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X-RAY DIFFRACTION
Materials and Methods page
4FYW
  •   Crystallization Hide
    Crystallization Experiments
    Method MICRODIALYSIS
    pH 5.7
    Temperature 298.0
    Details 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM CTP, pH 5.7, MICRODIALYSIS, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 121.3 α = 90
    b = 121.3 β = 90
    c = 142.25 γ = 120
     
    Space Group
    Space Group Name:    P 3 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Collection Date 2012-01-25
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.542
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 43.22
    Number Reflections(All) 70735
    Number Reflections(Observed) 70735
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.057
    Redundancy 5.35
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.18
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.45
    Mean I Over Sigma(Observed) 2.6
    Redundancy 5.28
    Number Unique Reflections(All) 6982
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 43.218
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 70735
    Number of Reflections(Observed) 70722
    Number of Reflections(R-Free) 3569
    Percent Reflections(Observed) 99.64
    R-Factor(Observed) 0.186
    R-Work 0.1838
    R-Free 0.2291
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.0296
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.1288
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.2637
    R-Factor(R-Free) 0.3248
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1288
    Shell Resolution(Low) 2.1592
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.2499
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1592
    Shell Resolution(Low) 2.1914
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.2516
    R-Factor(R-Free) 0.3272
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1914
    Shell Resolution(Low) 2.2257
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.2416
    R-Factor(R-Free) 0.3057
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2257
    Shell Resolution(Low) 2.2621
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.2559
    R-Factor(R-Free) 0.3465
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2621
    Shell Resolution(Low) 2.3011
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.2589
    R-Factor(R-Free) 0.3464
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3011
    Shell Resolution(Low) 2.343
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.2513
    R-Factor(R-Free) 0.3151
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.343
    Shell Resolution(Low) 2.3881
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.2369
    R-Factor(R-Free) 0.3303
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3881
    Shell Resolution(Low) 2.4368
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.2367
    R-Factor(R-Free) 0.2591
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4368
    Shell Resolution(Low) 2.4898
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2687
    R-Factor(R-Work) 0.2392
    R-Factor(R-Free) 0.2695
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4898
    Shell Resolution(Low) 2.5477
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.2231
    R-Factor(R-Free) 0.331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5477
    Shell Resolution(Low) 2.6114
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6114
    Shell Resolution(Low) 2.682
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2681
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.3239
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.682
    Shell Resolution(Low) 2.7609
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2154
    R-Factor(R-Free) 0.266
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7609
    Shell Resolution(Low) 2.85
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.85
    Shell Resolution(Low) 2.9518
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.2054
    R-Factor(R-Free) 0.2652
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9518
    Shell Resolution(Low) 3.07
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.257
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.07
    Shell Resolution(Low) 3.2097
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.261
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2097
    Shell Resolution(Low) 3.3788
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1902
    R-Factor(R-Free) 0.2953
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3788
    Shell Resolution(Low) 3.5904
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.1721
    R-Factor(R-Free) 0.226
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5904
    Shell Resolution(Low) 3.8675
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.2124
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8675
    Shell Resolution(Low) 4.2564
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.1429
    R-Factor(R-Free) 0.147
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2564
    Shell Resolution(Low) 4.8715
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.1357
    R-Factor(R-Free) 0.1654
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8715
    Shell Resolution(Low) 6.1348
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.1643
    R-Factor(R-Free) 0.1723
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1348
    Shell Resolution(Low) 43.2272
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2884
    R-Factor(R-Work) 0.1683
    R-Factor(R-Free) 0.1856
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.243
    f_plane_restr 0.005
    f_chiral_restr 0.078
    f_angle_d 1.128
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7083
    Nucleic Acid Atoms 0
    Heterogen Atoms 60
    Solvent Atoms 571
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) d*TREK
    Structure Solution PHENIX
    Structure Refinement PHENIX
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction D*trek version: 9.9.8.8D
    data collection D*trek version: 9.9.8.8D