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X-RAY DIFFRACTION
Materials and Methods page
4G0U
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 277.0
    Details 100mM magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 80.92 α = 90
    b = 175.8 β = 113.61
    c = 93.13 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX300HE
    Collection Date 2011-03-23
     
    Diffraction Radiation
    Monochromator Horizontally focusing single crystal monochromator (Crystal type Si(1 1 1))
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSRRC BEAMLINE BL13C1
    Wavelength List 0.97622
    Site NSRRC
    Beamline BL13C1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.7
    Resolution(Low) 30
    Number Reflections(All) 65343
    Number Reflections(Observed) 63644
    Percent Possible(Observed) 97.4
    B(Isotropic) From Wilson Plot 42.71
    Redundancy 3.0
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.75
    Percent Possible(All) 98.8
    R Merge I(Observed) 0.467
    Mean I Over Sigma(Observed) 2.6
    R-Sym I(Observed) 0.467
    Redundancy 3.1
    Number Unique Reflections(All) 3232
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 28.231
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 65471
    Number of Reflections(Observed) 63605
    Number of Reflections(R-Free) 3235
    Percent Reflections(Observed) 97.15
    R-Factor(All) 0.1591
    R-Factor(Observed) 0.1591
    R-Work 0.1562
    R-Free 0.2129
    R-Free Selection Details Randomly picked by PHENIX program
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.152
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6975
    Shell Resolution(Low) 2.7377
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2561
    R-Factor(R-Work) 0.2154
    R-Factor(R-Free) 0.2872
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7377
    Shell Resolution(Low) 2.7804
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2627
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.2853
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7804
    Shell Resolution(Low) 2.826
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.29
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.826
    Shell Resolution(Low) 2.8747
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.193
    R-Factor(R-Free) 0.2323
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8747
    Shell Resolution(Low) 2.9269
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1921
    R-Factor(R-Free) 0.2767
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9269
    Shell Resolution(Low) 2.9831
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1928
    R-Factor(R-Free) 0.2727
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9831
    Shell Resolution(Low) 3.044
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2555
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.044
    Shell Resolution(Low) 3.1101
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.1763
    R-Factor(R-Free) 0.2678
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1101
    Shell Resolution(Low) 3.1823
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2308
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1823
    Shell Resolution(Low) 3.2618
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.2386
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2618
    Shell Resolution(Low) 3.3498
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.1558
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3498
    Shell Resolution(Low) 3.4482
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.2144
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4482
    Shell Resolution(Low) 3.5593
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.1443
    R-Factor(R-Free) 0.1856
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5593
    Shell Resolution(Low) 3.6863
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.1477
    R-Factor(R-Free) 0.2179
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6863
    Shell Resolution(Low) 3.8335
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.1459
    R-Factor(R-Free) 0.1653
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8335
    Shell Resolution(Low) 4.0076
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.1458
    R-Factor(R-Free) 0.2155
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0076
    Shell Resolution(Low) 4.2182
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2604
    R-Factor(R-Work) 0.1321
    R-Factor(R-Free) 0.1885
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2182
    Shell Resolution(Low) 4.4815
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1246
    R-Factor(R-Free) 0.1923
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4815
    Shell Resolution(Low) 4.8259
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1288
    R-Factor(R-Free) 0.1713
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8259
    Shell Resolution(Low) 5.3087
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.1454
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3087
    Shell Resolution(Low) 6.0702
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2366
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0702
    Shell Resolution(Low) 7.6228
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2580
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.1871
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.6228
    Shell Resolution(Low) 28.2321
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2592
    R-Factor(R-Work) 0.1498
    R-Factor(R-Free) 0.1785
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.074
    f_dihedral_angle_d 16.466
    f_angle_d 1.192
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10676
    Nucleic Acid Atoms 820
    Heterogen Atoms 62
    Solvent Atoms 426
     
     
  •   Software and Computing Hide
    Computing
    Data Collection bluice
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX (phenix.automr: 1.6.4_486)
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building PHENIX version: (phenix.automr: 1.6.4_486)
    data collection bluice