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X-RAY DIFFRACTION
Materials and Methods page
4F5M
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.6
    Temperature 277.0
    Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 58.3 α = 90
    b = 108.94 β = 90
    c = 144.23 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 CCD
    Type ADSC QUANTUM 315
    Details Double Crystal
    Collection Date 2010-11-24
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength List 0.97946
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.65
    Resolution(Low) 60
    Number Reflections(All) 110828
    Number Reflections(Observed) 108279
    Percent Possible(Observed) 97.7
    R Merge I(Observed) 0.046
    B(Isotropic) From Wilson Plot 25.627
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.65
    Resolution(Low) 1.69
    Percent Possible(All) 96.5
    R Merge I(Observed) 0.393
    Mean I Over Sigma(Observed) 2.4
    R-Sym I(Observed) 0.393
    Redundancy 3.8
    Number Unique Reflections(All) 7826
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.65
    Resolution(Low) 37.092
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 108082
    Number of Reflections(R-Free) 5418
    Percent Reflections(Observed) 97.26
    R-Factor(Observed) 0.1774
    R-Work 0.1757
    R-Free 0.2103
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -0.261
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.6081
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.3471
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.65
    Shell Resolution(Low) 1.6687
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3342
    R-Factor(R-Work) 0.2736
    R-Factor(R-Free) 0.2941
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6687
    Shell Resolution(Low) 1.6884
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3302
    R-Factor(R-Work) 0.2737
    R-Factor(R-Free) 0.3442
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6884
    Shell Resolution(Low) 1.709
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3363
    R-Factor(R-Work) 0.2695
    R-Factor(R-Free) 0.3225
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.709
    Shell Resolution(Low) 1.7306
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3365
    R-Factor(R-Work) 0.2478
    R-Factor(R-Free) 0.3093
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7306
    Shell Resolution(Low) 1.7534
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 3314
    R-Factor(R-Work) 0.2466
    R-Factor(R-Free) 0.2742
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7534
    Shell Resolution(Low) 1.7774
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 3367
    R-Factor(R-Work) 0.2273
    R-Factor(R-Free) 0.2721
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7774
    Shell Resolution(Low) 1.8028
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3331
    R-Factor(R-Work) 0.223
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8028
    Shell Resolution(Low) 1.8297
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3378
    R-Factor(R-Work) 0.2102
    R-Factor(R-Free) 0.2319
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8297
    Shell Resolution(Low) 1.8583
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3363
    R-Factor(R-Work) 0.2072
    R-Factor(R-Free) 0.2711
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8583
    Shell Resolution(Low) 1.8887
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3391
    R-Factor(R-Work) 0.202
    R-Factor(R-Free) 0.2497
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8887
    Shell Resolution(Low) 1.9213
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3408
    R-Factor(R-Work) 0.1937
    R-Factor(R-Free) 0.2088
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9213
    Shell Resolution(Low) 1.9562
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3367
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2381
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9562
    Shell Resolution(Low) 1.9939
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3415
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.231
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9939
    Shell Resolution(Low) 2.0346
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 3365
    R-Factor(R-Work) 0.1802
    R-Factor(R-Free) 0.2636
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0346
    Shell Resolution(Low) 2.0788
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3448
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0788
    Shell Resolution(Low) 2.1272
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3396
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2384
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1272
    Shell Resolution(Low) 2.1803
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3426
    R-Factor(R-Work) 0.1683
    R-Factor(R-Free) 0.2303
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1803
    Shell Resolution(Low) 2.2393
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 3393
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.1894
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2393
    Shell Resolution(Low) 2.3052
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3432
    R-Factor(R-Work) 0.1725
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3052
    Shell Resolution(Low) 2.3796
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3458
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.2192
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3796
    Shell Resolution(Low) 2.4646
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3445
    R-Factor(R-Work) 0.174
    R-Factor(R-Free) 0.2329
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4646
    Shell Resolution(Low) 2.5633
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3452
    R-Factor(R-Work) 0.1797
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5633
    Shell Resolution(Low) 2.6799
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3487
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.2023
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6799
    Shell Resolution(Low) 2.8211
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3470
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1991
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8211
    Shell Resolution(Low) 2.9978
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3492
    R-Factor(R-Work) 0.1648
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9978
    Shell Resolution(Low) 3.2291
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3537
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2094
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2291
    Shell Resolution(Low) 3.5539
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3539
    R-Factor(R-Work) 0.1764
    R-Factor(R-Free) 0.2172
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5539
    Shell Resolution(Low) 4.0676
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3558
    R-Factor(R-Work) 0.1525
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0676
    Shell Resolution(Low) 5.1226
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 3596
    R-Factor(R-Work) 0.1435
    R-Factor(R-Free) 0.1654
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1226
    Shell Resolution(Low) 37.1012
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 3464
    R-Factor(R-Work) 0.1905
    R-Factor(R-Free) 0.2058
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.099
    f_dihedral_angle_d 13.99
    f_angle_d 1.315
    f_bond_d 0.011
     
    Coordinate Error
    Luzzati Sigma A(Observed) 0.22
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6179
    Nucleic Acid Atoms 0
    Heterogen Atoms 16
    Solvent Atoms 787
     
     
  •   Software and Computing Hide
    Computing
    Data Collection PROTEUM PLUS
    Data Reduction (intensity integration) PROTEUM PLUS
    Data Reduction (data scaling) PROTEUM PLUS
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building PHASER
    data collection PROTEUM version: PLUS