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X-RAY DIFFRACTION
Materials and Methods page
4MDF
  •   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 triphosphate, 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 = 53.03 α = 90
    b = 72.75 β = 90
    c = 119.46 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 2013-07-24
     
    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) 1.73
    Resolution(Low) 53
    Number Reflections(All) 49311
    Number Reflections(Observed) 49311
    Percent Possible(Observed) 100.0
     
    High Resolution Shell Details
    Resolution(High) 1.727
    Resolution(Low) 1.76
    Percent Possible(All) 99.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.727
    Resolution(Low) 48.465
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 49282
    Number of Reflections(Observed) 49036
    Number of Reflections(R-Free) 3896
    Percent Reflections(Observed) 99.53
    R-Factor(Observed) 0.1658
    R-Work 0.1632
    R-Free 0.196
    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) 1.7273
    Shell Resolution(Low) 1.7483
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1532
    R-Factor(R-Work) 0.2233
    R-Factor(R-Free) 0.2766
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7483
    Shell Resolution(Low) 1.7705
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1561
    R-Factor(R-Work) 0.1941
    R-Factor(R-Free) 0.2592
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7705
    Shell Resolution(Low) 1.7938
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1572
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7938
    Shell Resolution(Low) 1.8183
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1577
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8183
    Shell Resolution(Low) 1.8443
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1593
    R-Factor(R-Work) 0.1643
    R-Factor(R-Free) 0.2199
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8443
    Shell Resolution(Low) 1.8719
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1575
    R-Factor(R-Work) 0.1534
    R-Factor(R-Free) 0.2068
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8719
    Shell Resolution(Low) 1.9011
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 1598
    R-Factor(R-Work) 0.1488
    R-Factor(R-Free) 0.1802
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9011
    Shell Resolution(Low) 1.9323
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 1591
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.1975
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9323
    Shell Resolution(Low) 1.9656
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1635
    R-Factor(R-Work) 0.1475
    R-Factor(R-Free) 0.1938
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9656
    Shell Resolution(Low) 2.0013
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1585
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0013
    Shell Resolution(Low) 2.0398
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1602
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.1948
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0398
    Shell Resolution(Low) 2.0815
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1586
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.1897
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0815
    Shell Resolution(Low) 2.1267
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1587
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.1999
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1267
    Shell Resolution(Low) 2.1762
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1578
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.2235
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1762
    Shell Resolution(Low) 2.2306
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1599
    R-Factor(R-Work) 0.1517
    R-Factor(R-Free) 0.1664
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2306
    Shell Resolution(Low) 2.2909
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1611
    R-Factor(R-Work) 0.1562
    R-Factor(R-Free) 0.217
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2909
    Shell Resolution(Low) 2.3583
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1606
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.2177
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3583
    Shell Resolution(Low) 2.4345
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 1655
    R-Factor(R-Work) 0.1615
    R-Factor(R-Free) 0.208
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4345
    Shell Resolution(Low) 2.5215
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 1593
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.1964
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5215
    Shell Resolution(Low) 2.6224
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1620
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2116
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6224
    Shell Resolution(Low) 2.7418
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1620
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7418
    Shell Resolution(Low) 2.8863
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 1609
    R-Factor(R-Work) 0.1728
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8863
    Shell Resolution(Low) 3.0671
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1645
    R-Factor(R-Work) 0.1707
    R-Factor(R-Free) 0.1882
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0671
    Shell Resolution(Low) 3.3039
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1660
    R-Factor(R-Work) 0.1683
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3039
    Shell Resolution(Low) 3.6362
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1634
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6362
    Shell Resolution(Low) 4.1622
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1666
    R-Factor(R-Work) 0.1445
    R-Factor(R-Free) 0.1648
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1622
    Shell Resolution(Low) 5.2429
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1674
    R-Factor(R-Work) 0.1422
    R-Factor(R-Free) 0.1574
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2429
    Shell Resolution(Low) 48.4842
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1776
    R-Factor(R-Work) 0.1932
    R-Factor(R-Free) 0.1998
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.07
    f_dihedral_angle_d 20.11
    f_angle_d 1.126
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2738
    Nucleic Acid Atoms 169
    Heterogen Atoms 79
    Solvent Atoms 395
     
     
  •   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