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X-RAY DIFFRACTION
Materials and Methods page
4DVV
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 10% PEG 8000, 5% iso-propanol, 0.1M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 64.78 α = 90
    b = 68.08 β = 91.42
    c = 94.35 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR scanner 300 mm plate
    Collection Date 2011-06-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength 1
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.94
    Resolution(Low) 26.39
    Number Reflections(All) 61307
    Number Reflections(Observed) 58230
    Percent Possible(Observed) 95.4
    R Merge I(Observed) 0.058
    B(Isotropic) From Wilson Plot 35.88
    Redundancy 4.4
     
    High Resolution Shell Details
    Resolution(High) 1.94
    Resolution(Low) 1.97
    Percent Possible(All) 63.4
    R Merge I(Observed) 0.33
    Mean I Over Sigma(Observed) 2.23
    R-Sym I(Observed) 0.393
    Redundancy 2.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.94
    Resolution(Low) 26.39
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 61022
    Number of Reflections(Observed) 58216
    Number of Reflections(R-Free) 2944
    Percent Reflections(Observed) 95.4
    R-Factor(Observed) 0.1829
    R-Work 0.1811
    R-Free 0.2152
     
    Temperature Factor Modeling
    Mean Isotropic B Value 54.4834
    Anisotropic B[1][1] 3.7219
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -4.7081
    Anisotropic B[2][2] 1.6299
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.3518
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9708
    Number of Reflections(R-Free) 89
    Number of Reflections(R-Work) 1729
    R-Factor(R-Work) 0.2567
    R-Factor(R-Free) 0.2844
    Percent Reflections(Observed) 63.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9708
    Shell Resolution(Low) 2.0047
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2131
    R-Factor(R-Work) 0.2474
    R-Factor(R-Free) 0.2671
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0047
    Shell Resolution(Low) 2.0412
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2386
    R-Factor(R-Work) 0.2419
    R-Factor(R-Free) 0.2796
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0412
    Shell Resolution(Low) 2.0804
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2544
    R-Factor(R-Work) 0.2301
    R-Factor(R-Free) 0.2669
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0804
    Shell Resolution(Low) 2.1229
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2690
    R-Factor(R-Work) 0.2262
    R-Factor(R-Free) 0.2955
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1229
    Shell Resolution(Low) 2.169
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.2166
    R-Factor(R-Free) 0.2948
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.169
    Shell Resolution(Low) 2.2194
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.2075
    R-Factor(R-Free) 0.2204
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2194
    Shell Resolution(Low) 2.2749
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.1969
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2749
    Shell Resolution(Low) 2.3364
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.2043
    R-Factor(R-Free) 0.2346
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3364
    Shell Resolution(Low) 2.4051
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2771
    R-Factor(R-Work) 0.2022
    R-Factor(R-Free) 0.2664
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4051
    Shell Resolution(Low) 2.4827
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2709
    R-Factor(R-Work) 0.2164
    R-Factor(R-Free) 0.2669
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4827
    Shell Resolution(Low) 2.5713
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5713
    Shell Resolution(Low) 2.6742
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2747
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2497
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6742
    Shell Resolution(Low) 2.7958
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2735
    R-Factor(R-Work) 0.2013
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7958
    Shell Resolution(Low) 2.943
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2781
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2372
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.943
    Shell Resolution(Low) 3.1271
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2773
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.2638
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1271
    Shell Resolution(Low) 3.3681
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.1802
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3681
    Shell Resolution(Low) 3.7062
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.1679
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7062
    Shell Resolution(Low) 4.2406
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2750
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.1938
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2406
    Shell Resolution(Low) 5.3355
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2779
    R-Factor(R-Work) 0.1454
    R-Factor(R-Free) 0.1691
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3355
    Shell Resolution(Low) 26.3926
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.1755
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.052
    f_dihedral_angle_d 14.703
    f_angle_d 0.856
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5308
    Nucleic Acid Atoms 0
    Heterogen Atoms 386
    Solvent Atoms 378
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix