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X-RAY DIFFRACTION
Materials and Methods page
4JES
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7
    Temperature 293.0
    Details 1.1 M sodium malonate, 0.1 HEPES, 0.5% (v/v) Jeffamine ED-2001, pH 7.0, vapor diffusion, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.07 α = 90
    b = 75.07 β = 90
    c = 129.26 γ = 120
     
    Space Group
    Space Group Name:    P 63
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector pixel
    Type DECTRIS PILATUS 6M
    Collection Date 2012-02-25
     
    Diffraction Radiation
    Diffraction Protocol Single Wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 17-ID
    Wavelength List 1.0000
    Site APS
    Beamline 17-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.6
    Resolution(Low) 65.01
    Number Reflections(All) 54313
    Number Reflections(Observed) 54313
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.076
    Redundancy 10.2
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.63
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.01257
    Mean I Over Sigma(Observed) 2.1
    Redundancy 10.3
    Number Unique Reflections(All) 2687
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 37.535
    Cut-off Sigma(F) 1.72
    Number of Reflections(Observed) 54268
    Number of Reflections(R-Free) 2761
    Percent Reflections(Observed) 99.99
    R-Factor(Observed) 0.1626
    R-Work 0.1611
    R-Free 0.1901
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.8953
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.6276
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2554
    R-Factor(R-Work) 0.2386
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6276
    Shell Resolution(Low) 1.6572
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.2271
    R-Factor(R-Free) 0.2772
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6572
    Shell Resolution(Low) 1.6891
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2521
    R-Factor(R-Work) 0.2295
    R-Factor(R-Free) 0.2443
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6891
    Shell Resolution(Low) 1.7235
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.2367
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7235
    Shell Resolution(Low) 1.761
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2550
    R-Factor(R-Work) 0.2002
    R-Factor(R-Free) 0.237
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.761
    Shell Resolution(Low) 1.802
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2553
    R-Factor(R-Work) 0.2001
    R-Factor(R-Free) 0.2176
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.802
    Shell Resolution(Low) 1.8471
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.1771
    R-Factor(R-Free) 0.2
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8471
    Shell Resolution(Low) 1.897
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2549
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.2109
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.897
    Shell Resolution(Low) 1.9528
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2571
    R-Factor(R-Work) 0.1638
    R-Factor(R-Free) 0.1893
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9528
    Shell Resolution(Low) 2.0158
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2569
    R-Factor(R-Work) 0.1608
    R-Factor(R-Free) 0.2143
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0158
    Shell Resolution(Low) 2.0879
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1534
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0879
    Shell Resolution(Low) 2.1715
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2561
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1788
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1715
    Shell Resolution(Low) 2.2703
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.142
    R-Factor(R-Free) 0.1714
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2703
    Shell Resolution(Low) 2.39
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.1453
    R-Factor(R-Free) 0.153
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.39
    Shell Resolution(Low) 2.5397
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1529
    R-Factor(R-Free) 0.1789
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5397
    Shell Resolution(Low) 2.7357
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.1874
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7357
    Shell Resolution(Low) 3.0109
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.1923
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0109
    Shell Resolution(Low) 3.4463
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.1649
    R-Factor(R-Free) 0.1974
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4463
    Shell Resolution(Low) 4.341
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1409
    R-Factor(R-Free) 0.155
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.341
    Shell Resolution(Low) 37.5458
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.1581
    R-Factor(R-Free) 0.2054
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.926
    f_plane_restr 0.008
    f_chiral_restr 0.083
    f_angle_d 1.046
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2703
    Nucleic Acid Atoms 0
    Heterogen Atoms 77
    Solvent Atoms 259
     
     
  •   Software and Computing Hide
    Computing
    Data Collection JDIRECTOR
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_1148)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 0.1.27