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X-RAY DIFFRACTION
Materials and Methods page
3NE5
  •   Crystallization Hide
    Crystallization Experiments
    Method EVAPORATION
    pH 7.5
    Temperature 298.0
    Details 10 % PEG3350, 0.4M NH4SO4, 1% JM600, 5% Glycerol, 0.1M Bis-tris propane (7.5), EVAPORATION, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 160.27 α = 90
    b = 160.27 β = 90
    c = 682.84 γ = 120
     
    Space Group
    Space Group Name:    H 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-04-09
     
    Diffraction Radiation
    Monochromator Cryo-Cooled Si(111) double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9792
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.9
    Resolution(Low) 39.5
    Number Reflections(Observed) 75498
    Percent Possible(Observed) 93.2
    R Merge I(Observed) 0.09
    Redundancy 1.4
     
    High Resolution Shell Details
    Resolution(High) 2.898
    Resolution(Low) 3.0
    Percent Possible(All) 90.9
    R Merge I(Observed) 0.493
    Mean I Over Sigma(Observed) 1.5
    Redundancy 1.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.898
    Resolution(Low) 39.493
    Cut-off Sigma(F) 0.09
    Number of Reflections(Observed) 59612
    Number of Reflections(R-Free) 2975
    Percent Reflections(Observed) 78.93
    R-Factor(Observed) 0.231
    R-Work 0.229
    R-Free 0.267
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 69.29
    Anisotropic B[1][1] 3.572
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.572
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -7.143
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.898
    Shell Resolution(Low) 2.945
    Number of Reflections(R-Free) 84
    Number of Reflections(R-Work) 2066
    R-Factor(R-Work) 0.368
    R-Factor(R-Free) 0.428
    Percent Reflections(Observed) 61.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.945
    Shell Resolution(Low) 2.996
    Number of Reflections(R-Free) 110
    Number of Reflections(R-Work) 2170
    R-Factor(R-Work) 0.355
    R-Factor(R-Free) 0.366
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.996
    Shell Resolution(Low) 3.051
    Number of Reflections(R-Free) 97
    Number of Reflections(R-Work) 2151
    R-Factor(R-Work) 0.346
    R-Factor(R-Free) 0.395
    Percent Reflections(Observed) 63.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.051
    Shell Resolution(Low) 3.109
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2222
    R-Factor(R-Work) 0.33
    R-Factor(R-Free) 0.384
    Percent Reflections(Observed) 66.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.109
    Shell Resolution(Low) 3.173
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2288
    R-Factor(R-Work) 0.314
    R-Factor(R-Free) 0.36
    Percent Reflections(Observed) 68.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.173
    Shell Resolution(Low) 3.242
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2339
    R-Factor(R-Work) 0.293
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.242
    Shell Resolution(Low) 3.317
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2428
    R-Factor(R-Work) 0.285
    R-Factor(R-Free) 0.374
    Percent Reflections(Observed) 71.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.317
    Shell Resolution(Low) 3.4
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2538
    R-Factor(R-Work) 0.274
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4
    Shell Resolution(Low) 3.492
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2561
    R-Factor(R-Work) 0.261
    R-Factor(R-Free) 0.307
    Percent Reflections(Observed) 76.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.492
    Shell Resolution(Low) 3.595
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.258
    R-Factor(R-Free) 0.285
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.595
    Shell Resolution(Low) 3.711
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.313
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.711
    Shell Resolution(Low) 3.843
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2748
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.843
    Shell Resolution(Low) 3.997
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2825
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.279
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.997
    Shell Resolution(Low) 4.179
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2857
    R-Factor(R-Work) 0.191
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.179
    Shell Resolution(Low) 4.399
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 2909
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.399
    Shell Resolution(Low) 4.674
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3035
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.213
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.674
    Shell Resolution(Low) 5.034
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3089
    R-Factor(R-Work) 0.158
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.034
    Shell Resolution(Low) 5.539
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3143
    R-Factor(R-Work) 0.182
    R-Factor(R-Free) 0.243
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.539
    Shell Resolution(Low) 6.338
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3181
    R-Factor(R-Work) 0.208
    R-Factor(R-Free) 0.225
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.338
    Shell Resolution(Low) 7.975
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3222
    R-Factor(R-Work) 0.209
    R-Factor(R-Free) 0.242
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.975
    Shell Resolution(Low) 39.496
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3522
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.224
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.223
    f_plane_restr 0.003
    f_chiral_restr 0.046
    f_angle_d 0.683
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12854
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 19
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine)
     
    Software
    data extraction pdb_extract version: 3.100
    refinement phenix
    molecular replacement Phaser
    data scaling SCALEPACK