POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4I1D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 4.5
    Temperature 289.0
    Details 0.2M Lithium Sulfate, 0.1M Sodium Acetate:Acetic Acid:HCl, 50% (v/v) PEG400, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 136.64 α = 90
    b = 136.64 β = 90
    c = 185.63 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details mirror
    Collection Date 2011-04-09
     
    Diffraction Radiation
    Monochromator Si 111 crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97921
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.2
    Resolution(Low) 50
    Number Reflections(All) 100645
    Number Reflections(Observed) 100645
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.094
    Redundancy 4.8
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.24
    Percent Possible(All) 90.2
    R Merge I(Observed) 0.545
    Mean I Over Sigma(Observed) 1.9
    Redundancy 2.3
    Number Unique Reflections(All) 4572
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.201
    Resolution(Low) 49.892
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 100533
    Number of Reflections(Observed) 100533
    Number of Reflections(R-Free) 5020
    Percent Reflections(Observed) 98.76
    R-Factor(All) 0.1739
    R-Factor(Observed) 0.1739
    R-Work 0.172
    R-Free 0.2092
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 7.5273
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 7.5273
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -15.0546
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2011
    Shell Resolution(Low) 2.2261
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.2869
    R-Factor(R-Free) 0.3683
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2261
    Shell Resolution(Low) 2.2523
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 2927
    R-Factor(R-Work) 0.2684
    R-Factor(R-Free) 0.3338
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2523
    Shell Resolution(Low) 2.2797
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3062
    R-Factor(R-Work) 0.2532
    R-Factor(R-Free) 0.3149
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2797
    Shell Resolution(Low) 2.3086
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3099
    R-Factor(R-Work) 0.2489
    R-Factor(R-Free) 0.3112
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3086
    Shell Resolution(Low) 2.339
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3074
    R-Factor(R-Work) 0.2396
    R-Factor(R-Free) 0.3267
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.339
    Shell Resolution(Low) 2.371
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 3207
    R-Factor(R-Work) 0.2192
    R-Factor(R-Free) 0.2786
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.371
    Shell Resolution(Low) 2.4049
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 3187
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2842
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4049
    Shell Resolution(Low) 2.4408
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3227
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.2606
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4408
    Shell Resolution(Low) 2.4789
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 3166
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2647
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4789
    Shell Resolution(Low) 2.5196
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3178
    R-Factor(R-Work) 0.2164
    R-Factor(R-Free) 0.2525
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5196
    Shell Resolution(Low) 2.563
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 3210
    R-Factor(R-Work) 0.2093
    R-Factor(R-Free) 0.2719
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.563
    Shell Resolution(Low) 2.6096
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3163
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.2661
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6096
    Shell Resolution(Low) 2.6598
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3242
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.2663
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6598
    Shell Resolution(Low) 2.7141
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3192
    R-Factor(R-Work) 0.1967
    R-Factor(R-Free) 0.216
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7141
    Shell Resolution(Low) 2.7731
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3224
    R-Factor(R-Work) 0.1981
    R-Factor(R-Free) 0.2562
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7731
    Shell Resolution(Low) 2.8376
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3213
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2192
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8376
    Shell Resolution(Low) 2.9085
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3199
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9085
    Shell Resolution(Low) 2.9872
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3198
    R-Factor(R-Work) 0.2089
    R-Factor(R-Free) 0.2512
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9872
    Shell Resolution(Low) 3.0751
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3217
    R-Factor(R-Work) 0.2114
    R-Factor(R-Free) 0.2524
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0751
    Shell Resolution(Low) 3.1743
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3249
    R-Factor(R-Work) 0.1988
    R-Factor(R-Free) 0.2558
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1743
    Shell Resolution(Low) 3.2877
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3203
    R-Factor(R-Work) 0.1901
    R-Factor(R-Free) 0.2341
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2877
    Shell Resolution(Low) 3.4193
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3231
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4193
    Shell Resolution(Low) 3.5749
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3202
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.2001
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5749
    Shell Resolution(Low) 3.7633
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3224
    R-Factor(R-Work) 0.1471
    R-Factor(R-Free) 0.1741
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7633
    Shell Resolution(Low) 3.999
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3212
    R-Factor(R-Work) 0.137
    R-Factor(R-Free) 0.1679
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.999
    Shell Resolution(Low) 4.3076
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3246
    R-Factor(R-Work) 0.1316
    R-Factor(R-Free) 0.1624
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3076
    Shell Resolution(Low) 4.7408
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3248
    R-Factor(R-Work) 0.1241
    R-Factor(R-Free) 0.1458
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7408
    Shell Resolution(Low) 5.4261
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3285
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1857
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4261
    Shell Resolution(Low) 6.8336
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3329
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1823
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8336
    Shell Resolution(Low) 49.9051
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3373
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.1994
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.067
    f_dihedral_angle_d 14.421
    f_angle_d 1.026
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9926
    Nucleic Acid Atoms 0
    Heterogen Atoms 372
    Solvent Atoms 243
     
     
  •   Software and Computing Hide
    Computing
    Data Collection sbc-collect
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution SHELXD/MLPHARE/DM/ARP/wARP/HKL3000
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building SHELXD/MLPHARE/DM/ARP/wARP/HKL3000
    data collection sbc-collect