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X-RAY DIFFRACTION
Materials and Methods page
3UMP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.75
    Temperature 291.0
    Details 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 43.86 α = 90
    b = 88.91 β = 90
    c = 176.4 γ = 90
     
    Space Group
    Space Group Name:    P 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2010-09-09
     
    Diffraction Radiation
    Monochromator SI(311) AND SI(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength List 0.97627
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.85
    Resolution(Low) 50
    Number Reflections(All) 113930
    Number Reflections(Observed) 109841
    Percent Possible(Observed) 96.4
    R Merge I(Observed) 0.052
    B(Isotropic) From Wilson Plot 37.411
     
    High Resolution Shell Details
    Resolution(High) 1.849
    Resolution(Low) 1.96
    Percent Possible(All) 96.2
    R Merge I(Observed) 0.46
    Mean I Over Sigma(Observed) 2.07
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.849
    Resolution(Low) 49.046
    Cut-off Sigma(F) 1.21
    Number of Reflections(all) 113930
    Number of Reflections(Observed) 109841
    Number of Reflections(R-Free) 5471
    Percent Reflections(Observed) 96.41
    R-Factor(Observed) 0.1739
    R-Work 0.1721
    R-Free 0.2087
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.1342
    Anisotropic B[1][1] -2.7434
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.6697
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0737
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.849
    Shell Resolution(Low) 1.8705
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3261
    R-Factor(R-Work) 0.2743
    R-Factor(R-Free) 0.3089
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8705
    Shell Resolution(Low) 1.8925
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3574
    R-Factor(R-Work) 0.2601
    R-Factor(R-Free) 0.2897
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8925
    Shell Resolution(Low) 1.9155
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 3484
    R-Factor(R-Work) 0.2633
    R-Factor(R-Free) 0.2912
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9155
    Shell Resolution(Low) 1.9398
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3518
    R-Factor(R-Work) 0.2404
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9398
    Shell Resolution(Low) 1.9653
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3512
    R-Factor(R-Work) 0.2318
    R-Factor(R-Free) 0.2842
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9653
    Shell Resolution(Low) 1.9922
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3603
    R-Factor(R-Work) 0.2231
    R-Factor(R-Free) 0.2528
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9922
    Shell Resolution(Low) 2.0207
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3513
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.2693
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0207
    Shell Resolution(Low) 2.0509
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3495
    R-Factor(R-Work) 0.2047
    R-Factor(R-Free) 0.2872
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0509
    Shell Resolution(Low) 2.0829
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3623
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.2525
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0829
    Shell Resolution(Low) 2.1171
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3521
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.2747
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1171
    Shell Resolution(Low) 2.1536
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3544
    R-Factor(R-Work) 0.1828
    R-Factor(R-Free) 0.2102
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1536
    Shell Resolution(Low) 2.1927
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3554
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.2068
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1927
    Shell Resolution(Low) 2.2349
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3517
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.2046
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2349
    Shell Resolution(Low) 2.2805
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3511
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2805
    Shell Resolution(Low) 2.3301
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3514
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.2124
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3301
    Shell Resolution(Low) 2.3843
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3499
    R-Factor(R-Work) 0.1795
    R-Factor(R-Free) 0.2034
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3843
    Shell Resolution(Low) 2.4439
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3535
    R-Factor(R-Work) 0.183
    R-Factor(R-Free) 0.2293
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4439
    Shell Resolution(Low) 2.51
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3445
    R-Factor(R-Work) 0.1717
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.51
    Shell Resolution(Low) 2.5839
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3571
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.2485
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5839
    Shell Resolution(Low) 2.6673
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3474
    R-Factor(R-Work) 0.1797
    R-Factor(R-Free) 0.2342
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6673
    Shell Resolution(Low) 2.7626
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3517
    R-Factor(R-Work) 0.18
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7626
    Shell Resolution(Low) 2.8732
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3444
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.1883
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8732
    Shell Resolution(Low) 3.0039
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3479
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1944
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0039
    Shell Resolution(Low) 3.1623
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3381
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.2174
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1623
    Shell Resolution(Low) 3.3604
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3436
    R-Factor(R-Work) 0.1732
    R-Factor(R-Free) 0.218
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3604
    Shell Resolution(Low) 3.6197
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3416
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2104
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6197
    Shell Resolution(Low) 3.9839
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3403
    R-Factor(R-Work) 0.1512
    R-Factor(R-Free) 0.1745
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9839
    Shell Resolution(Low) 4.56
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3303
    R-Factor(R-Work) 0.1327
    R-Factor(R-Free) 0.1785
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.56
    Shell Resolution(Low) 5.7437
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3345
    R-Factor(R-Work) 0.1511
    R-Factor(R-Free) 0.1753
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7437
    Shell Resolution(Low) 49.0636
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3378
    R-Factor(R-Work) 0.1608
    R-Factor(R-Free) 0.1564
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 21.073
    f_plane_restr 0.005
    f_chiral_restr 0.071
    f_angle_d 1.369
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4541
    Nucleic Acid Atoms 0
    Heterogen Atoms 130
    Solvent Atoms 438
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    density modification DM
    molecular replacement Phaser
    data reduction Xscale