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X-RAY DIFFRACTION
Materials and Methods page
4H86
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.4
    Temperature 298.0
    Details Protein Solution (40 mg/ml Ahp1 protein, in Milli-Q water containing 10mM DTT) mixed in a 1:1 ratio with the well solution (0.1 M BIS-TRIS pH 5.4, 2.0 M Ammonium Sulfate) Cryoprotected with 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 149.05 α = 90
    b = 149.05 β = 90
    c = 149.05 γ = 90
     
    Space Group
    Space Group Name:    I 21 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2011-11-08
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97915
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(All) 37056
    Number Reflections(Observed) 37056
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.125
    B(Isotropic) From Wilson Plot 29.79
    Redundancy 44.8
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.03
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.765
    Redundancy 45.0
    Number Unique Reflections(All) 1844
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.004
    Resolution(Low) 35.131
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 37055
    Number of Reflections(Observed) 37007
    Number of Reflections(R-Free) 1863
    Percent Reflections(Observed) 99.87
    R-Factor(All) 0.1584
    R-Factor(Observed) 0.1584
    R-Work 0.1576
    R-Free 0.1734
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.7781
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0036
    Shell Resolution(Low) 2.0578
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2690
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.2048
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0578
    Shell Resolution(Low) 2.1183
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.2169
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1183
    Shell Resolution(Low) 2.1867
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.1859
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1867
    Shell Resolution(Low) 2.2648
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.1652
    R-Factor(R-Free) 0.2005
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2648
    Shell Resolution(Low) 2.3555
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3555
    Shell Resolution(Low) 2.4626
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.2006
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4626
    Shell Resolution(Low) 2.5924
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.242
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5924
    Shell Resolution(Low) 2.7548
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.1744
    R-Factor(R-Free) 0.2067
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7548
    Shell Resolution(Low) 2.9674
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2689
    R-Factor(R-Work) 0.1655
    R-Factor(R-Free) 0.1664
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9674
    Shell Resolution(Low) 3.2658
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.1722
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2658
    Shell Resolution(Low) 3.7379
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2721
    R-Factor(R-Work) 0.1388
    R-Factor(R-Free) 0.1448
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7379
    Shell Resolution(Low) 4.7076
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.1261
    R-Factor(R-Free) 0.139
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7076
    Shell Resolution(Low) 35.1366
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2819
    R-Factor(R-Work) 0.1714
    R-Factor(R-Free) 0.1795
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 11.438
    f_plane_restr 0.004
    f_chiral_restr 0.066
    f_angle_d 0.907
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1422
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 246
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution PHENIX:PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL