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X-RAY DIFFRACTION
Materials and Methods page
4H3S
  •   Crystallization Hide
    Crystallization Experiments
    Method Batch under oil
    pH 7.5
    Temperature 287.15
    Details 3.5 micro L of protein solution (13.9 mg/ml protein in 200mM NaCl, 5% (v/v) glycerol, 2mM DTT, 0.025% (w/v) NaN3, 20mM HEPES buffer, pH 7.5) with 2.0 micro L of precipitant solution (50mM NH4Br, 50mM KC2H3O2, 100mM HEPES, pH 7.5 and 20%(w/v) PEG 20K, Batch under oil, temperature 287.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 176.61 α = 90
    b = 176.61 β = 90
    c = 72.19 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2008-04-12
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL11-1
    Wavelength List 1.1696
    Site SSRL
    Beamline BL11-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.15
    Resolution(Low) 76.47
    Number Reflections(Observed) 70276
    Percent Possible(Observed) 99.86
    R Merge I(Observed) 0.068
    B(Isotropic) From Wilson Plot 33.55
    Redundancy 11.2
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.27
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.348
    Mean I Over Sigma(Observed) 3.0
    Redundancy 4.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MRSAD
    reflnsShellList 2.15
    Resolution(Low) 52.495
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 70197
    Number of Reflections(Observed) 70196
    Number of Reflections(R-Free) 3541
    Percent Reflections(Observed) 99.76
    R-Factor(Observed) 0.1611
    R-Work 0.1603
    R-Free 0.1756
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.1794
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.2858
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1794
    Shell Resolution(Low) 2.2106
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2244
    R-Factor(R-Free) 0.224
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2106
    Shell Resolution(Low) 2.2436
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2199
    R-Factor(R-Free) 0.2102
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2436
    Shell Resolution(Low) 2.2786
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.2166
    R-Factor(R-Free) 0.2458
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2786
    Shell Resolution(Low) 2.316
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.2164
    R-Factor(R-Free) 0.258
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.316
    Shell Resolution(Low) 2.3559
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.1978
    R-Factor(R-Free) 0.1909
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3559
    Shell Resolution(Low) 2.3988
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1897
    R-Factor(R-Free) 0.2003
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3988
    Shell Resolution(Low) 2.4449
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.1901
    R-Factor(R-Free) 0.2191
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4449
    Shell Resolution(Low) 2.4948
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.1934
    R-Factor(R-Free) 0.2375
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4948
    Shell Resolution(Low) 2.5491
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.2393
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5491
    Shell Resolution(Low) 2.6084
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.1752
    R-Factor(R-Free) 0.2076
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6084
    Shell Resolution(Low) 2.6736
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.1707
    R-Factor(R-Free) 0.2255
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6736
    Shell Resolution(Low) 2.7459
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2003
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7459
    Shell Resolution(Low) 2.8267
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.1724
    R-Factor(R-Free) 0.1828
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8267
    Shell Resolution(Low) 2.9179
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.1736
    R-Factor(R-Free) 0.2319
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9179
    Shell Resolution(Low) 3.0222
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.1828
    R-Factor(R-Free) 0.2059
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0222
    Shell Resolution(Low) 3.1432
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2081
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1432
    Shell Resolution(Low) 3.2862
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2862
    Shell Resolution(Low) 3.4594
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4594
    Shell Resolution(Low) 3.6761
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.1474
    R-Factor(R-Free) 0.157
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6761
    Shell Resolution(Low) 3.9598
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1394
    R-Factor(R-Free) 0.1481
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9598
    Shell Resolution(Low) 4.3582
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.119
    R-Factor(R-Free) 0.1291
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3582
    Shell Resolution(Low) 4.9884
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2716
    R-Factor(R-Work) 0.1171
    R-Factor(R-Free) 0.1164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9884
    Shell Resolution(Low) 6.2832
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.1466
    R-Factor(R-Free) 0.1538
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2832
    Shell Resolution(Low) 52.5105
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2809
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.148
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.045
    f_dihedral_angle_d 13.584
    f_angle_d 0.714
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4790
    Nucleic Acid Atoms 0
    Heterogen Atoms 75
    Solvent Atoms 447
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BluIce
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: dev_1096)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_1096)
    model building PHENIX
    data collection BluIce