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X-RAY DIFFRACTION
Materials and Methods page
4D9W
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 291.0
    Details 1.9 M cesium chloride, 50% DMSO, 50 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 93.1 α = 90
    b = 93.1 β = 90
    c = 130.9 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Details Collimating Mirror
    Collection Date 2010-06-25
     
    Diffraction Radiation
    Monochromator Double Crystal Si(111)
    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) 1.38
    Resolution(Low) 50
    Number Reflections(All) 68072
    Number Reflections(Observed) 68072
    Percent Possible(Observed) 98.6
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 1.38
    Resolution(Low) 1.4
    Percent Possible(All) 99.9
    Mean I Over Sigma(Observed) 3.4
    R-Sym I(Observed) 0.5
    Redundancy 5.9
    Number Unique Reflections(All) 3373
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.381
    Resolution(Low) 22.302
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 68231
    Number of Reflections(Observed) 64916
    Number of Reflections(R-Free) 3315
    Percent Reflections(Observed) 94.11
    R-Factor(All) 0.1107
    R-Factor(Observed) 0.1107
    R-Work 0.1091
    R-Free 0.1402
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -1.1688
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.1688
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.3376
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.381
    Shell Resolution(Low) 1.401
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2348
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.2128
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.401
    Shell Resolution(Low) 1.4219
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2394
    R-Factor(R-Work) 0.1362
    R-Factor(R-Free) 0.171
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4219
    Shell Resolution(Low) 1.4442
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2415
    R-Factor(R-Work) 0.1304
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4442
    Shell Resolution(Low) 1.4678
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2453
    R-Factor(R-Work) 0.1238
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4678
    Shell Resolution(Low) 1.4931
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2486
    R-Factor(R-Work) 0.1166
    R-Factor(R-Free) 0.1692
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4931
    Shell Resolution(Low) 1.5203
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2445
    R-Factor(R-Work) 0.1034
    R-Factor(R-Free) 0.1519
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5203
    Shell Resolution(Low) 1.5495
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2488
    R-Factor(R-Work) 0.0986
    R-Factor(R-Free) 0.147
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5495
    Shell Resolution(Low) 1.5811
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2536
    R-Factor(R-Work) 0.0899
    R-Factor(R-Free) 0.1413
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5811
    Shell Resolution(Low) 1.6155
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2513
    R-Factor(R-Work) 0.0915
    R-Factor(R-Free) 0.1363
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6155
    Shell Resolution(Low) 1.6531
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.0863
    R-Factor(R-Free) 0.1663
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6531
    Shell Resolution(Low) 1.6944
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2589
    R-Factor(R-Work) 0.0878
    R-Factor(R-Free) 0.125
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6944
    Shell Resolution(Low) 1.7402
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2543
    R-Factor(R-Work) 0.0839
    R-Factor(R-Free) 0.1229
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7402
    Shell Resolution(Low) 1.7914
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.0873
    R-Factor(R-Free) 0.1254
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7914
    Shell Resolution(Low) 1.8492
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2533
    R-Factor(R-Work) 0.0848
    R-Factor(R-Free) 0.1135
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8492
    Shell Resolution(Low) 1.9152
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2557
    R-Factor(R-Work) 0.0937
    R-Factor(R-Free) 0.1251
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9152
    Shell Resolution(Low) 1.9919
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2605
    R-Factor(R-Work) 0.0951
    R-Factor(R-Free) 0.1284
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9919
    Shell Resolution(Low) 2.0824
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.0963
    R-Factor(R-Free) 0.1242
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0824
    Shell Resolution(Low) 2.1921
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.0912
    R-Factor(R-Free) 0.1098
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1921
    Shell Resolution(Low) 2.3294
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.0961
    R-Factor(R-Free) 0.1352
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3294
    Shell Resolution(Low) 2.509
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1069
    R-Factor(R-Free) 0.1262
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.509
    Shell Resolution(Low) 2.7611
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1094
    R-Factor(R-Free) 0.1425
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7611
    Shell Resolution(Low) 3.1596
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.1112
    R-Factor(R-Free) 0.144
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1596
    Shell Resolution(Low) 3.9771
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2725
    R-Factor(R-Work) 0.1236
    R-Factor(R-Free) 0.1309
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9771
    Shell Resolution(Low) 22.3047
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2816
    R-Factor(R-Work) 0.145
    R-Factor(R-Free) 0.165
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.089
    f_dihedral_angle_d 14.07
    f_angle_d 1.275
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2428
    Nucleic Acid Atoms 0
    Heterogen Atoms 70
    Solvent Atoms 474
     
     
  •   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_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building PHASER
    data collection MAR345dtb