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X-RAY DIFFRACTION
Materials and Methods page
4FYV
  •   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 dCTP, pH 5.7, MICRODIALYSIS, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 120.68 α = 90
    b = 120.68 β = 90
    c = 142.52 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 CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-01-18
     
    Diffraction Radiation
    Monochromator Rosenbaum-Rock double crystal sagittal focusing monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(All) 70569
    Number Reflections(Observed) 70569
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.107
    Redundancy 23.1
     
    High Resolution Shell Details
    Resolution(High) 2.0976
    Resolution(Low) 2.18
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.562
    Redundancy 21.1
    Number Unique Reflections(All) 6979
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 2.0976
    Resolution(Low) 49.062
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 70565
    Number of Reflections(R-Free) 3564
    Percent Reflections(Observed) 99.84
    R-Factor(Observed) 0.1771
    R-Work 0.1751
    R-Free 0.2152
     
    Temperature Factor Modeling
    Mean Isotropic B Value 56.7152
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0976
    Shell Resolution(Low) 2.1263
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2550
    R-Factor(R-Work) 0.2158
    R-Factor(R-Free) 0.2451
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1263
    Shell Resolution(Low) 2.1567
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.2129
    R-Factor(R-Free) 0.2907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1567
    Shell Resolution(Low) 2.1889
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.2053
    R-Factor(R-Free) 0.2756
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1889
    Shell Resolution(Low) 2.2231
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2499
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2231
    Shell Resolution(Low) 2.2595
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.1945
    R-Factor(R-Free) 0.2354
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2595
    Shell Resolution(Low) 2.2985
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2592
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2985
    Shell Resolution(Low) 2.3403
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.1977
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3403
    Shell Resolution(Low) 2.3853
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.1919
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3853
    Shell Resolution(Low) 2.434
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2681
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.2376
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.434
    Shell Resolution(Low) 2.4869
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1881
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4869
    Shell Resolution(Low) 2.5447
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5447
    Shell Resolution(Low) 2.6084
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.1882
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6084
    Shell Resolution(Low) 2.6789
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.1865
    R-Factor(R-Free) 0.2499
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6789
    Shell Resolution(Low) 2.7577
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7577
    Shell Resolution(Low) 2.8467
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.195
    R-Factor(R-Free) 0.2572
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8467
    Shell Resolution(Low) 2.9485
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2702
    R-Factor(R-Work) 0.1974
    R-Factor(R-Free) 0.2693
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9485
    Shell Resolution(Low) 3.0665
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.1885
    R-Factor(R-Free) 0.2488
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0665
    Shell Resolution(Low) 3.206
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1914
    R-Factor(R-Free) 0.2313
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.206
    Shell Resolution(Low) 3.375
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.2395
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.375
    Shell Resolution(Low) 3.5864
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.2049
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5864
    Shell Resolution(Low) 3.8632
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.1699
    R-Factor(R-Free) 0.2114
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8632
    Shell Resolution(Low) 4.2518
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.1478
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2518
    Shell Resolution(Low) 4.8666
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.1417
    R-Factor(R-Free) 0.1716
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8666
    Shell Resolution(Low) 6.1295
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2764
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1295
    Shell Resolution(Low) 49.0756
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2902
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.1671
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.069
    f_plane_restr 0.005
    f_chiral_restr 0.076
    f_angle_d 1.122
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7082
    Nucleic Acid Atoms 0
    Heterogen Atoms 63
    Solvent Atoms 496
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution PHENIX
    Structure Refinement PHENIX
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL