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X-RAY DIFFRACTION
Materials and Methods page
2YMD
  •   Crystallization Hide
    Crystallization Experiments
    Details 400 MM (NH4)H2PO4
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 203.57 α = 90
    b = 140.06 β = 99.08
    c = 126.53 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 PIXEL (PILATUS 6M)
    Type DECTRIS
    Collection Date 2011-06-02
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength 1.00
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.96
    Resolution(Low) 46.9
    Number Reflections(Observed) 249028
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.01
    B(Isotropic) From Wilson Plot 22.28
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.96
    Resolution(Low) 2.19
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.08
    Mean I Over Sigma(Observed) 1.0
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.96
    Resolution(Low) 46.903
    Cut-off Sigma(F) 1.42
    Number of Reflections(Observed) 239406
    Number of Reflections(R-Free) 2294
    Percent Reflections(Observed) 95.78
    R-Factor(Observed) 0.1595
    R-Work 0.1591
    R-Free 0.2011
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.2
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9609
    Shell Resolution(Low) 2.0036
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 12058
    R-Factor(R-Work) 0.2593
    R-Factor(R-Free) 0.2862
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0036
    Shell Resolution(Low) 2.0502
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 13761
    R-Factor(R-Work) 0.2356
    R-Factor(R-Free) 0.3124
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0502
    Shell Resolution(Low) 2.1014
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 14212
    R-Factor(R-Work) 0.2121
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1014
    Shell Resolution(Low) 2.1583
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 14470
    R-Factor(R-Work) 0.1995
    R-Factor(R-Free) 0.2371
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1583
    Shell Resolution(Low) 2.2218
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 14718
    R-Factor(R-Work) 0.1968
    R-Factor(R-Free) 0.2327
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2218
    Shell Resolution(Low) 2.2935
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 14802
    R-Factor(R-Work) 0.1888
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2935
    Shell Resolution(Low) 2.3754
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 14981
    R-Factor(R-Work) 0.1764
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3754
    Shell Resolution(Low) 2.4706
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 15090
    R-Factor(R-Work) 0.1739
    R-Factor(R-Free) 0.2323
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4706
    Shell Resolution(Low) 2.583
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 15098
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.583
    Shell Resolution(Low) 2.7191
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 15157
    R-Factor(R-Work) 0.1661
    R-Factor(R-Free) 0.2193
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7191
    Shell Resolution(Low) 2.8895
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 15304
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.2228
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8895
    Shell Resolution(Low) 3.1125
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 15367
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.1932
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1125
    Shell Resolution(Low) 3.4257
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 15463
    R-Factor(R-Work) 0.1364
    R-Factor(R-Free) 0.1762
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4257
    Shell Resolution(Low) 3.9212
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 15427
    R-Factor(R-Work) 0.1301
    R-Factor(R-Free) 0.1767
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9212
    Shell Resolution(Low) 4.9394
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 15559
    R-Factor(R-Work) 0.1161
    R-Factor(R-Free) 0.1365
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9394
    Shell Resolution(Low) 46.9162
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 15645
    R-Factor(R-Work) 0.1641
    R-Factor(R-Free) 0.1917
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.073
    f_dihedral_angle_d 14.086
    f_angle_d 1.061
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16864
    Nucleic Acid Atoms 0
    Heterogen Atoms 264
    Solvent Atoms 2665
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building MOLREP