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X-RAY DIFFRACTION
Materials and Methods page
4MDE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 298.0
    Details 100 mM sodium citrate, pH 5.0, 2 mM guanosine diphosphate, 100mM magnesium chloride,18-24% PEG 6000,1.1 mM short DNA strand , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.44 α = 90
    b = 73.12 β = 90
    c = 119.04 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 130
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2013-08-14
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -999.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.8
    Resolution(Low) 46.2
    Number Reflections(All) 44706
    Number Reflections(Observed) 43723
    Percent Possible(Observed) 97.8
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 97.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method molecular refinement
    reflnsShellList 1.8
    Resolution(Low) 40.995
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 44862
    Number of Reflections(Observed) 43651
    Number of Reflections(R-Free) 3439
    Percent Reflections(Observed) 97.33
    R-Factor(Observed) 0.1675
    R-Work 0.1644
    R-Free 0.2056
    R-Free Selection Details 8% of data chosen at random
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8247
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 1642
    R-Factor(R-Work) 0.2228
    R-Factor(R-Free) 0.2708
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8247
    Shell Resolution(Low) 1.8507
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1562
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.2732
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8507
    Shell Resolution(Low) 1.8784
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1565
    R-Factor(R-Work) 0.1925
    R-Factor(R-Free) 0.2308
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8784
    Shell Resolution(Low) 1.9077
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1539
    R-Factor(R-Work) 0.1795
    R-Factor(R-Free) 0.2035
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9077
    Shell Resolution(Low) 1.939
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1620
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.2408
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9724
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 1616
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2471
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9724
    Shell Resolution(Low) 2.0083
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1587
    R-Factor(R-Work) 0.1746
    R-Factor(R-Free) 0.2242
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0083
    Shell Resolution(Low) 2.0469
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1562
    R-Factor(R-Work) 0.1687
    R-Factor(R-Free) 0.2305
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0469
    Shell Resolution(Low) 2.0887
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1619
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0887
    Shell Resolution(Low) 2.1341
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1564
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1341
    Shell Resolution(Low) 2.1838
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1601
    R-Factor(R-Work) 0.1563
    R-Factor(R-Free) 0.2082
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1838
    Shell Resolution(Low) 2.2384
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1588
    R-Factor(R-Work) 0.1632
    R-Factor(R-Free) 0.2155
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2384
    Shell Resolution(Low) 2.2989
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1578
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.2374
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2989
    Shell Resolution(Low) 2.3665
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1621
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.2292
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3665
    Shell Resolution(Low) 2.4429
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 1607
    R-Factor(R-Work) 0.1653
    R-Factor(R-Free) 0.235
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4429
    Shell Resolution(Low) 2.5302
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1600
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2327
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5302
    Shell Resolution(Low) 2.6315
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 1633
    R-Factor(R-Work) 0.1755
    R-Factor(R-Free) 0.2114
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6315
    Shell Resolution(Low) 2.7512
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1592
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.2185
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7512
    Shell Resolution(Low) 2.8962
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1626
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.1884
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8962
    Shell Resolution(Low) 3.0776
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1618
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.1901
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0776
    Shell Resolution(Low) 3.3152
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1663
    R-Factor(R-Work) 0.1679
    R-Factor(R-Free) 0.1853
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3152
    Shell Resolution(Low) 3.6486
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1676
    R-Factor(R-Work) 0.1611
    R-Factor(R-Free) 0.1945
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6486
    Shell Resolution(Low) 4.1761
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1637
    R-Factor(R-Work) 0.1466
    R-Factor(R-Free) 0.1792
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1761
    Shell Resolution(Low) 5.2597
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1637
    R-Factor(R-Work) 0.1432
    R-Factor(R-Free) 0.1736
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2597
    Shell Resolution(Low) 41.006
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1659
    R-Factor(R-Work) 0.1788
    R-Factor(R-Free) 0.2136
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.071
    f_dihedral_angle_d 15.352
    f_angle_d 1.084
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2738
    Nucleic Acid Atoms 202
    Heterogen Atoms 58
    Solvent Atoms 440
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.2_1309)
    model building PHENIX
    data collection CBASS