POP-OUT | CLOSE

An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IX2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 289.0
    Details 0.86 sodium/potassium buffer, 0.15 M MOPS buffer, 0.02 M sodium fluoride, 0.01 M IMP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 167.18 α = 90
    b = 167.16 β = 90
    c = 93.08 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2012-04-24
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.9792
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.15
    Resolution(Low) 38.1
    Number Reflections(All) 71185
    Number Reflections(Observed) 71185
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.195
    B(Isotropic) From Wilson Plot 32.6
    Redundancy 7.3
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.19
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.921
    Mean I Over Sigma(Observed) 2.66
    Redundancy 6.7
    Number Unique Reflections(All) 3518
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.146
    Resolution(Low) 38.1
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 71179
    Number of Reflections(Observed) 71179
    Number of Reflections(R-Free) 3606
    Percent Reflections(Observed) 99.69
    R-Factor(Observed) 0.2114
    R-Work 0.2077
    R-Free 0.258
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.3149
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1466
    Shell Resolution(Low) 2.1836
    Number of Reflections(Observed) 3357
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3191
    R-Factor(R-Work) 0.2274
    R-Factor(R-Free) 0.3323
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1836
    Shell Resolution(Low) 2.2233
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 3369
    R-Factor(R-Work) 0.2319
    R-Factor(R-Free) 0.3007
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2233
    Shell Resolution(Low) 2.2661
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3321
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.2692
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2661
    Shell Resolution(Low) 2.3123
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3362
    R-Factor(R-Work) 0.2267
    R-Factor(R-Free) 0.3258
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3123
    Shell Resolution(Low) 2.3626
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3369
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.2651
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3626
    Shell Resolution(Low) 2.4175
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3357
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.2946
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4175
    Shell Resolution(Low) 2.478
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3355
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.2706
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.478
    Shell Resolution(Low) 2.5449
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3376
    R-Factor(R-Work) 0.2179
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5449
    Shell Resolution(Low) 2.6198
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3354
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.2197
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6198
    Shell Resolution(Low) 2.7044
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3337
    R-Factor(R-Work) 0.2138
    R-Factor(R-Free) 0.2889
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7044
    Shell Resolution(Low) 2.801
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3347
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.2684
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.801
    Shell Resolution(Low) 2.9131
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3366
    R-Factor(R-Work) 0.2099
    R-Factor(R-Free) 0.2976
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9131
    Shell Resolution(Low) 3.0456
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3381
    R-Factor(R-Work) 0.2042
    R-Factor(R-Free) 0.24
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0456
    Shell Resolution(Low) 3.2061
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3394
    R-Factor(R-Work) 0.2057
    R-Factor(R-Free) 0.2583
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2061
    Shell Resolution(Low) 3.4068
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3380
    R-Factor(R-Work) 0.1943
    R-Factor(R-Free) 0.2483
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4068
    Shell Resolution(Low) 3.6696
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3421
    R-Factor(R-Work) 0.1828
    R-Factor(R-Free) 0.258
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6696
    Shell Resolution(Low) 4.0385
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3385
    R-Factor(R-Work) 0.1841
    R-Factor(R-Free) 0.2046
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0385
    Shell Resolution(Low) 4.6218
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3448
    R-Factor(R-Work) 0.1788
    R-Factor(R-Free) 0.2199
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6218
    Shell Resolution(Low) 5.8191
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3460
    R-Factor(R-Work) 0.2029
    R-Factor(R-Free) 0.2371
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8191
    Shell Resolution(Low) 36.2902
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3599
    R-Factor(R-Work) 0.2563
    R-Factor(R-Free) 0.3206
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.556
    f_plane_restr 0.003
    f_chiral_restr 0.043
    f_angle_d 0.707
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9738
    Nucleic Acid Atoms 0
    Heterogen Atoms 96
    Solvent Atoms 873
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SBC-collect
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution MOLREP, HKL3000
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL