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X-RAY DIFFRACTION
Materials and Methods page
4G0W
  •   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 = 80.66 α = 90
    b = 176.42 β = 112.04
    c = 93.64 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 ADSC QUANTUM 315r
    Collection Date 2012-03-14
     
    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 BL13B1
    Wavelength List 1.0000
    Site NSRRC
    Beamline BL13B1
     
     
  •   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) 66542
    Number Reflections(Observed) 65943
    Percent Possible(Observed) 99.1
    B(Isotropic) From Wilson Plot 43.27
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.75
    Percent Possible(All) 91.7
    R Merge I(Observed) 0.424
    Mean I Over Sigma(Observed) 2.52
    R-Sym I(Observed) 0.424
    Redundancy 3.1
    Number Unique Reflections(All) 3034
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.696
    Resolution(Low) 27.49
    Cut-off Sigma(F) 1.37
    Number of Reflections(all) 66698
    Number of Reflections(Observed) 65898
    Number of Reflections(R-Free) 3340
    Percent Reflections(Observed) 98.8
    R-Factor(All) 0.1677
    R-Factor(Observed) 0.1677
    R-Work 0.1652
    R-Free 0.2154
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 44.8366
    Anisotropic B[1][1] 0.1508
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.7989
    Anisotropic B[2][2] -0.0833
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.0675
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6958
    Shell Resolution(Low) 2.7343
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2208
    R-Factor(R-Work) 0.27
    R-Factor(R-Free) 0.3317
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7343
    Shell Resolution(Low) 2.7751
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2481
    R-Factor(R-Work) 0.2717
    R-Factor(R-Free) 0.3481
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7751
    Shell Resolution(Low) 2.8184
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2533
    R-Factor(R-Work) 0.2625
    R-Factor(R-Free) 0.3199
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8184
    Shell Resolution(Low) 2.8646
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.2502
    R-Factor(R-Free) 0.3131
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8646
    Shell Resolution(Low) 2.9139
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2627
    R-Factor(R-Work) 0.2363
    R-Factor(R-Free) 0.299
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9139
    Shell Resolution(Low) 2.9668
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.2226
    R-Factor(R-Free) 0.3059
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9668
    Shell Resolution(Low) 3.0238
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.2142
    R-Factor(R-Free) 0.2928
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0238
    Shell Resolution(Low) 3.0855
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.2493
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0855
    Shell Resolution(Low) 3.1525
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.2255
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1525
    Shell Resolution(Low) 3.2257
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1641
    R-Factor(R-Free) 0.2188
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2257
    Shell Resolution(Low) 3.3062
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.1614
    R-Factor(R-Free) 0.2088
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3062
    Shell Resolution(Low) 3.3955
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1561
    R-Factor(R-Free) 0.1974
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3955
    Shell Resolution(Low) 3.4952
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.1532
    R-Factor(R-Free) 0.2023
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4952
    Shell Resolution(Low) 3.6078
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.147
    R-Factor(R-Free) 0.2099
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6078
    Shell Resolution(Low) 3.7364
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.1471
    R-Factor(R-Free) 0.1874
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7364
    Shell Resolution(Low) 3.8856
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.1451
    R-Factor(R-Free) 0.1741
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8856
    Shell Resolution(Low) 4.0619
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.1436
    R-Factor(R-Free) 0.1921
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0619
    Shell Resolution(Low) 4.2753
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.136
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2753
    Shell Resolution(Low) 4.5421
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2627
    R-Factor(R-Work) 0.1254
    R-Factor(R-Free) 0.1954
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5421
    Shell Resolution(Low) 4.891
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1385
    R-Factor(R-Free) 0.1786
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.891
    Shell Resolution(Low) 5.3799
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1564
    R-Factor(R-Free) 0.2081
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3799
    Shell Resolution(Low) 6.1507
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1846
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1507
    Shell Resolution(Low) 7.7207
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1752
    R-Factor(R-Free) 0.2267
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7207
    Shell Resolution(Low) 27.491
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1493
    R-Factor(R-Free) 0.1756
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.073
    f_dihedral_angle_d 17.511
    f_angle_d 1.158
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10704
    Nucleic Acid Atoms 820
    Heterogen Atoms 66
    Solvent Atoms 420
     
     
  •   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: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHENIX version: (phenix.automr: 1.6.4_486)
    data collection bluice