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X-RAY DIFFRACTION
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4HUB
Re-refined structure
Text THIS ENTRY 4HUB REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1FFKSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1FFK: N.BAN, P.NISSEN, J.HANSEN, P.B.MOORE, T.A.STEITZ
 
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 211.66 α = 90
    b = 299.67 β = 90
    c = 573.77 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Radiation
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.404
    Resolution(Low) 85.478
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 666777
    Number of Reflections(Observed) 666777
    Number of Reflections(R-Free) 6672
    Percent Reflections(Observed) 95.49
    R-Factor(All) 0.167
    R-Factor(Observed) 0.166
    R-Work 0.1656
    R-Free 0.2062
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.404
    Shell Resolution(Low) 2.4308
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 15697
    R-Factor(R-Work) 0.277
    R-Factor(R-Free) 0.3194
    Percent Reflections(Observed) 69.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4308
    Shell Resolution(Low) 2.4594
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 16850
    R-Factor(R-Work) 0.2569
    R-Factor(R-Free) 0.315
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4594
    Shell Resolution(Low) 2.4894
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 17611
    R-Factor(R-Work) 0.2502
    R-Factor(R-Free) 0.3109
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4894
    Shell Resolution(Low) 2.5209
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 18432
    R-Factor(R-Work) 0.2494
    R-Factor(R-Free) 0.2719
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5209
    Shell Resolution(Low) 2.5541
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 19386
    R-Factor(R-Work) 0.2489
    R-Factor(R-Free) 0.2963
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5541
    Shell Resolution(Low) 2.5891
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 20385
    R-Factor(R-Work) 0.2482
    R-Factor(R-Free) 0.3105
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5891
    Shell Resolution(Low) 2.6261
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 21533
    R-Factor(R-Work) 0.2463
    R-Factor(R-Free) 0.3153
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6261
    Shell Resolution(Low) 2.6653
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 22653
    R-Factor(R-Work) 0.2391
    R-Factor(R-Free) 0.3118
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6653
    Shell Resolution(Low) 2.707
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 22944
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.2688
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.707
    Shell Resolution(Low) 2.7513
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 22969
    R-Factor(R-Work) 0.2337
    R-Factor(R-Free) 0.2897
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7513
    Shell Resolution(Low) 2.7988
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 22924
    R-Factor(R-Work) 0.2255
    R-Factor(R-Free) 0.2951
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7988
    Shell Resolution(Low) 2.8497
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 22954
    R-Factor(R-Work) 0.2241
    R-Factor(R-Free) 0.2407
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8497
    Shell Resolution(Low) 2.9045
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 23001
    R-Factor(R-Work) 0.2181
    R-Factor(R-Free) 0.2984
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9045
    Shell Resolution(Low) 2.9638
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 22986
    R-Factor(R-Work) 0.2143
    R-Factor(R-Free) 0.2634
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9638
    Shell Resolution(Low) 3.0282
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 22957
    R-Factor(R-Work) 0.2074
    R-Factor(R-Free) 0.2619
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0282
    Shell Resolution(Low) 3.0987
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 22938
    R-Factor(R-Work) 0.1965
    R-Factor(R-Free) 0.2322
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0987
    Shell Resolution(Low) 3.1762
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 22929
    R-Factor(R-Work) 0.183
    R-Factor(R-Free) 0.2147
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1762
    Shell Resolution(Low) 3.262
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 23001
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.2203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.262
    Shell Resolution(Low) 3.358
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 22988
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.358
    Shell Resolution(Low) 3.4664
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 23041
    R-Factor(R-Work) 0.1612
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4664
    Shell Resolution(Low) 3.5903
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 22975
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.2033
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5903
    Shell Resolution(Low) 3.7341
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 23062
    R-Factor(R-Work) 0.1405
    R-Factor(R-Free) 0.1799
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7341
    Shell Resolution(Low) 3.904
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 23077
    R-Factor(R-Work) 0.1343
    R-Factor(R-Free) 0.1606
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.904
    Shell Resolution(Low) 4.1098
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 22997
    R-Factor(R-Work) 0.1284
    R-Factor(R-Free) 0.1725
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1098
    Shell Resolution(Low) 4.3673
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 23150
    R-Factor(R-Work) 0.1263
    R-Factor(R-Free) 0.1652
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3673
    Shell Resolution(Low) 4.7045
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 23168
    R-Factor(R-Work) 0.1219
    R-Factor(R-Free) 0.1622
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7045
    Shell Resolution(Low) 5.1779
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 23071
    R-Factor(R-Work) 0.1196
    R-Factor(R-Free) 0.1463
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1779
    Shell Resolution(Low) 5.927
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 23266
    R-Factor(R-Work) 0.1223
    R-Factor(R-Free) 0.1538
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.927
    Shell Resolution(Low) 7.4667
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 23371
    R-Factor(R-Work) 0.1406
    R-Factor(R-Free) 0.1862
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.4667
    Shell Resolution(Low) 85.5317
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 23789
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1822
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.057
    f_dihedral_angle_d 13.827
    f_angle_d 1.078
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 32583
    Nucleic Acid Atoms 62785
    Heterogen Atoms 277
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DENZO
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building CNS
    data collection DENZO