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X-RAY DIFFRACTION
Materials and Methods page
4IIJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.7
    Temperature 293.0
    Details 4-10% PEG 4000, 4-6% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/Imidazole , pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.53 α = 90
    b = 155.91 β = 90
    c = 181.02 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 2M
    Collection Date 2012-01-26
     
    Diffraction Radiation
    Monochromator vertically collimating mirror (M1, focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry, and a toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06DA
    Wavelength List 0.999870
    Site SLS
    Beamline X06DA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.6
    Resolution(Low) 62.3
    Number Reflections(All) 90649
    Number Reflections(Observed) 90604
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 61.5
    Redundancy 26.7
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.67
    Percent Possible(All) 99.9
    Mean I Over Sigma(Observed) 1.07
    Redundancy 25.7
    Number Unique Reflections(All) 6591
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method Difference Fourier
    reflnsShellList 2.6
    Resolution(Low) 62.275
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 90649
    Number of Reflections(Observed) 90582
    Number of Reflections(R-Free) 4511
    Percent Reflections(Observed) 99.94
    R-Factor(All) 0.1993
    R-Factor(Observed) 0.1993
    R-Work 0.1974
    R-Free 0.2353
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 7.9029
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 18.5304
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.1876
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.6296
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2819
    R-Factor(R-Work) 0.3093
    R-Factor(R-Free) 0.3437
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6296
    Shell Resolution(Low) 2.6605
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2824
    R-Factor(R-Work) 0.3063
    R-Factor(R-Free) 0.362
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6605
    Shell Resolution(Low) 2.6929
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2807
    R-Factor(R-Work) 0.3133
    R-Factor(R-Free) 0.3197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6929
    Shell Resolution(Low) 2.727
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2870
    R-Factor(R-Work) 0.2994
    R-Factor(R-Free) 0.3216
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.727
    Shell Resolution(Low) 2.7629
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2792
    R-Factor(R-Work) 0.2797
    R-Factor(R-Free) 0.3366
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7629
    Shell Resolution(Low) 2.8008
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2857
    R-Factor(R-Work) 0.2794
    R-Factor(R-Free) 0.3165
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8008
    Shell Resolution(Low) 2.8408
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2839
    R-Factor(R-Work) 0.2682
    R-Factor(R-Free) 0.312
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8408
    Shell Resolution(Low) 2.8832
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2862
    R-Factor(R-Work) 0.2617
    R-Factor(R-Free) 0.3053
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8832
    Shell Resolution(Low) 2.9282
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2851
    R-Factor(R-Work) 0.2653
    R-Factor(R-Free) 0.3089
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9282
    Shell Resolution(Low) 2.9762
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2851
    R-Factor(R-Work) 0.2519
    R-Factor(R-Free) 0.3114
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9762
    Shell Resolution(Low) 3.0275
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2855
    R-Factor(R-Work) 0.2352
    R-Factor(R-Free) 0.2755
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0275
    Shell Resolution(Low) 3.0826
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2818
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.278
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0826
    Shell Resolution(Low) 3.1419
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2868
    R-Factor(R-Work) 0.2287
    R-Factor(R-Free) 0.2628
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1419
    Shell Resolution(Low) 3.206
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2855
    R-Factor(R-Work) 0.2263
    R-Factor(R-Free) 0.304
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.206
    Shell Resolution(Low) 3.2757
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2871
    R-Factor(R-Work) 0.2292
    R-Factor(R-Free) 0.3
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2757
    Shell Resolution(Low) 3.3519
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 2838
    R-Factor(R-Work) 0.2165
    R-Factor(R-Free) 0.2699
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3519
    Shell Resolution(Low) 3.4357
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2846
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.2497
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4357
    Shell Resolution(Low) 3.5286
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2845
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.2597
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5286
    Shell Resolution(Low) 3.6324
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2855
    R-Factor(R-Work) 0.1929
    R-Factor(R-Free) 0.2449
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6324
    Shell Resolution(Low) 3.7497
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2862
    R-Factor(R-Work) 0.1833
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7497
    Shell Resolution(Low) 3.8837
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2862
    R-Factor(R-Work) 0.1757
    R-Factor(R-Free) 0.2144
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8837
    Shell Resolution(Low) 4.0391
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2889
    R-Factor(R-Work) 0.1729
    R-Factor(R-Free) 0.2099
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0391
    Shell Resolution(Low) 4.2229
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2882
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.1975
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2229
    Shell Resolution(Low) 4.4455
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2908
    R-Factor(R-Work) 0.15
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4455
    Shell Resolution(Low) 4.724
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2880
    R-Factor(R-Work) 0.1411
    R-Factor(R-Free) 0.1644
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.724
    Shell Resolution(Low) 5.0885
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 2880
    R-Factor(R-Work) 0.1536
    R-Factor(R-Free) 0.2
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0885
    Shell Resolution(Low) 5.6003
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2903
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2472
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6003
    Shell Resolution(Low) 6.41
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2939
    R-Factor(R-Work) 0.2025
    R-Factor(R-Free) 0.2437
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.41
    Shell Resolution(Low) 8.0732
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2966
    R-Factor(R-Work) 0.1878
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0732
    Shell Resolution(Low) 62.2929
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3077
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2062
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.057
    f_dihedral_angle_d 14.812
    f_angle_d 0.805
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16571
    Nucleic Acid Atoms 0
    Heterogen Atoms 141
    Solvent Atoms 92
     
     
  •   Software and Computing Hide
    Computing
    Data Collection REMDAQ
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHENIX (phenix.refine: 1.7.3_928)
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHENIX version: (phenix.refine: 1.7.3_928)
    data collection REMDAQ