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X-RAY DIFFRACTION
Materials and Methods page
4FYX
  •   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 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 121.21 α = 90
    b = 121.21 β = 90
    c = 141.76 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 2012-01-19
     
    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) 2.09
    Resolution(Low) 50
    Number Reflections(All) 71745
    Number Reflections(Observed) 71745
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.145
    Redundancy 22.3
     
    High Resolution Shell Details
    Resolution(High) 2.0889
    Resolution(Low) 2.18
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.684
    Redundancy 20.3
    Number Unique Reflections(All) 7107
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0889
    Resolution(Low) 49.22
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 71777
    Number of Reflections(Observed) 71741
    Number of Reflections(R-Free) 3630
    Percent Reflections(Observed) 99.95
    R-Factor(Observed) 0.1676
    R-Work 0.1652
    R-Free 0.2125
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.2654
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0889
    Shell Resolution(Low) 2.1164
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2560
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.254
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1164
    Shell Resolution(Low) 2.1454
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2603
    R-Factor(R-Work) 0.1935
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1454
    Shell Resolution(Low) 2.176
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2569
    R-Factor(R-Work) 0.1874
    R-Factor(R-Free) 0.2465
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.176
    Shell Resolution(Low) 2.2085
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.1772
    R-Factor(R-Free) 0.2467
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2085
    Shell Resolution(Low) 2.243
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.2386
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.243
    Shell Resolution(Low) 2.2798
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2571
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2798
    Shell Resolution(Low) 2.3191
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.1773
    R-Factor(R-Free) 0.2325
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3191
    Shell Resolution(Low) 2.3613
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.1738
    R-Factor(R-Free) 0.2622
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3613
    Shell Resolution(Low) 2.4067
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.1706
    R-Factor(R-Free) 0.2293
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4067
    Shell Resolution(Low) 2.4558
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.2495
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4558
    Shell Resolution(Low) 2.5092
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.2037
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5092
    Shell Resolution(Low) 2.5676
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2581
    R-Factor(R-Work) 0.1639
    R-Factor(R-Free) 0.221
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5676
    Shell Resolution(Low) 2.6318
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1696
    R-Factor(R-Free) 0.2647
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6318
    Shell Resolution(Low) 2.703
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.179
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.703
    Shell Resolution(Low) 2.7825
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.1772
    R-Factor(R-Free) 0.2303
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7825
    Shell Resolution(Low) 2.8723
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.1809
    R-Factor(R-Free) 0.2392
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8723
    Shell Resolution(Low) 2.9749
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.1737
    R-Factor(R-Free) 0.2561
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9749
    Shell Resolution(Low) 3.094
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2041
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.094
    Shell Resolution(Low) 3.2348
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2223
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2348
    Shell Resolution(Low) 3.4053
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2152
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4053
    Shell Resolution(Low) 3.6186
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.1848
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6186
    Shell Resolution(Low) 3.8979
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.2063
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8979
    Shell Resolution(Low) 4.29
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1374
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.29
    Shell Resolution(Low) 4.9102
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1311
    R-Factor(R-Free) 0.1721
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9102
    Shell Resolution(Low) 6.1845
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.1677
    R-Factor(R-Free) 0.2026
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1845
    Shell Resolution(Low) 49.2341
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2820
    R-Factor(R-Work) 0.1755
    R-Factor(R-Free) 0.1831
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.029
    f_plane_restr 0.005
    f_chiral_restr 0.077
    f_angle_d 1.07
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7149
    Nucleic Acid Atoms 0
    Heterogen Atoms 118
    Solvent Atoms 634
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL