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X-RAY DIFFRACTION
Materials and Methods page
4FYY
  •   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 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 121.13 α = 90
    b = 121.13 β = 90
    c = 141.44 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) 1.94
    Resolution(Low) 50
    Number Reflections(All) 89121
    Number Reflections(Observed) 89121
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.137
    Redundancy 22.0
     
    High Resolution Shell Details
    Resolution(High) 1.9395
    Resolution(Low) 2.01
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.608
    Redundancy 19.5
    Number Unique Reflections(All) 8794
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9395
    Resolution(Low) 49.179
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 89196
    Number of Reflections(Observed) 89119
    Number of Reflections(R-Free) 4462
    Percent Reflections(Observed) 99.98
    R-Factor(Observed) 0.1948
    R-Work 0.1926
    R-Free 0.2365
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 41.2092
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9395
    Shell Resolution(Low) 1.9615
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2784
    R-Factor(R-Work) 0.2003
    R-Factor(R-Free) 0.2355
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9615
    Shell Resolution(Low) 1.9846
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2777
    R-Factor(R-Work) 0.1996
    R-Factor(R-Free) 0.2702
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9846
    Shell Resolution(Low) 2.0088
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2779
    R-Factor(R-Work) 0.2065
    R-Factor(R-Free) 0.2672
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0088
    Shell Resolution(Low) 2.0342
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2772
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.2624
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0342
    Shell Resolution(Low) 2.061
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2829
    R-Factor(R-Work) 0.2017
    R-Factor(R-Free) 0.2829
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.061
    Shell Resolution(Low) 2.0892
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2770
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0892
    Shell Resolution(Low) 2.1191
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2812
    R-Factor(R-Work) 0.1837
    R-Factor(R-Free) 0.2151
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1191
    Shell Resolution(Low) 2.1507
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2799
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1507
    Shell Resolution(Low) 2.1843
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2780
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.2439
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1843
    Shell Resolution(Low) 2.2201
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2768
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.2341
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2201
    Shell Resolution(Low) 2.2584
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2805
    R-Factor(R-Work) 0.1791
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2584
    Shell Resolution(Low) 2.2995
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2826
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2389
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2995
    Shell Resolution(Low) 2.3437
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.2168
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3437
    Shell Resolution(Low) 2.3915
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2800
    R-Factor(R-Work) 0.1837
    R-Factor(R-Free) 0.2517
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3915
    Shell Resolution(Low) 2.4435
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2828
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4435
    Shell Resolution(Low) 2.5004
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2815
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.2089
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5004
    Shell Resolution(Low) 2.5629
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2804
    R-Factor(R-Work) 0.183
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5629
    Shell Resolution(Low) 2.6322
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2819
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.2716
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6322
    Shell Resolution(Low) 2.7096
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2809
    R-Factor(R-Work) 0.1837
    R-Factor(R-Free) 0.2339
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7096
    Shell Resolution(Low) 2.7971
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2807
    R-Factor(R-Work) 0.1898
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7971
    Shell Resolution(Low) 2.897
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2827
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.2304
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.897
    Shell Resolution(Low) 3.013
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2840
    R-Factor(R-Work) 0.196
    R-Factor(R-Free) 0.2455
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.013
    Shell Resolution(Low) 3.1501
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2853
    R-Factor(R-Work) 0.2006
    R-Factor(R-Free) 0.2683
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1501
    Shell Resolution(Low) 3.3162
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2819
    R-Factor(R-Work) 0.2043
    R-Factor(R-Free) 0.2469
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3162
    Shell Resolution(Low) 3.5239
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2842
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2366
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5239
    Shell Resolution(Low) 3.7959
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2865
    R-Factor(R-Work) 0.1902
    R-Factor(R-Free) 0.2399
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7959
    Shell Resolution(Low) 4.1777
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2857
    R-Factor(R-Work) 0.1842
    R-Factor(R-Free) 0.2401
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1777
    Shell Resolution(Low) 4.7818
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 2858
    R-Factor(R-Work) 0.1811
    R-Factor(R-Free) 0.2392
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7818
    Shell Resolution(Low) 6.0228
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2888
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2116
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0228
    Shell Resolution(Low) 49.195
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 3038
    R-Factor(R-Work) 0.2134
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.002
    f_plane_restr 0.005
    f_chiral_restr 0.077
    f_angle_d 1.139
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7140
    Nucleic Acid Atoms 0
    Heterogen Atoms 120
    Solvent Atoms 574
     
     
  •   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