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X-RAY DIFFRACTION
Materials and Methods page
4GYR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 298.0
    Details 24%(w/v)PEG4000,50mM MgCl2,100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.09 α = 90
    b = 78.09 β = 90
    c = 397.54 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2012-01-01
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 1.033
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.8
    Resolution(Low) 50
    Number Reflections(All) 33600
    Number Reflections(Observed) 33519
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.114
    B(Isotropic) From Wilson Plot 40.3
    Redundancy 9.0
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.85
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.171
    Mean I Over Sigma(Observed) 18.1
    Redundancy 4.6
    Number Unique Reflections(All) 1634
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 40.045
    Cut-off Sigma(F) 1.91
    Number of Reflections(Observed) 33489
    Number of Reflections(R-Free) 2026
    Percent Reflections(Observed) 99.87
    R-Factor(Observed) 0.2594
    R-Work 0.2562
    R-Free 0.3068
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.7
    Anisotropic B[1][1] 4.9635
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 4.9635
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -9.2344
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8003
    Shell Resolution(Low) 2.8703
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2234
    R-Factor(R-Work) 0.2964
    R-Factor(R-Free) 0.3626
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8703
    Shell Resolution(Low) 2.9478
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2233
    R-Factor(R-Work) 0.299
    R-Factor(R-Free) 0.3564
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9478
    Shell Resolution(Low) 3.0346
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2251
    R-Factor(R-Work) 0.2832
    R-Factor(R-Free) 0.3523
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0346
    Shell Resolution(Low) 3.1325
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2274
    R-Factor(R-Work) 0.2856
    R-Factor(R-Free) 0.3742
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1325
    Shell Resolution(Low) 3.2444
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2237
    R-Factor(R-Work) 0.2822
    R-Factor(R-Free) 0.3457
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2444
    Shell Resolution(Low) 3.3742
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2246
    R-Factor(R-Work) 0.267
    R-Factor(R-Free) 0.3305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3742
    Shell Resolution(Low) 3.5277
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2231
    R-Factor(R-Work) 0.2772
    R-Factor(R-Free) 0.3105
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5277
    Shell Resolution(Low) 3.7136
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2267
    R-Factor(R-Work) 0.2596
    R-Factor(R-Free) 0.3561
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7136
    Shell Resolution(Low) 3.946
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2232
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.3148
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.946
    Shell Resolution(Low) 4.2504
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2244
    R-Factor(R-Work) 0.2264
    R-Factor(R-Free) 0.2945
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2504
    Shell Resolution(Low) 4.6776
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2247
    R-Factor(R-Work) 0.2131
    R-Factor(R-Free) 0.2497
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6776
    Shell Resolution(Low) 5.353
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2252
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.2907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.353
    Shell Resolution(Low) 6.7391
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2252
    R-Factor(R-Work) 0.2783
    R-Factor(R-Free) 0.3044
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7391
    Shell Resolution(Low) 40.0494
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2263
    R-Factor(R-Work) 0.2586
    R-Factor(R-Free) 0.2402
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.059
    f_dihedral_angle_d 17.386
    f_angle_d 0.906
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6806
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 116
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MC-2 diffractometer software from EMBL
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phnix.autoMR
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building Phnix.autoMR
    data collection MC-2 version: diffractometer software from EMBL