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X-RAY DIFFRACTION
Materials and Methods page
3O44
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7.6
    Temperature 293.0
    Details 20 mM HEPES, 10% PEG 2000, 20 mM Cobalt(III) Hexammine Choride, 1 mM C10E8, pH 7.6, vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 172.35 α = 90
    b = 182.86 β = 90
    c = 430.39 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2009-01-01
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2009-01-01
     
    Diffraction Radiation
    Monochromator Liquid nitrogen-cooled double crystal
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator Liquid nitrogen-cooled double crystal
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 1.00
    Site SSRL
    Beamline BL12-2
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 1.25499, 1.25462, 1.03317
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.88
    Resolution(Low) 100
    Number Reflections(Observed) 299154
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.096
    B(Isotropic) From Wilson Plot 66.7
    Redundancy 4.6
     
    High Resolution Shell Details
    Resolution(High) 2.88
    Resolution(Low) 3.0
    Percent Possible(All) 96.3
    R Merge I(Observed) 0.505
    Redundancy 4.3
    Number Unique Reflections(All) 28859
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.88
    Resolution(Low) 43.956
    Cut-off Sigma(F) 0.1
    Number of Reflections(Observed) 275516
    Number of Reflections(R-Free) 13889
    Percent Reflections(Observed) 90.75
    R-Factor(Observed) 0.2192
    R-Work 0.2176
    R-Free 0.2486
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 55.2557
    Anisotropic B[1][1] 9.461
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 14.9775
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -24.4384
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.88
    Shell Resolution(Low) 2.9201
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 6193
    R-Factor(R-Work) 0.3161
    R-Factor(R-Free) 0.341
    Percent Reflections(Observed) 65.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9201
    Shell Resolution(Low) 2.9545
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7469
    R-Factor(R-Work) 0.3001
    R-Factor(R-Free) 0.3512
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9545
    Shell Resolution(Low) 2.9905
    Number of Reflections(R-Free) 430
    Number of Reflections(R-Work) 7694
    R-Factor(R-Work) 0.3057
    R-Factor(R-Free) 0.3674
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9905
    Shell Resolution(Low) 3.0283
    Number of Reflections(R-Free) 435
    Number of Reflections(R-Work) 7764
    R-Factor(R-Work) 0.2946
    R-Factor(R-Free) 0.3378
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0283
    Shell Resolution(Low) 3.0682
    Number of Reflections(R-Free) 436
    Number of Reflections(R-Work) 7912
    R-Factor(R-Work) 0.2884
    R-Factor(R-Free) 0.3269
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0682
    Shell Resolution(Low) 3.1102
    Number of Reflections(R-Free) 452
    Number of Reflections(R-Work) 8077
    R-Factor(R-Work) 0.278
    R-Factor(R-Free) 0.3436
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1102
    Shell Resolution(Low) 3.1546
    Number of Reflections(R-Free) 457
    Number of Reflections(R-Work) 8135
    R-Factor(R-Work) 0.2843
    R-Factor(R-Free) 0.33
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1546
    Shell Resolution(Low) 3.2017
    Number of Reflections(R-Free) 430
    Number of Reflections(R-Work) 8264
    R-Factor(R-Work) 0.2756
    R-Factor(R-Free) 0.3142
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2017
    Shell Resolution(Low) 3.2517
    Number of Reflections(R-Free) 438
    Number of Reflections(R-Work) 8401
    R-Factor(R-Work) 0.2628
    R-Factor(R-Free) 0.3119
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2517
    Shell Resolution(Low) 3.305
    Number of Reflections(R-Free) 453
    Number of Reflections(R-Work) 8532
    R-Factor(R-Work) 0.2685
    R-Factor(R-Free) 0.2987
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.305
    Shell Resolution(Low) 3.3619
    Number of Reflections(R-Free) 457
    Number of Reflections(R-Work) 8436
    R-Factor(R-Work) 0.2589
    R-Factor(R-Free) 0.3087
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3619
    Shell Resolution(Low) 3.4231
    Number of Reflections(R-Free) 438
    Number of Reflections(R-Work) 8605
    R-Factor(R-Work) 0.2528
