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X-RAY DIFFRACTION
Materials and Methods page
4DVS
  •   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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 64.64 α = 90
    b = 68.22 β = 91.48
    c = 94.02 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 2011-06-05
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength 1
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(All) 49234
    Number Reflections(Observed) 43523
    Percent Possible(Observed) 88.4
    R Merge I(Observed) 0.058
    B(Isotropic) From Wilson Plot 34.5
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.14
    Percent Possible(All) 46.8
    R Merge I(Observed) 0.447
    Mean I Over Sigma(Observed) 1.49
    R-Sym I(Observed) 0.076
    Redundancy 3.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 25.067
    Cut-off Sigma(F) 1.42
    Number of Reflections(all) 49376
    Number of Reflections(Observed) 41640
    Number of Reflections(R-Free) 2070
    Percent Reflections(Observed) 84.41
    R-Factor(Observed) 0.1947
    R-Work 0.1927
    R-Free 0.2319
     
    Temperature Factor Modeling
    Mean Isotropic B Value 56.4595
    Anisotropic B[1][1] 6.3432
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -5.0073
    Anisotropic B[2][2] 2.1836
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -8.5268
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0798
    Shell Resolution(Low) 2.1282
    Number of Reflections(R-Free) 35
    Number of Reflections(R-Work) 1222
    R-Factor(R-Work) 0.2707
    R-Factor(R-Free) 0.2968
    Percent Reflections(Observed) 38.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1282
    Shell Resolution(Low) 2.1813
    Number of Reflections(R-Free) 72
    Number of Reflections(R-Work) 1651
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.3154
    Percent Reflections(Observed) 53.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1813
    Shell Resolution(Low) 2.2403
    Number of Reflections(R-Free) 94
    Number of Reflections(R-Work) 2043
    R-Factor(R-Work) 0.2508
    R-Factor(R-Free) 0.3027
    Percent Reflections(Observed) 65.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2403
    Shell Resolution(Low) 2.3062
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2303
    R-Factor(R-Work) 0.2434
    R-Factor(R-Free) 0.3038
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3062
    Shell Resolution(Low) 2.3805
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2525
    R-Factor(R-Work) 0.2268
    R-Factor(R-Free) 0.3058
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3805
    Shell Resolution(Low) 2.4656
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.2307
    R-Factor(R-Free) 0.2801
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4656
    Shell Resolution(Low) 2.5642
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2843
    R-Factor(R-Work) 0.2214
    R-Factor(R-Free) 0.2676
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5642
    Shell Resolution(Low) 2.6808
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2907
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6808
    Shell Resolution(Low) 2.8219
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2993
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.2483
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8219
    Shell Resolution(Low) 2.9984
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 2974
    R-Factor(R-Work) 0.2131
    R-Factor(R-Free) 0.2526
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9984
    Shell Resolution(Low) 3.2295
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3042
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2615
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2295
    Shell Resolution(Low) 3.5537
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3036
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2256
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5537
    Shell Resolution(Low) 4.066
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3062
    R-Factor(R-Work) 0.1757
    R-Factor(R-Free) 0.2138
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.066
    Shell Resolution(Low) 5.1156
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3061
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.1969
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1156
    Shell Resolution(Low) 25.0687
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 3205
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.2025
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.01
    f_chiral_restr 0.033
    f_dihedral_angle_d 11.647
    f_angle_d 0.526
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5308
    Nucleic Acid Atoms 0
    Heterogen Atoms 384
    Solvent Atoms 241
     
     
  •   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_1069)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix