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X-RAY DIFFRACTION
Materials and Methods page
3RAE
  •   Crystallization Hide
    Crystallization Experiments
    Method LIQUID DIFFUSION
    pH 6.5
    Temperature 304.0
    Details 50mM sodium cacodylate, 7% isopropanol, pH 6.5, LIQUID DIFFUSION, temperature 304K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 157.83 α = 90
    b = 157.83 β = 90
    c = 211.15 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-09-26
     
    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) 2.6
    Resolution(Low) 50
    Number Reflections(All) 94010
    Number Reflections(Observed) 93164
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.085
    B(Isotropic) From Wilson Plot 71.22
    Redundancy 4.5
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.69
    Percent Possible(All) 95.3
    R Merge I(Observed) 0.84
    Mean I Over Sigma(Observed) 1.2
    R-Sym I(Observed) 0.84
    Redundancy 3.5
    Number Unique Reflections(All) 8838
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 41.832
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 67471
    Number of Reflections(Observed) 67471
    Number of Reflections(R-Free) 6838
    Percent Reflections(Observed) 99.45
    R-Factor(Observed) 0.1899
    R-Work 0.1857
    R-Free 0.2264
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 6.8001
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 6.8001
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -13.6002
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9
    Shell Resolution(Low) 2.933
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 1992
    R-Factor(R-Work) 0.2806
    R-Factor(R-Free) 0.3562
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.933
    Shell Resolution(Low) 2.9675
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 2026
    R-Factor(R-Work) 0.2641
    R-Factor(R-Free) 0.3285
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9675
    Shell Resolution(Low) 3.0036
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 2026
    R-Factor(R-Work) 0.247
    R-Factor(R-Free) 0.3191
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0036
    Shell Resolution(Low) 3.0417
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 2011
    R-Factor(R-Work) 0.2587
    R-Factor(R-Free) 0.3335
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0417
    Shell Resolution(Low) 3.0817
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 1997
    R-Factor(R-Work) 0.2488
    R-Factor(R-Free) 0.3145
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0817
    Shell Resolution(Low) 3.1239
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 1999
    R-Factor(R-Work) 0.2369
    R-Factor(R-Free) 0.2939
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1239
    Shell Resolution(Low) 3.1685
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 2043
    R-Factor(R-Work) 0.2287
    R-Factor(R-Free) 0.2911
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1685
    Shell Resolution(Low) 3.2158
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 2029
    R-Factor(R-Work) 0.2347
    R-Factor(R-Free) 0.2821
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2158
    Shell Resolution(Low) 3.266
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 1977
    R-Factor(R-Work) 0.2276
    R-Factor(R-Free) 0.3225
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.266
    Shell Resolution(Low) 3.3195
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 2026
    R-Factor(R-Work) 0.2132
    R-Factor(R-Free) 0.2817
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3195
    Shell Resolution(Low) 3.3767
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 2018
    R-Factor(R-Work) 0.2028
    R-Factor(R-Free) 0.2433
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3767
    Shell Resolution(Low) 3.4381
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 1978
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2461
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4381
    Shell Resolution(Low) 3.5042
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 2040
    R-Factor(R-Work) 0.1888
    R-Factor(R-Free) 0.2496
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5042
    Shell Resolution(Low) 3.5757
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 1998
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.2378
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5757
    Shell Resolution(Low) 3.6534
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 2038
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.2557
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6534
    Shell Resolution(Low) 3.7383
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 2000
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7383
    Shell Resolution(Low) 3.8318
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 2041
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.2432
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8318
    Shell Resolution(Low) 3.9353
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 2010
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.211
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9353
    Shell Resolution(Low) 4.051
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 2038
    R-Factor(R-Work) 0.1616
    R-Factor(R-Free) 0.1987
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.051
    Shell Resolution(Low) 4.1816
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 2023
    R-Factor(R-Work) 0.1576
    R-Factor(R-Free) 0.211
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1816
    Shell Resolution(Low) 4.3309
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 2029
    R-Factor(R-Work) 0.1526
    R-Factor(R-Free) 0.1858
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3309
    Shell Resolution(Low) 4.5041
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 2012
    R-Factor(R-Work) 0.1345
    R-Factor(R-Free) 0.2002
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5041
    Shell Resolution(Low) 4.7089
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 2024
    R-Factor(R-Work) 0.1363
    R-Factor(R-Free) 0.1594
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7089
    Shell Resolution(Low) 4.9568
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 2064
    R-Factor(R-Work) 0.15
    R-Factor(R-Free) 0.1766
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9568
    Shell Resolution(Low) 5.2668
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 2051
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.1956
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2668
    Shell Resolution(Low) 5.6725
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2019
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6725
    Shell Resolution(Low) 6.2417
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 2059
    R-Factor(R-Work) 0.1872
    R-Factor(R-Free) 0.2442
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2417
    Shell Resolution(Low) 7.141
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 2057
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2062
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.141
    Shell Resolution(Low) 8.9822
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 2074
    R-Factor(R-Work) 0.155
    R-Factor(R-Free) 0.1669
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.9822
    Shell Resolution(Low) 41.8368
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 1934
    R-Factor(R-Work) 0.1854
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 89.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.077
    f_dihedral_angle_d 16.839
    f_angle_d 1.221
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10338
    Nucleic Acid Atoms 730
    Heterogen Atoms 58
    Solvent Atoms 54
     
     
  •   Software and Computing Hide
    Computing
    Data Collection GDE
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.6.1_357)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.1_357)
    model building Phaser
    data collection GDE