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X-RAY DIFFRACTION
Materials and Methods page
4JER
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7.8
    Temperature 293.0
    Details 0.2 M potassium sodium tartarate tetrahydrate, 20% (w/v) PEG 3350, pH 7.8, vapor diffusion, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.34 α = 90
    b = 70.34 β = 90
    c = 74.84 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2012-02-25
     
    Diffraction Radiation
    Diffraction Protocol Single Wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 17-ID
    Wavelength List 1.0000
    Site APS
    Beamline 17-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.1
    Resolution(Low) 51.26
    Number Reflections(All) 76552
    Number Reflections(Observed) 76552
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.042
    Redundancy 8.3
     
    High Resolution Shell Details
    Resolution(High) 1.1
    Resolution(Low) 1.12
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.755
    Mean I Over Sigma(Observed) 2.9
    Redundancy 8.2
    Number Unique Reflections(All) 3745
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.1
    Resolution(Low) 33.036
    Cut-off Sigma(F) 1.72
    Number of Reflections(Observed) 76478
    Number of Reflections(R-Free) 3844
    Percent Reflections(Observed) 99.95
    R-Factor(Observed) 0.1391
    R-Work 0.1387
    R-Free 0.146
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.9167
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1
    Shell Resolution(Low) 1.1139
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2149
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1139
    Shell Resolution(Low) 1.1286
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1852
    R-Factor(R-Free) 0.1948
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1286
    Shell Resolution(Low) 1.1441
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.1639
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1441
    Shell Resolution(Low) 1.1604
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.1576
    R-Factor(R-Free) 0.1621
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1604
    Shell Resolution(Low) 1.1777
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.1414
    R-Factor(R-Free) 0.1631
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1777
    Shell Resolution(Low) 1.1961
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1424
    R-Factor(R-Free) 0.155
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1961
    Shell Resolution(Low) 1.2157
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1354
    R-Factor(R-Free) 0.1586
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2157
    Shell Resolution(Low) 1.2367
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1325
    R-Factor(R-Free) 0.1433
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2367
    Shell Resolution(Low) 1.2592
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1233
    R-Factor(R-Free) 0.1331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2592
    Shell Resolution(Low) 1.2834
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.1228
    R-Factor(R-Free) 0.1587
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2834
    Shell Resolution(Low) 1.3096
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1144
    R-Factor(R-Free) 0.1325
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3096
    Shell Resolution(Low) 1.3381
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1073
    R-Factor(R-Free) 0.1431
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3381
    Shell Resolution(Low) 1.3692
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1067
    R-Factor(R-Free) 0.1322
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3692
    Shell Resolution(Low) 1.4034
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.1066
    R-Factor(R-Free) 0.1337
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4034
    Shell Resolution(Low) 1.4414
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.1029
    R-Factor(R-Free) 0.1181
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4414
    Shell Resolution(Low) 1.4838
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.0997
    R-Factor(R-Free) 0.1354
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4838
    Shell Resolution(Low) 1.5317
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.1003
    R-Factor(R-Free) 0.1184
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5317
    Shell Resolution(Low) 1.5864
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.0991
    R-Factor(R-Free) 0.1085
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5864
    Shell Resolution(Low) 1.65
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1062
    R-Factor(R-Free) 0.1083
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.65
    Shell Resolution(Low) 1.7251
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.1118
    R-Factor(R-Free) 0.1247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7251
    Shell Resolution(Low) 1.816
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.1186
    R-Factor(R-Free) 0.1328
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.816
    Shell Resolution(Low) 1.9298
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2692
    R-Factor(R-Work) 0.1249
    R-Factor(R-Free) 0.1305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9298
    Shell Resolution(Low) 2.0787
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2716
    R-Factor(R-Work) 0.1275
    R-Factor(R-Free) 0.1342
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0787
    Shell Resolution(Low) 2.2879
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.1334
    R-Factor(R-Free) 0.1428
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2879
    Shell Resolution(Low) 2.6188
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2764
    R-Factor(R-Work) 0.1494
    R-Factor(R-Free) 0.1768
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6188
    Shell Resolution(Low) 3.299
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2763
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.1455
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.299
    Shell Resolution(Low) 33.051
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2950
    R-Factor(R-Work) 0.1617
    R-Factor(R-Free) 0.1676
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.08
    f_plane_restr 0.009
    f_chiral_restr 0.092
    f_angle_d 1.214
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1381
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 220
     
     
  •   Software and Computing Hide
    Computing
    Data Collection JDIRECTOR
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_1131)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 0.1.27
    data collection Mosflm