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X-RAY DIFFRACTION
Materials and Methods page
4IYQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 290.0
    Details EB Synergy screen c10: 40% iso-propanol, 15% PEG 8000, 100mM imidazole/HCl, EhchA.00496.a.A1.PB00060 at 21mg/ml, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 87.49 α = 90
    b = 32.58 β = 119.65
    c = 89.08 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 315r
    Collection Date 2012-05-12
     
    Diffraction Radiation
    Monochromator Single crystal, cylindrically bent, Si(220)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.1
    Wavelength List 0.977408
    Site ALS
    Beamline 5.0.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.55
    Resolution(Low) 20
    Number Reflections(All) 14800
    Number Reflections(Observed) 14664
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.114
    B(Isotropic) From Wilson Plot 35.579
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.55
    Resolution(Low) 2.62
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.489
    Mean I Over Sigma(Observed) 2.76
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.55
    Resolution(Low) 19.355
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 14800
    Number of Reflections(Observed) 14656
    Number of Reflections(R-Free) 740
    Percent Reflections(Observed) 99.69
    R-Factor(Observed) 0.171
    R-Work 0.1684
    R-Free 0.219
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic, TLS
    Mean Isotropic B Value 21.7883
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.55
    Shell Resolution(Low) 2.7464
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.2096
    R-Factor(R-Free) 0.2987
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7464
    Shell Resolution(Low) 3.0219
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2740
    R-Factor(R-Work) 0.2018
    R-Factor(R-Free) 0.2626
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0219
    Shell Resolution(Low) 3.457
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2772
    R-Factor(R-Work) 0.1811
    R-Factor(R-Free) 0.2509
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.457
    Shell Resolution(Low) 4.3473
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2776
    R-Factor(R-Work) 0.148
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3473
    Shell Resolution(Low) 19.3552
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2886
    R-Factor(R-Work) 0.1503
    R-Factor(R-Free) 0.1872
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.165
    f_plane_restr 0.005
    f_chiral_restr 0.043
    f_angle_d 1.044
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2480
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 72
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BOS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_1269)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser version: 2.5.1
    data reduction Xscale