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X-RAY DIFFRACTION
Materials and Methods page
4HEV
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 298.0
    Details 10-12mg/ml enzyme in 50mM NaPO4, 2mM EDTA, pH 6.5; and 10-15% polyethylene glycol (PEG) 2,000 monomethyl ester, 0.2-0.3M K2HPO4, 0.1M D,L-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.6 α = 90
    b = 67.63 β = 106.13
    c = 99.41 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 ADSC QUANTUM 4
    Collection Date 2008-08-18
     
    Diffraction Radiation
    Monochromator Si111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X12B
    Wavelength List 0.9500
    Site NSLS
    Beamline X12B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.5
    Resolution(Low) 40.47
    Number Reflections(All) 32607
    Number Reflections(Observed) 31857
    Percent Possible(Observed) 97.7
    R Merge I(Observed) 0.069
    B(Isotropic) From Wilson Plot 43.51
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.59
    Percent Possible(All) 92.7
    R Merge I(Observed) 0.463
    Mean I Over Sigma(Observed) 3.2
    Redundancy 3.3
    Number Unique Reflections(All) 3218
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 40.469
    Cut-off Sigma(F) 1.42
    Number of Reflections(all) 32607
    Number of Reflections(Observed) 30530
    Number of Reflections(R-Free) 1514
    Percent Reflections(Observed) 93.32
    R-Factor(All) 0.20657
    R-Factor(Observed) 0.2044
    R-Work 0.2021
    R-Free 0.2477
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic/TLS
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5003
    Shell Resolution(Low) 2.581
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2249
    R-Factor(R-Work) 0.2469
    R-Factor(R-Free) 0.3243
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.581
    Shell Resolution(Low) 2.6732
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2432
    R-Factor(R-Work) 0.2325
    R-Factor(R-Free) 0.2971
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6732
    Shell Resolution(Low) 2.7802
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2533
    R-Factor(R-Work) 0.2409
    R-Factor(R-Free) 0.3018
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7802
    Shell Resolution(Low) 2.9067
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.2475
    R-Factor(R-Free) 0.3344
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9067
    Shell Resolution(Low) 3.0599
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2301
    R-Factor(R-Free) 0.3109
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0599
    Shell Resolution(Low) 3.2515
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.2318
    R-Factor(R-Free) 0.2926
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2515
    Shell Resolution(Low) 3.5025
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2744
    R-Factor(R-Work) 0.2162
    R-Factor(R-Free) 0.2586
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5025
    Shell Resolution(Low) 3.8547
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.2222
    R-Factor(R-Free) 0.2798
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8547
    Shell Resolution(Low) 4.4119
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4119
    Shell Resolution(Low) 5.5562
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2814
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.1851
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5562
    Shell Resolution(Low) 40.4746
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2830
    R-Factor(R-Work) 0.1871
    R-Factor(R-Free) 0.212
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.002
    f_chiral_restr 0.042
    f_dihedral_angle_d 11.815
    f_angle_d 0.549
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6398
    Nucleic Acid Atoms 0
    Heterogen Atoms 32
    Solvent Atoms 153
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building PHASER
    data collection CBASS