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X-RAY DIFFRACTION
Materials and Methods page
4OO8
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 8
    Temperature 293.0
    Details 12% PEG 3350, 100mM Tris-HCl, 200mM ammonium acetate, 150mM NaCl, 100mM NDSB-256, pH 8.0, vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 76.71 α = 97.68
    b = 105.69 β = 98.43
    c = 126.82 γ = 100.31
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2013-11-12
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL32XU
    Wavelength List 1.000
    Site SPRING-8
    Beamline BL32XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.5
    Resolution(Low) 46.88
    Number Reflections(Observed) 130485
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.063
    B(Isotropic) From Wilson Plot 59.84
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.65
    Percent Possible(All) 96.2
    R Merge I(Observed) 0.011
    Mean I Over Sigma(Observed) 2.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 46.701
    Cut-off Sigma(F) 1.98
    Number of Reflections(all) 130396
    Number of Reflections(Observed) 130396
    Number of Reflections(R-Free) 6521
    Percent Reflections(Observed) 98.53
    R-Factor(All) 0.2235
    R-Factor(Observed) 0.2235
    R-Work 0.2219
    R-Free 0.2536
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 80.5122
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.5284
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4151
    R-Factor(R-Work) 0.3414
    R-Factor(R-Free) 0.3789
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5284
    Shell Resolution(Low) 2.5582
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4100
    R-Factor(R-Work) 0.3223
    R-Factor(R-Free) 0.3575
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5582
    Shell Resolution(Low) 2.5894
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4100
    R-Factor(R-Work) 0.318
    R-Factor(R-Free) 0.3414
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5894
    Shell Resolution(Low) 2.6221
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.3158
    R-Factor(R-Free) 0.3573
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6221
    Shell Resolution(Low) 2.6566
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4127
    R-Factor(R-Work) 0.3124
    R-Factor(R-Free) 0.3438
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6566
    Shell Resolution(Low) 2.693
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4068
    R-Factor(R-Work) 0.2998
    R-Factor(R-Free) 0.3239
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.693
    Shell Resolution(Low) 2.7315
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4110
    R-Factor(R-Work) 0.2951
    R-Factor(R-Free) 0.3468
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7315
    Shell Resolution(Low) 2.7723
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4128
    R-Factor(R-Work) 0.2912
    R-Factor(R-Free) 0.3449
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7723
    Shell Resolution(Low) 2.8156
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4125
    R-Factor(R-Work) 0.2887
    R-Factor(R-Free) 0.3274
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8156
    Shell Resolution(Low) 2.8617
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4109
    R-Factor(R-Work) 0.2781
    R-Factor(R-Free) 0.3203
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8617
    Shell Resolution(Low) 2.9111
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4098
    R-Factor(R-Work) 0.2932
    R-Factor(R-Free) 0.3091
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9111
    Shell Resolution(Low) 2.964
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4169
    R-Factor(R-Work) 0.2945
    R-Factor(R-Free) 0.3288
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.964
    Shell Resolution(Low) 3.021
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4113
    R-Factor(R-Work) 0.2877
    R-Factor(R-Free) 0.3027
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.021
    Shell Resolution(Low) 3.0826
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4151
    R-Factor(R-Work) 0.2786
    R-Factor(R-Free) 0.3069
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0826
    Shell Resolution(Low) 3.1497
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.2666
    R-Factor(R-Free) 0.3017
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1497
    Shell Resolution(Low) 3.2229
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4156
    R-Factor(R-Work) 0.2584
    R-Factor(R-Free) 0.3039
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2229
    Shell Resolution(Low) 3.3035
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4148
    R-Factor(R-Work) 0.2487
    R-Factor(R-Free) 0.287
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3035
    Shell Resolution(Low) 3.3928
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4085
    R-Factor(R-Work) 0.2462
    R-Factor(R-Free) 0.2745
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3928
    Shell Resolution(Low) 3.4926
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4182
    R-Factor(R-Work) 0.2434
    R-Factor(R-Free) 0.2689
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4926
    Shell Resolution(Low) 3.6053
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4134
    R-Factor(R-Work) 0.2395
    R-Factor(R-Free) 0.2652
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6053
    Shell Resolution(Low) 3.7341
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4143
    R-Factor(R-Work) 0.2204
    R-Factor(R-Free) 0.2419
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7341
    Shell Resolution(Low) 3.8835
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4132
    R-Factor(R-Work) 0.2152
    R-Factor(R-Free) 0.2595
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8835
    Shell Resolution(Low) 4.0602
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4186
    R-Factor(R-Work) 0.2075
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0602
    Shell Resolution(Low) 4.2741
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4154
    R-Factor(R-Work) 0.1974
    R-Factor(R-Free) 0.2368
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2741
    Shell Resolution(Low) 4.5417
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4132
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.2377
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5417
    Shell Resolution(Low) 4.892
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4152
    R-Factor(R-Work) 0.1844
    R-Factor(R-Free) 0.1994
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.892
    Shell Resolution(Low) 5.3836
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4165
    R-Factor(R-Work) 0.1881
    R-Factor(R-Free) 0.2341
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3836
    Shell Resolution(Low) 6.1612
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4171
    R-Factor(R-Work) 0.1994
    R-Factor(R-Free) 0.2253
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1612
    Shell Resolution(Low) 7.7566
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4183
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2076
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7566
    Shell Resolution(Low) 46.7096
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 4021
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.1874
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.58
    f_plane_restr 0.002
    f_chiral_restr 0.022
    f_angle_d 0.526
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 18997
    Nucleic Acid Atoms 5012
    Heterogen Atoms 0
    Solvent Atoms 144
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8.3_1479)
     
    Software
    data extraction PDB_EXTRACT version: 3.14
    refinement phenix
    data reduction Xscale