell Resolution(Low) 2.3389
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 1676
    R-Factor(R-Work) 0.2173
    R-Factor(R-Free) 0.2353
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3389
    Shell Resolution(Low) 2.3812
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1726
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.2653
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3812
    Shell Resolution(Low) 2.4268
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 1695
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4268
    Shell Resolution(Low) 2.476
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 1788
    R-Factor(R-Work) 0.2009
    R-Factor(R-Free) 0.2344
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.476
    Shell Resolution(Low) 2.5296
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 1680
    R-Factor(R-Work) 0.1923
    R-Factor(R-Free) 0.247
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5296
    Shell Resolution(Low) 2.588
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1725
    R-Factor(R-Work) 0.1967
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.588
    Shell Resolution(Low) 2.6523
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1712
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2408
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6523
    Shell Resolution(Low) 2.7235
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 1717
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2568
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7235
    Shell Resolution(Low) 2.8029
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 1690
    R-Factor(R-Work) 0.1941
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8029
    Shell Resolution(Low) 2.8926
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1782
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8926
    Shell Resolution(Low) 2.9949
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1765
    R-Factor(R-Work) 0.1997
    R-Factor(R-Free) 0.2579
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9949
    Shell Resolution(Low) 3.1135
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 1735
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2405
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1135
    Shell Resolution(Low) 3.2534
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 1701
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.2253
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2534
    Shell Resolution(Low) 3.4224
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1765
    R-Factor(R-Work) 0.1679
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4224
    Shell Resolution(Low) 3.6331
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 1777
    R-Factor(R-Work) 0.1663
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6331
    Shell Resolution(Low) 3.9076
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 1708
    R-Factor(R-Work) 0.153
    R-Factor(R-Free) 0.1845
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9076
    Shell Resolution(Low) 4.2898
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 1723
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.1851
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2898
    Shell Resolution(Low) 4.8857
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 1798
    R-Factor(R-Work) 0.1418
    R-Factor(R-Free) 0.1657
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8857
    Shell Resolution(Low) 6.0653
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 1789
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.2068
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0653
    Shell Resolution(Low) 13.7009
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 1711
    R-Factor(R-Work) 0.1581
    R-Factor(R-Free) 0.1716
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.129
    f_plane_restr 0.003
    f_chiral_restr 0.045
    f_angle_d 0.763
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2443
    Nucleic Acid Atoms 627
    Heterogen Atoms 3
    Solvent Atoms 354
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Mar
    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