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X-RAY DIFFRACTION
Materials and Methods page
4DBC
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 2 uL of protein solution(15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 mM deaza-PLP, 50 mM L-aspartate) mixed with 2 uL reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA), VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 84.29 α = 90
    b = 155.25 β = 90
    c = 77.96 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2010-02-03
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength 1.033
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.5
    Resolution(Low) 28.62
    Number Reflections(All) 81931
    Number Reflections(Observed) 80890
    Percent Possible(Observed) 98.7
    R Merge I(Observed) 0.038
    Redundancy 4.24
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.54
    Percent Possible(All) 93.9
    R Merge I(Observed) 0.543
    Mean I Over Sigma(Observed) 2.03
    R-Sym I(Observed) 0.543
    Redundancy 2.73
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 28.617
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 80854
    Number of Reflections(R-Free) 4061
    Percent Reflections(Observed) 98.74
    R-Factor(Observed) 0.1704
    R-Work 0.1692
    R-Free 0.1935
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.3233
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.8079
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.5153
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.5177
    Number of Reflections(R-Free) 111
    Number of Reflections(R-Work) 2464
    R-Factor(R-Work) 0.368
    R-Factor(R-Free) 0.363
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5177
    Shell Resolution(Low) 1.5362
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2510
    R-Factor(R-Work) 0.3231
    R-Factor(R-Free) 0.3203
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5362
    Shell Resolution(Low) 1.5556
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2568
    R-Factor(R-Work) 0.2975
    R-Factor(R-Free) 0.2939
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5556
    Shell Resolution(Low) 1.5761
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.286
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5761
    Shell Resolution(Low) 1.5977
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.2551
    R-Factor(R-Free) 0.291
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5977
    Shell Resolution(Low) 1.6205
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.2426
    R-Factor(R-Free) 0.3078
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6205
    Shell Resolution(Low) 1.6447
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2353
    R-Factor(R-Free) 0.2549
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6447
    Shell Resolution(Low) 1.6704
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.2078
    R-Factor(R-Free) 0.2164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6704
    Shell Resolution(Low) 1.6978
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.2079
    R-Factor(R-Free) 0.2482
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6978
    Shell Resolution(Low) 1.727
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.2094
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.727
    Shell Resolution(Low) 1.7584
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2256
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7584
    Shell Resolution(Low) 1.7922
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1887
    R-Factor(R-Free) 0.2448
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7922
    Shell Resolution(Low) 1.8288
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1842
    R-Factor(R-Free) 0.2253
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8288
    Shell Resolution(Low) 1.8686
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2454
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8686
    Shell Resolution(Low) 1.912
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1779
    R-Factor(R-Free) 0.1841
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.912
    Shell Resolution(Low) 1.9598
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.1949
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9598
    Shell Resolution(Low) 2.0128
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0128
    Shell Resolution(Low) 2.072
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2069
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.072
    Shell Resolution(Low) 2.1389
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1389
    Shell Resolution(Low) 2.2153
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.162
    R-Factor(R-Free) 0.173
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2153
    Shell Resolution(Low) 2.304
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.1581
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.304
    Shell Resolution(Low) 2.4088
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1632
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4088
    Shell Resolution(Low) 2.5357
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.1816
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5357
    Shell Resolution(Low) 2.6945
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.2064
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6945
    Shell Resolution(Low) 2.9023
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.1787
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9023
    Shell Resolution(Low) 3.194
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.1848
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.194
    Shell Resolution(Low) 3.6554
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2730
    R-Factor(R-Work) 0.1561
    R-Factor(R-Free) 0.1764
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6554
    Shell Resolution(Low) 4.6023
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2747
    R-Factor(R-Work) 0.1361
    R-Factor(R-Free) 0.1562
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6023
    Shell Resolution(Low) 28.6218
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.1692
    R-Factor(R-Free) 0.1724
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.01
    f_chiral_restr 0.115
    f_dihedral_angle_d 12.866
    f_angle_d 1.607
    f_bond_d 0.016
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3065
    Nucleic Acid Atoms 0
    Heterogen Atoms 48
    Solvent Atoms 447
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building MOLREP