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X-RAY DIFFRACTION
Materials and Methods page
4K50
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 289.0
    Details 0.16 M ammonium sulfate, 0.08 M sodium acetate, pH 4.6, 20% (w/v) PEG 4000, and 20% (v/v) glycerol and directly frozen , VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.75 α = 90.01
    b = 113.89 β = 90.49
    c = 122.6 γ = 90
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type NOIR-1
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength List 1.00
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.5
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.93
    Resolution(Low) 49.07
    Number Reflections(Observed) 61473
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.108
    Redundancy 1.98
     
    High Resolution Shell Details
    Resolution(High) 2.93
    Resolution(Low) 3.03
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.438
    Mean I Over Sigma(Observed) 1.6
    Redundancy 1.98
    Number Unique Reflections(All) 6165
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.93
    Resolution(Low) 45.303
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 61310
    Number of Reflections(R-Free) 3069
    Percent Reflections(Observed) 98.15
    R-Factor(Observed) 0.1935
    R-Work 0.1907
    R-Free 0.2474
     
    Temperature Factor Modeling
    Mean Isotropic B Value 37.7811
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.93
    Shell Resolution(Low) 2.9758
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.3199
    R-Factor(R-Free) 0.3808
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9758
    Shell Resolution(Low) 3.0246
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2596
    R-Factor(R-Work) 0.3063
    R-Factor(R-Free) 0.3725
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0246
    Shell Resolution(Low) 3.0767
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.3008
    R-Factor(R-Free) 0.4297
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0767
    Shell Resolution(Low) 3.1327
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.2837
    R-Factor(R-Free) 0.3564
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1327
    Shell Resolution(Low) 3.1929
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.2617
    R-Factor(R-Free) 0.3178
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1929
    Shell Resolution(Low) 3.2581
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.2539
    R-Factor(R-Free) 0.378
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2581
    Shell Resolution(Low) 3.3289
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.2426
    R-Factor(R-Free) 0.3192
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3289
    Shell Resolution(Low) 3.4063
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.2428
    R-Factor(R-Free) 0.3091
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4063
    Shell Resolution(Low) 3.4914
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.2201
    R-Factor(R-Free) 0.2714
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4914
    Shell Resolution(Low) 3.5858
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.2186
    R-Factor(R-Free) 0.3103
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5858
    Shell Resolution(Low) 3.6913
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.2066
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6913
    Shell Resolution(Low) 3.8104
    Number of Reflections(R-Free) 100
    Number of Reflections(R-Work) 2750
    R-Factor(R-Work) 0.1845
    R-Factor(R-Free) 0.2256
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8104
    Shell Resolution(Low) 3.9465
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.179
    R-Factor(R-Free) 0.2496
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9465
    Shell Resolution(Low) 4.1044
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1044
    Shell Resolution(Low) 4.291
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.1529
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.291
    Shell Resolution(Low) 4.5171
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1449
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5171
    Shell Resolution(Low) 4.7998
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.1395
    R-Factor(R-Free) 0.1792
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7998
    Shell Resolution(Low) 5.1699
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.1443
    R-Factor(R-Free) 0.1912
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1699
    Shell Resolution(Low) 5.6893
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1508
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6893
    Shell Resolution(Low) 6.5105
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.2212
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5105
    Shell Resolution(Low) 8.1946
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.1946
    Shell Resolution(Low) 45.3085
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2571
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.173
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.788
    f_plane_restr 0.007
    f_chiral_restr 0.052
    f_angle_d 1.187
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14740
    Nucleic Acid Atoms 3928
    Heterogen Atoms 111
    Solvent Atoms 408
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) DTREK
    Data Reduction (data scaling) DTREK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction D*trek version: 9.9.9.1L
    data collection D*trek