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X-RAY DIFFRACTION
Materials and Methods page
4EDI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 298.0
    Details 5% PEG8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 86.75 α = 90
    b = 86.75 β = 90
    c = 251.68 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
    Type ADSC QUANTUM 315
    Collection Date 2010-07-25
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.97949
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2
    Resolution(Low) 100
    Number Reflections(Observed) 65257
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.053
    B(Isotropic) From Wilson Plot 25.677
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 1.998
    Resolution(Low) 2.07
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.218
    Redundancy 4.0
    Number Unique Reflections(All) 6436
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.998
    Resolution(Low) 59.595
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 65223
    Number of Reflections(R-Free) 3311
    Percent Reflections(Observed) 98.63
    R-Factor(Observed) 0.1715
    R-Work 0.1703
    R-Free 0.193
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.5746
    Anisotropic B[1][1] 2.3459
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.3459
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.6918
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.998
    Shell Resolution(Low) 2.0266
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2490
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2209
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0266
    Shell Resolution(Low) 2.0569
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2582
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.211
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0569
    Shell Resolution(Low) 2.089
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2541
    R-Factor(R-Work) 0.1774
    R-Factor(R-Free) 0.2044
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.089
    Shell Resolution(Low) 2.1233
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2604
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.2088
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1233
    Shell Resolution(Low) 2.1599
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.1635
    R-Factor(R-Free) 0.1861
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1599
    Shell Resolution(Low) 2.1992
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2582
    R-Factor(R-Work) 0.1615
    R-Factor(R-Free) 0.1782
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1992
    Shell Resolution(Low) 2.2415
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2560
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1828
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2415
    Shell Resolution(Low) 2.2872
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.1601
    R-Factor(R-Free) 0.1723
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2872
    Shell Resolution(Low) 2.3369
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2564
    R-Factor(R-Work) 0.1544
    R-Factor(R-Free) 0.1775
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3369
    Shell Resolution(Low) 2.3913
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2552
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.1869
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3913
    Shell Resolution(Low) 2.4511
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2580
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.2135
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4511
    Shell Resolution(Low) 2.5174
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2576
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.185
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5174
    Shell Resolution(Low) 2.5915
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2555
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.1739
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5915
    Shell Resolution(Low) 2.6751
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2589
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.1922
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6751
    Shell Resolution(Low) 2.7707
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7707
    Shell Resolution(Low) 2.8817
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2586
    R-Factor(R-Work) 0.1622
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8817
    Shell Resolution(Low) 3.0128
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0128
    Shell Resolution(Low) 3.1716
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.168
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1716
    Shell Resolution(Low) 3.3703
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1811
    R-Factor(R-Free) 0.1989
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3703
    Shell Resolution(Low) 3.6305
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6305
    Shell Resolution(Low) 3.9958
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2562
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.1958
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9958
    Shell Resolution(Low) 4.5738
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2551
    R-Factor(R-Work) 0.1534
    R-Factor(R-Free) 0.1565
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5738
    Shell Resolution(Low) 5.7618
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2524
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7618
    Shell Resolution(Low) 59.6215
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.2112
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.036
    f_plane_restr 0.005
    f_chiral_restr 0.065
    f_angle_d 1.058
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4824
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 245
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser version: 2.1.4
    data reduction SCALEPACK