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X-RAY DIFFRACTION
Materials and Methods page
4GD0
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 291.15
    Details 100 mM Tris, 1 mM DTT, 10 % DMSO, 12% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 91.43 α = 90
    b = 64.99 β = 96.1
    c = 70.2 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 113.15
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Details morror
    Collection Date 2010-10-21
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type BESSY BEAMLINE 14.2
    Wavelength List 0.91841
    Site BESSY
    Beamline 14.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.29
    Resolution(Low) 50
    Number Reflections(All) 99752
    Number Reflections(Observed) 99752
    Percent Possible(Observed) 97.1
    B(Isotropic) From Wilson Plot 8.85
    Redundancy 2.7
     
    High Resolution Shell Details
    Resolution(High) 1.29
    Resolution(Low) 1.31
    Percent Possible(All) 81.5
    Mean I Over Sigma(Observed) 3.02
    Redundancy 1.7
    Number Unique Reflections(All) 4187
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.29
    Resolution(Low) 16.275
    Cut-off Sigma(F) 1.0
    Number of Reflections(all) 96177
    Number of Reflections(Observed) 96177
    Number of Reflections(R-Free) 9637
    Percent Reflections(Observed) 93.7
    R-Factor(Observed) 0.1651
    R-Work 0.1628
    R-Free 0.1855
    R-Free Selection Details Random, 10%
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic
    Anisotropic B[1][1] -0.0306
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.7146
    Anisotropic B[2][2] -1.1613
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.1919
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.29
    Shell Resolution(Low) 1.3047
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 2231
    R-Factor(R-Work) 0.2279
    R-Factor(R-Free) 0.2657
    Percent Reflections(Observed) 72.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3047
    Shell Resolution(Low) 1.3201
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 2451
    R-Factor(R-Work) 0.2221
    R-Factor(R-Free) 0.2705
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3201
    Shell Resolution(Low) 1.3362
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.2019
    R-Factor(R-Free) 0.2233
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3362
    Shell Resolution(Low) 1.3531
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.1897
    R-Factor(R-Free) 0.2407
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3531
    Shell Resolution(Low) 1.3709
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.1872
    R-Factor(R-Free) 0.2176
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3709
    Shell Resolution(Low) 1.3896
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.2209
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3896
    Shell Resolution(Low) 1.4095
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 2876
    R-Factor(R-Work) 0.1784
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4095
    Shell Resolution(Low) 1.4305
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 2784
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.2193
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4305
    Shell Resolution(Low) 1.4528
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 2869
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.2092
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4528
    Shell Resolution(Low) 1.4766
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 2916
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.1929
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4766
    Shell Resolution(Low) 1.5021
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 2855
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.2
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5021
    Shell Resolution(Low) 1.5294
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 2904
    R-Factor(R-Work) 0.1531
    R-Factor(R-Free) 0.1837
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5294
    Shell Resolution(Low) 1.5588
    Number of Reflections(R-Free) 327
    Number of Reflections(R-Work) 2957
    R-Factor(R-Work) 0.1506
    R-Factor(R-Free) 0.1745
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5588
    Shell Resolution(Low) 1.5906
    Number of Reflections(R-Free) 375
    Number of Reflections(R-Work) 2860
    R-Factor(R-Work) 0.1514
    R-Factor(R-Free) 0.1871
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5906
    Shell Resolution(Low) 1.6251
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 2914
    R-Factor(R-Work) 0.1499
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6251
    Shell Resolution(Low) 1.6629
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 2908
    R-Factor(R-Work) 0.1564
    R-Factor(R-Free) 0.1832
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6629
    Shell Resolution(Low) 1.7044
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 3006
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.1985
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7044
    Shell Resolution(Low) 1.7505
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 2962
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7505
    Shell Resolution(Low) 1.8019
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 2977
    R-Factor(R-Work) 0.1605
    R-Factor(R-Free) 0.1971
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8019
    Shell Resolution(Low) 1.86
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 3010
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1795
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.86
    Shell Resolution(Low) 1.9264
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 3023
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9264
    Shell Resolution(Low) 2.0034
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 3052
    R-Factor(R-Work) 0.1593
    R-Factor(R-Free) 0.1931
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0034
    Shell Resolution(Low) 2.0943
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 3057
    R-Factor(R-Work) 0.1588
    R-Factor(R-Free) 0.1711
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0943
    Shell Resolution(Low) 2.2045
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 3061
    R-Factor(R-Work) 0.1547
    R-Factor(R-Free) 0.1771
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2045
    Shell Resolution(Low) 2.3423
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 3072
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.1721
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3423
    Shell Resolution(Low) 2.5225
    Number of Reflections(R-Free) 359
    Number of Reflections(R-Work) 3022
    R-Factor(R-Work) 0.1559
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5225
    Shell Resolution(Low) 2.7752
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 3095
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7752
    Shell Resolution(Low) 3.1742
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 3102
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.1635
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1742
    Shell Resolution(Low) 3.9894
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 3047
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1627
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9894
    Shell Resolution(Low) 16.275
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 2858
    R-Factor(R-Work) 0.1826
    R-Factor(R-Free) 0.1871
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.069
    f_dihedral_angle_d 12.416
    f_angle_d 1.06
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2857
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 524
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.2_869)
    model building Phaser
    data collection MAR345dtb