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X-RAY DIFFRACTION
Materials and Methods page
4GDL
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 136.6 α = 90
    b = 58.4 β = 130.04
    c = 91.8 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-11-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.2
    Wavelength List 1.0092
    Site ALS
    Beamline 5.0.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.88
    Resolution(Low) 50
    Number Reflections(Observed) 12548
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.056
    Redundancy 4.4
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 92.4
    R Merge I(Observed) 0.541
    Redundancy 3.7
    Number Unique Reflections(All) 1174
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.875
    Resolution(Low) 36.224
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 12465
    Number of Reflections(R-Free) 1263
    Percent Reflections(Observed) 97.41
    R-Factor(Observed) 0.2186
    R-Work 0.2146
    R-Free 0.254
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 138.769
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8753
    Shell Resolution(Low) 2.9903
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 1081
    R-Factor(R-Work) 0.3301
    R-Factor(R-Free) 0.4281
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9903
    Shell Resolution(Low) 3.1264
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1222
    R-Factor(R-Work) 0.304
    R-Factor(R-Free) 0.3126
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1264
    Shell Resolution(Low) 3.2911
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.2506
    R-Factor(R-Free) 0.2864
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2911
    Shell Resolution(Low) 3.4971
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1253
    R-Factor(R-Work) 0.2514
    R-Factor(R-Free) 0.2919
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4971
    Shell Resolution(Low) 3.7669
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1258
    R-Factor(R-Work) 0.2354
    R-Factor(R-Free) 0.3062
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7669
    Shell Resolution(Low) 4.1455
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1269
    R-Factor(R-Work) 0.2207
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1455
    Shell Resolution(Low) 4.7442
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1267
    R-Factor(R-Work) 0.1802
    R-Factor(R-Free) 0.2081
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7442
    Shell Resolution(Low) 5.9729
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1287
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.2265
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9729
    Shell Resolution(Low) 36.2267
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1308
    R-Factor(R-Work) 0.2006
    R-Factor(R-Free) 0.245
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 9.914
    f_plane_restr 0.003
    f_chiral_restr 0.037
    f_angle_d 0.51
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3226
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL