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X-RAY DIFFRACTION
Materials and Methods page
3LTN
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 295.0
    Details 4-5% isopropanol, optimised mixture of salts, 50mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 122.51 α = 90
    b = 122.51 β = 90
    c = 178.3 γ = 120
     
    Space Group
    Space Group Name:    P 32
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-08-07
     
    Diffraction Radiation
    Monochromator Double Crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I03
    Wavelength List 0.9763
    Site DIAMOND
    Beamline I03
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.1
    Resolution(Low) 50
    Number Reflections(All) 54325
    Number Reflections(Observed) 53890
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.075
    B(Isotropic) From Wilson Plot 98.815
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.21
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.408
    Mean I Over Sigma(Observed) 3.563
    R-Sym I(Observed) 0.408
    Redundancy 5.8
    Number Unique Reflections(All) 5435
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.1
    Resolution(Low) 34.127
    Cut-off Sigma(F) 1.97
    Number of Reflections(Observed) 53839
    Number of Reflections(R-Free) 5392
    Percent Reflections(Observed) 99.15
    R-Factor(Observed) 0.1902
    R-Work 0.186
    R-Free 0.2277
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic+TLS
    Mean Isotropic B Value 112.623
    Anisotropic B[1][1] -13.7173
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -13.7173
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.8126
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1001
    Shell Resolution(Low) 3.1353
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 1665
    R-Factor(R-Work) 0.2805
    R-Factor(R-Free) 0.3314
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1353
    Shell Resolution(Low) 3.1722
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 1597
    R-Factor(R-Work) 0.2635
    R-Factor(R-Free) 0.2883
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1722
    Shell Resolution(Low) 3.2108
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 1666
    R-Factor(R-Work) 0.2676
    R-Factor(R-Free) 0.3428
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2108
    Shell Resolution(Low) 3.2515
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 1583
    R-Factor(R-Work) 0.2479
    R-Factor(R-Free) 0.3407
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2515
    Shell Resolution(Low) 3.2942
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1666
    R-Factor(R-Work) 0.2192
    R-Factor(R-Free) 0.2302
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2942
    Shell Resolution(Low) 3.3393
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 1633
    R-Factor(R-Work) 0.2106
    R-Factor(R-Free) 0.2714
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3393
    Shell Resolution(Low) 3.387
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 1642
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.2693
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.387
    Shell Resolution(Low) 3.4375
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 1610
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.2834
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4375
    Shell Resolution(Low) 3.4911
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1685
    R-Factor(R-Work) 0.2135
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4911
    Shell Resolution(Low) 3.5483
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 1607
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2674
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5483
    Shell Resolution(Low) 3.6094
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1652
    R-Factor(R-Work) 0.2228
    R-Factor(R-Free) 0.2725
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6094
    Shell Resolution(Low) 3.675
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1605
    R-Factor(R-Work) 0.2267
    R-Factor(R-Free) 0.3219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.675
    Shell Resolution(Low) 3.7456
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 1639
    R-Factor(R-Work) 0.1959
    R-Factor(R-Free) 0.2312
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7456
    Shell Resolution(Low) 3.8219
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 1608
    R-Factor(R-Work) 0.1793
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8219
    Shell Resolution(Low) 3.9049
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1620
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.2283
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9049
    Shell Resolution(Low) 3.9956
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 1599
    R-Factor(R-Work) 0.1505
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9956
    Shell Resolution(Low) 4.0954
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 1654
    R-Factor(R-Work) 0.1656
    R-Factor(R-Free) 0.2092
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0954
    Shell Resolution(Low) 4.2059
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 1634
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.2091
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2059
    Shell Resolution(Low) 4.3295
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1620
    R-Factor(R-Work) 0.1562
    R-Factor(R-Free) 0.2004
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3295
    Shell Resolution(Low) 4.4689
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1597
    R-Factor(R-Work) 0.1378
    R-Factor(R-Free) 0.1814
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4689
    Shell Resolution(Low) 4.6283
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1603
    R-Factor(R-Work) 0.1236
    R-Factor(R-Free) 0.151
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6283
    Shell Resolution(Low) 4.8131
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 1632
    R-Factor(R-Work) 0.133
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8131
    Shell Resolution(Low) 5.0315
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 1612
    R-Factor(R-Work) 0.1494
    R-Factor(R-Free) 0.1967
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0315
    Shell Resolution(Low) 5.2958
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 1641
    R-Factor(R-Work) 0.1683
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2958
    Shell Resolution(Low) 5.6263
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 1616
    R-Factor(R-Work) 0.1767
    R-Factor(R-Free) 0.2313
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6263
    Shell Resolution(Low) 6.0585
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 1633
    R-Factor(R-Work) 0.1882
    R-Factor(R-Free) 0.2172
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0585
    Shell Resolution(Low) 6.6641
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 1588
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6641
    Shell Resolution(Low) 7.619
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 1652
    R-Factor(R-Work) 0.1836
    R-Factor(R-Free) 0.2198
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.619
    Shell Resolution(Low) 9.564
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 1614
    R-Factor(R-Work) 0.1729
    R-Factor(R-Free) 0.1954
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.564
    Shell Resolution(Low) 34.1288
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1274
    R-Factor(R-Work) 0.2166
    R-Factor(R-Free) 0.2603
    Percent Reflections(Observed) 78.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.083
    f_dihedral_angle_d 20.094
    f_angle_d 1.308
    f_bond_d 0.025
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10282
    Nucleic Acid Atoms 730
    Heterogen Atoms 54
    Solvent Atoms 5
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution phaser
    Structure Refinement PHENIX (phenix.refine)
     
    Software
    refinement PHENIX version: (phenix.refine)
    model building phaser