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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4ES4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 293.0
    Details 0.1M Na/K phosphate pH5.8, 6% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 132.49 α = 90
    b = 132.49 β = 90
    c = 145.68 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2011-06-20
     
    Diffraction Radiation
    Monochromator SAGITTALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97939
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(Observed) 33268
    Percent Possible(Observed) 99.8
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.748
    Mean I Over Sigma(Observed) 5.03
    R-Sym I(Observed) 0.748
    Redundancy 11.0
    Number Unique Reflections(All) 3258
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 39.165
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 31417
    Number of Reflections(Observed) 31417
    Number of Reflections(R-Free) 1914
    Percent Reflections(Observed) 94.33
    R-Factor(All) 0.2469
    R-Factor(Observed) 0.2469
    R-Work 0.2445
    R-Free 0.2826
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 82.2457
    Anisotropic B[1][1] -11.0281
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -11.0281
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 22.0563
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8975
    Shell Resolution(Low) 2.9699
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 1784
    R-Factor(R-Work) 0.3298
    R-Factor(R-Free) 0.3762
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9699
    Shell Resolution(Low) 3.0502
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1961
    R-Factor(R-Work) 0.317
    R-Factor(R-Free) 0.3978
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0502
    Shell Resolution(Low) 3.1399
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1979
    R-Factor(R-Work) 0.3252
    R-Factor(R-Free) 0.3708
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1399
    Shell Resolution(Low) 3.2412
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2000
    R-Factor(R-Work) 0.2973
    R-Factor(R-Free) 0.3764
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2412
    Shell Resolution(Low) 3.357
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2093
    R-Factor(R-Work) 0.2931
    R-Factor(R-Free) 0.3738
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.357
    Shell Resolution(Low) 3.4913
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2105
    R-Factor(R-Work) 0.2682
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4913
    Shell Resolution(Low) 3.6501
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2144
    R-Factor(R-Work) 0.2452
    R-Factor(R-Free) 0.3321
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6501
    Shell Resolution(Low) 3.8424
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2122
    R-Factor(R-Work) 0.2227
    R-Factor(R-Free) 0.2678
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8424
    Shell Resolution(Low) 4.0829
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2140
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.2823
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0829
    Shell Resolution(Low) 4.3977
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2177
    R-Factor(R-Work) 0.202
    R-Factor(R-Free) 0.2062
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3977
    Shell Resolution(Low) 4.8395
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2187
    R-Factor(R-Work) 0.1951
    R-Factor(R-Free) 0.2623
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8395
    Shell Resolution(Low) 5.5382
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2224
    R-Factor(R-Work) 0.2408
    R-Factor(R-Free) 0.2984
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5382
    Shell Resolution(Low) 6.9711
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2270
    R-Factor(R-Work) 0.2665
    R-Factor(R-Free) 0.2741
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9711
    Shell Resolution(Low) 39.1686
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2317
    R-Factor(R-Work) 0.2424
    R-Factor(R-Free) 0.2455
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.091
    f_dihedral_angle_d 19.104
    f_angle_d 1.367
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9074
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.6.2_432)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.2_432)
    model building Phaser
    data collection HKL-2000