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X-RAY DIFFRACTION
Materials and Methods page
4KRE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9
    Temperature 291.0
    Details 13% PEG 3350, 9% iso-propanol, 0.1M Tris pH 9.0, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.47 α = 90
    b = 98.63 β = 110.96
    c = 73.21 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 2012-06-19
     
    Diffraction Radiation
    Monochromator Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.75
    Resolution(Low) 50
    Number Reflections(All) 91609
    Number Reflections(Observed) 91609
    Percent Possible(Observed) 98.0
    R Merge I(Observed) 0.055
    B(Isotropic) From Wilson Plot 31.826
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.8
    Percent Possible(All) 85.3
    R Merge I(Observed) 0.422
    Mean I Over Sigma(Observed) 1.96
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.754
    Resolution(Low) 32.926
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 91605
    Number of Reflections(Observed) 91605
    Number of Reflections(R-Free) 4581
    Percent Reflections(Observed) 98.08
    R-Factor(Observed) 0.172
    R-Work 0.1705
    R-Free 0.2019
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.8155
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.754
    Shell Resolution(Low) 1.7741
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2206
    R-Factor(R-Work) 0.2751
    R-Factor(R-Free) 0.3005
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7741
    Shell Resolution(Low) 1.7949
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.2405
    R-Factor(R-Free) 0.2582
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7949
    Shell Resolution(Low) 1.8168
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2819
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.3084
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8168
    Shell Resolution(Low) 1.8398
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2934
    R-Factor(R-Work) 0.2098
    R-Factor(R-Free) 0.2657
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8398
    Shell Resolution(Low) 1.864
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2956
    R-Factor(R-Work) 0.1881
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.864
    Shell Resolution(Low) 1.8896
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2941
    R-Factor(R-Work) 0.1855
    R-Factor(R-Free) 0.2457
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8896
    Shell Resolution(Low) 1.9166
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2945
    R-Factor(R-Work) 0.1818
    R-Factor(R-Free) 0.2065
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9166
    Shell Resolution(Low) 1.9452
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2921
    R-Factor(R-Work) 0.1811
    R-Factor(R-Free) 0.2163
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9452
    Shell Resolution(Low) 1.9756
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2967
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9756
    Shell Resolution(Low) 2.0079
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2913
    R-Factor(R-Work) 0.1773
    R-Factor(R-Free) 0.2154
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0079
    Shell Resolution(Low) 2.0426
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2946
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2099
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0426
    Shell Resolution(Low) 2.0797
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2967
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.2063
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0797
    Shell Resolution(Low) 2.1197
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2934
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1197
    Shell Resolution(Low) 2.1629
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2937
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.2237
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1629
    Shell Resolution(Low) 2.21
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2960
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.1931
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.21
    Shell Resolution(Low) 2.2614
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2928
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1945
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2614
    Shell Resolution(Low) 2.3179
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2925
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3179
    Shell Resolution(Low) 2.3806
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2961
    R-Factor(R-Work) 0.1585
    R-Factor(R-Free) 0.2047
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3806
    Shell Resolution(Low) 2.4506
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2949
    R-Factor(R-Work) 0.1623
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4506
    Shell Resolution(Low) 2.5297
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2956
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5297
    Shell Resolution(Low) 2.62
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2935
    R-Factor(R-Work) 0.1641
    R-Factor(R-Free) 0.1992
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.62
    Shell Resolution(Low) 2.7249
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2926
    R-Factor(R-Work) 0.1749
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7249
    Shell Resolution(Low) 2.8488
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2928
    R-Factor(R-Work) 0.1749
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8488
    Shell Resolution(Low) 2.9989
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2914
    R-Factor(R-Work) 0.1832
    R-Factor(R-Free) 0.2188
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9989
    Shell Resolution(Low) 3.1867
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2968
    R-Factor(R-Work) 0.1739
    R-Factor(R-Free) 0.2143
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1867
    Shell Resolution(Low) 3.4325
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2911
    R-Factor(R-Work) 0.18
    R-Factor(R-Free) 0.1847
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4325
    Shell Resolution(Low) 3.7775
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2938
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7775
    Shell Resolution(Low) 4.323
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2927
    R-Factor(R-Work) 0.15
    R-Factor(R-Free) 0.1735
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.323
    Shell Resolution(Low) 5.4426
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2946
    R-Factor(R-Work) 0.1542
    R-Factor(R-Free) 0.1654
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4426
    Shell Resolution(Low) 32.926
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2832
    R-Factor(R-Work) 0.1834
    R-Factor(R-Free) 0.2125
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.455
    f_plane_restr 0.006
    f_chiral_restr 0.083
    f_angle_d 1.184
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6433
    Nucleic Acid Atoms 234
    Heterogen Atoms 0
    Solvent Atoms 470
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale