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X-RAY DIFFRACTION
Materials and Methods page
4AFY
  •   Crystallization Hide
    Crystallization Experiments
    pH 7
    Details HEPES 0.1 M PH 8.0, NAH2PO4 0.8 M K2HPO4 0.8 M
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 104.33 α = 90
    b = 104.33 β = 90
    c = 154.24 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD (QUANTUM 315R)
    Type ADSC
    Collection Date 2008-12-04
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SOLEIL BEAMLINE PROXIMA 1
    Wavelength 0.9793
    Site SOLEIL
    Beamline PROXIMA 1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.01
    Resolution(Low) 50
    Number Reflections(Observed) 57232
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 43.8
    Redundancy 13.6
     
    High Resolution Shell Details
    Resolution(High) 2.01
    Resolution(Low) 2.06
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.38
    Mean I Over Sigma(Observed) 5.8
    Redundancy 8.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.01
    Resolution(Low) 43.209
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 57230
    Number of Reflections(R-Free) 2890
    Percent Reflections(Observed) 99.95
    R-Factor(Observed) 0.2101
    R-Work 0.2085
    R-Free 0.239
     
    Temperature Factor Modeling
    Mean Isotropic B Value 46.8
    Anisotropic B[1][1] 0.5263
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.5263
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.0526
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0101
    Shell Resolution(Low) 2.043
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2510
    R-Factor(R-Work) 0.2794
    R-Factor(R-Free) 0.2905
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.043
    Shell Resolution(Low) 2.0783
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2554
    R-Factor(R-Work) 0.2478
    R-Factor(R-Free) 0.2971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0783
    Shell Resolution(Low) 2.1161
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2573
    R-Factor(R-Work) 0.2486
    R-Factor(R-Free) 0.3036
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1161
    Shell Resolution(Low) 2.1568
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2537
    R-Factor(R-Work) 0.2421
    R-Factor(R-Free) 0.2806
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1568
    Shell Resolution(Low) 2.2008
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.2433
    R-Factor(R-Free) 0.3225
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2008
    Shell Resolution(Low) 2.2486
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2549
    R-Factor(R-Work) 0.2389
    R-Factor(R-Free) 0.2869
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2486
    Shell Resolution(Low) 2.3009
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2561
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.2805
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3009
    Shell Resolution(Low) 2.3585
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2589
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.3132
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3585
    Shell Resolution(Low) 2.4222
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2572
    R-Factor(R-Work) 0.2351
    R-Factor(R-Free) 0.2628
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4222
    Shell Resolution(Low) 2.4935
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.2203
    R-Factor(R-Free) 0.2774
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4935
    Shell Resolution(Low) 2.574
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2531
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.2725
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.574
    Shell Resolution(Low) 2.666
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.2115
    R-Factor(R-Free) 0.2612
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.666
    Shell Resolution(Low) 2.7727
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.2169
    R-Factor(R-Free) 0.2411
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7727
    Shell Resolution(Low) 2.8989
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.2098
    R-Factor(R-Free) 0.2343
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8989
    Shell Resolution(Low) 3.0517
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2599
    R-Factor(R-Work) 0.2191
    R-Factor(R-Free) 0.2517
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0517
    Shell Resolution(Low) 3.2428
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2573
    R-Factor(R-Work) 0.2087
    R-Factor(R-Free) 0.2225
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2428
    Shell Resolution(Low) 3.4931
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.2091
    R-Factor(R-Free) 0.2423
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4931
    Shell Resolution(Low) 3.8444
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.2038
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8444
    Shell Resolution(Low) 4.4002
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1734
    R-Factor(R-Free) 0.1906
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4002
    Shell Resolution(Low) 5.542
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.1742
    R-Factor(R-Free) 0.2053
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.542
    Shell Resolution(Low) 43.2185
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2837
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.077
    f_dihedral_angle_d 15.952
    f_angle_d 1.407
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3912
    Nucleic Acid Atoms 92
    Heterogen Atoms 5
    Solvent Atoms 268
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution BALBES
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building BALBES