POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3K9F
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 295.0
    Details 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 = 122.41 α = 90
    b = 122.41 β = 90
    c = 178.29 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
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I03
    Wavelength List 0.97630
    Site DIAMOND
    Beamline I03
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(Observed) 64923
    Percent Possible(Observed) 98.1
    R Merge I(Observed) 0.074
    B(Isotropic) From Wilson Plot 80.77
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    R Merge I(Observed) 0.422
    Mean I Over Sigma(Observed) 2.19
    R-Sym I(Observed) 0.422
    Redundancy 5.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 26.731
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 64564
    Number of Reflections(R-Free) 6484
    Percent Reflections(Observed) 97.64
    R-Factor(Observed) 0.1867
    R-Work 0.1831
    R-Free 0.2182
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic+TLS
    Mean Isotropic B Value 88.666
    Anisotropic B[1][1] -2.415
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.415
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.829
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9004
    Shell Resolution(Low) 2.9333
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 1915
    R-Factor(R-Work) 0.2548
    R-Factor(R-Free) 0.2933
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9333
    Shell Resolution(Low) 2.9678
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 1968
    R-Factor(R-Work) 0.2428
    R-Factor(R-Free) 0.2851
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9678
    Shell Resolution(Low) 3.0039
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 1962
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.261
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0039
    Shell Resolution(Low) 3.0419
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 1937
    R-Factor(R-Work) 0.237
    R-Factor(R-Free) 0.2732
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0419
    Shell Resolution(Low) 3.0819
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 2006
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.284
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0819
    Shell Resolution(Low) 3.124
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 1943
    R-Factor(R-Work) 0.2183
    R-Factor(R-Free) 0.2664
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.124
    Shell Resolution(Low) 3.1686
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 1947
    R-Factor(R-Work) 0.2372
    R-Factor(R-Free) 0.2547
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1686
    Shell Resolution(Low) 3.2158
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 2056
    R-Factor(R-Work) 0.2485
    R-Factor(R-Free) 0.3158
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2158
    Shell Resolution(Low) 3.266
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 1874
    R-Factor(R-Work) 0.2513
    R-Factor(R-Free) 0.306
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.266
    Shell Resolution(Low) 3.3194
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 2018
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.2841
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3194
    Shell Resolution(Low) 3.3766
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 1984
    R-Factor(R-Work) 0.2279
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3766
    Shell Resolution(Low) 3.4378
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 1946
    R-Factor(R-Work) 0.2227
    R-Factor(R-Free) 0.2591
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4378
    Shell Resolution(Low) 3.5038
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 2002
    R-Factor(R-Work) 0.2075
    R-Factor(R-Free) 0.2464
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5038
    Shell Resolution(Low) 3.5752
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 1968
    R-Factor(R-Work) 0.1954
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5752
    Shell Resolution(Low) 3.6527
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 2007
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2359
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6527
    Shell Resolution(Low) 3.7375
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 2019
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2103
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7375
    Shell Resolution(Low) 3.8307
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 1921
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.1895
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8307
    Shell Resolution(Low) 3.9339
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 2017
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9339
    Shell Resolution(Low) 4.0493
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 1910
    R-Factor(R-Work) 0.1505
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0493
    Shell Resolution(Low) 4.1796
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 1980
    R-Factor(R-Work) 0.1525
    R-Factor(R-Free) 0.1806
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1796
    Shell Resolution(Low) 4.3283
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 2006
    R-Factor(R-Work) 0.1453
    R-Factor(R-Free) 0.1779
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3283
    Shell Resolution(Low) 4.5009
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 1950
    R-Factor(R-Work) 0.1326
    R-Factor(R-Free) 0.1639
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5009
    Shell Resolution(Low) 4.7047
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 1978
    R-Factor(R-Work) 0.1251
    R-Factor(R-Free) 0.1599
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7047
    Shell Resolution(Low) 4.9512
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 1936
    R-Factor(R-Work) 0.1344
    R-Factor(R-Free) 0.1719
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9512
    Shell Resolution(Low) 5.2592
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 1981
    R-Factor(R-Work) 0.1503
    R-Factor(R-Free) 0.1711
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2592
    Shell Resolution(Low) 5.6617
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 1983
    R-Factor(R-Work) 0.1535
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6617
    Shell Resolution(Low) 6.225
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 1968
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.225
    Shell Resolution(Low) 7.1109
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 2012
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1109
    Shell Resolution(Low) 8.9036
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 1886
    R-Factor(R-Work) 0.1617
    R-Factor(R-Free) 0.1941
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.9036
    Shell Resolution(Low) 26.7318
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 1000
    R-Factor(R-Work) 0.2171
    R-Factor(R-Free) 0.2575
    Percent Reflections(Observed) 50.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.095
    f_dihedral_angle_d 19.692
    f_angle_d 1.403
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10721
    Nucleic Acid Atoms 730
    Heterogen Atoms 54
    Solvent Atoms 14
     
     
  •   Software and Computing Hide
    Computing
    Data Collection GDA
    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
    data collection GDA