    R-Factor(R-Free) 0.3048
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4231
    Shell Resolution(Low) 3.4889
    Number of Reflections(R-Free) 465
    Number of Reflections(R-Work) 8759
    R-Factor(R-Work) 0.2513
    R-Factor(R-Free) 0.2874
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4889
    Shell Resolution(Low) 3.5601
    Number of Reflections(R-Free) 495
    Number of Reflections(R-Work) 8754
    R-Factor(R-Work) 0.2351
    R-Factor(R-Free) 0.2653
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5601
    Shell Resolution(Low) 3.6374
    Number of Reflections(R-Free) 488
    Number of Reflections(R-Work) 8906
    R-Factor(R-Work) 0.2354
    R-Factor(R-Free) 0.2807
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6374
    Shell Resolution(Low) 3.722
    Number of Reflections(R-Free) 469
    Number of Reflections(R-Work) 8987
    R-Factor(R-Work) 0.2279
    R-Factor(R-Free) 0.2685
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.722
    Shell Resolution(Low) 3.815
    Number of Reflections(R-Free) 496
    Number of Reflections(R-Work) 9012
    R-Factor(R-Work) 0.2172
    R-Factor(R-Free) 0.2641
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.815
    Shell Resolution(Low) 3.9181
    Number of Reflections(R-Free) 453
    Number of Reflections(R-Work) 9021
    R-Factor(R-Work) 0.2139
    R-Factor(R-Free) 0.2306
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9181
    Shell Resolution(Low) 4.0333
    Number of Reflections(R-Free) 504
    Number of Reflections(R-Work) 9109
    R-Factor(R-Work) 0.1994
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0333
    Shell Resolution(Low) 4.1634
    Number of Reflections(R-Free) 510
    Number of Reflections(R-Work) 9114
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2342
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1634
    Shell Resolution(Low) 4.3121
    Number of Reflections(R-Free) 455
    Number of Reflections(R-Work) 9280
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3121
    Shell Resolution(Low) 4.4846
    Number of Reflections(R-Free) 483
    Number of Reflections(R-Work) 9339
    R-Factor(R-Work) 0.1714
    R-Factor(R-Free) 0.1933
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4846
    Shell Resolution(Low) 4.6885
    Number of Reflections(R-Free) 492
    Number of Reflections(R-Work) 9357
    R-Factor(R-Work) 0.1627
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6885
    Shell Resolution(Low) 4.9354
    Number of Reflections(R-Free) 511
    Number of Reflections(R-Work) 9372
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.1815
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9354
    Shell Resolution(Low) 5.2441
    Number of Reflections(R-Free) 493
    Number of Reflections(R-Work) 9444
    R-Factor(R-Work) 0.1598
    R-Factor(R-Free) 0.1749
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2441
    Shell Resolution(Low) 5.6482
    Number of Reflections(R-Free) 453
    Number of Reflections(R-Work) 9474
    R-Factor(R-Work) 0.1763
    R-Factor(R-Free) 0.2109
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6482
    Shell Resolution(Low) 6.2152
    Number of Reflections(R-Free) 509
    Number of Reflections(R-Work) 9465
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2159
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2152
    Shell Resolution(Low) 7.1113
    Number of Reflections(R-Free) 487
    Number of Reflections(R-Work) 9532
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.226
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1113
    Shell Resolution(Low) 8.9471
    Number of Reflections(R-Free) 484
    Number of Reflections(R-Work) 9598
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.9471
    Shell Resolution(Low) 43.9609
    Number of Reflections(R-Free) 514
    Number of Reflections(R-Work) 9622
    R-Factor(R-Work) 0.2201
    R-Factor(R-Free) 0.2184
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.078
    f_plane_restr 0.004
    f_chiral_restr 0.068
    f_angle_d 1.053
    f_bond_d 0.008
     
    Coordinate Error
    Luzzati ESD(Observed) 0.4156
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 62298
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 650
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SHELXD
    Structure Refinement PHENIX (phenix.refine: 1.5_2)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    phasing SHELX
    data scaling SCALEPACK
    reflection data processing DENZO