POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4EKQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 277.0
    Details 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.21 α = 90
    b = 76.07 β = 93.01
    c = 52.81 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 2010-11-22
     
    Diffraction Radiation
    Monochromator two flat Si(111) crystals, mounted in a model DCM from Khozu
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.116
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.54
    Resolution(Low) 50
    Number Reflections(Observed) 52590
    Percent Possible(Observed) 93.4
    R Merge I(Observed) 0.043
    B(Isotropic) From Wilson Plot 21.656
     
    High Resolution Shell Details
    Resolution(High) 1.54
    Resolution(Low) 1.62
    Percent Possible(All) 96.3
    R Merge I(Observed) 0.337
    Mean I Over Sigma(Observed) 3.11
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.54
    Resolution(Low) 48.143
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 52589
    Number of Reflections(R-Free) 2116
    Percent Reflections(Observed) 93.41
    R-Factor(Observed) 0.1763
    R-Work 0.1751
    R-Free 0.2041
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.0271
    Anisotropic B[1][1] -1.0043
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.6146
    Anisotropic B[2][2] 0.8528
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.1515
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.54
    Shell Resolution(Low) 1.5758
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3458
    R-Factor(R-Work) 0.2206
    R-Factor(R-Free) 0.2472
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5758
    Shell Resolution(Low) 1.6152
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3460
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6152
    Shell Resolution(Low) 1.6589
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3452
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.2583
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6589
    Shell Resolution(Low) 1.7077
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3399
    R-Factor(R-Work) 0.2015
    R-Factor(R-Free) 0.2603
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7077
    Shell Resolution(Low) 1.7629
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3436
    R-Factor(R-Work) 0.1902
    R-Factor(R-Free) 0.2444
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7629
    Shell Resolution(Low) 1.8259
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3392
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2128
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8259
    Shell Resolution(Low) 1.899
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3393
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.899
    Shell Resolution(Low) 1.9854
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3393
    R-Factor(R-Work) 0.1663
    R-Factor(R-Free) 0.184
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9854
    Shell Resolution(Low) 2.0901
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3377
    R-Factor(R-Work) 0.1631
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0901
    Shell Resolution(Low) 2.221
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3329
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2136
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.221
    Shell Resolution(Low) 2.3925
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3363
    R-Factor(R-Work) 0.1641
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3925
    Shell Resolution(Low) 2.6333
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3320
    R-Factor(R-Work) 0.1695
    R-Factor(R-Free) 0.1991
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6333
    Shell Resolution(Low) 3.0142
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3271
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.2069
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0142
    Shell Resolution(Low) 3.7974
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 3256
    R-Factor(R-Work) 0.1635
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7974
    Shell Resolution(Low) 48.1668
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3174
    R-Factor(R-Work) 0.1765
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 86.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.221
    f_plane_restr 0.01
    f_chiral_restr 0.124
    f_angle_d 1.775
    f_bond_d 0.021
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2748
    Nucleic Acid Atoms 0
    Heterogen Atoms 75
    Solvent Atoms 295
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX (phenix.refine: 1.7.1_743)
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale