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X-RAY DIFFRACTION
Materials and Methods page
4M9N
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7.5
    Temperature 291.0
    Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.52 α = 90
    b = 79.21 β = 106.24
    c = 54.69 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 104
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details mirrors
    Collection Date 2013-01-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.28
    Resolution(Low) 14
    Percent Possible(Observed) 97.5
    R Merge I(Observed) 0.053
    B(Isotropic) From Wilson Plot 33.48
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 2.275
    Resolution(Low) 2.36
    Percent Possible(All) 81.9
    R Merge I(Observed) 0.245
    Redundancy 2.3
    Number Unique Reflections(All) 1657
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method Isomorphous replacement
    reflnsShellList 2.275
    Resolution(Low) 13.923
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 36691
    Number of Reflections(R-Free) 3646
    Percent Reflections(Observed) 91.35
    R-Factor(Observed) 0.1951
    R-Work 0.1915
    R-Free 0.2267
     
    Temperature Factor Modeling
    Mean Isotropic B Value 34.6408
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2751
    Shell Resolution(Low) 2.3049
    Number of Reflections(R-Free) 92
    Number of Reflections(R-Work) 740
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.3147
    Percent Reflections(Observed) 54.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3049
    Shell Resolution(Low) 2.3363
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 939
    R-Factor(R-Work) 0.2485
    R-Factor(R-Free) 0.2956
    Percent Reflections(Observed) 67.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3363
    Shell Resolution(Low) 2.3695
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 1017
    R-Factor(R-Work) 0.2442
    R-Factor(R-Free) 0.3329
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3695
    Shell Resolution(Low) 2.4047
    Number of Reflections(R-Free) 82
    Number of Reflections(R-Work) 1122
    R-Factor(R-Work) 0.2436
    R-Factor(R-Free) 0.2921
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4047
    Shell Resolution(Low) 2.4421
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1166
    R-Factor(R-Work) 0.2287
    R-Factor(R-Free) 0.2904
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4421
    Shell Resolution(Low) 2.4819
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1283
    R-Factor(R-Work) 0.2348
    R-Factor(R-Free) 0.2857
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4819
    Shell Resolution(Low) 2.5245
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1291
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.3313
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5245
    Shell Resolution(Low) 2.5701
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1310
    R-Factor(R-Work) 0.2408
    R-Factor(R-Free) 0.2959
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5701
    Shell Resolution(Low) 2.6192
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1307
    R-Factor(R-Work) 0.2218
    R-Factor(R-Free) 0.3038
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6192
    Shell Resolution(Low) 2.6723
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1296
    R-Factor(R-Work) 0.2235
    R-Factor(R-Free) 0.2922
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6723
    Shell Resolution(Low) 2.73
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1346
    R-Factor(R-Work) 0.2313
    R-Factor(R-Free) 0.2696
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.73
    Shell Resolution(Low) 2.793
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1264
    R-Factor(R-Work) 0.2145
    R-Factor(R-Free) 0.3046
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.793
    Shell Resolution(Low) 2.8623
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1381
    R-Factor(R-Work) 0.2197
    R-Factor(R-Free) 0.2266
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8623
    Shell Resolution(Low) 2.9389
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 1369
    R-Factor(R-Work) 0.2138
    R-Factor(R-Free) 0.2609
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9389
    Shell Resolution(Low) 3.0246
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1358
    R-Factor(R-Work) 0.2209
    R-Factor(R-Free) 0.263
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0246
    Shell Resolution(Low) 3.1211
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1319
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2639
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1211
    Shell Resolution(Low) 3.2313
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 1320
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.2614
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2313
    Shell Resolution(Low) 3.359
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1339
    R-Factor(R-Work) 0.1937
    R-Factor(R-Free) 0.2626
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.359
    Shell Resolution(Low) 3.5095
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 1369
    R-Factor(R-Work) 0.1887
    R-Factor(R-Free) 0.2007
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5095
    Shell Resolution(Low) 3.6913
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1366
    R-Factor(R-Work) 0.1701
    R-Factor(R-Free) 0.2278
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6913
    Shell Resolution(Low) 3.9177
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 1345
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.2128
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9177
    Shell Resolution(Low) 4.2124
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1370
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1576
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2124
    Shell Resolution(Low) 4.6222
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1348
    R-Factor(R-Work) 0.1486
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6222
    Shell Resolution(Low) 5.2592
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1341
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.1711
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2592
    Shell Resolution(Low) 6.5113
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1396
    R-Factor(R-Work) 0.1849
    R-Factor(R-Free) 0.185
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5113
    Shell Resolution(Low) 13.923
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 1343
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.1817
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.468
    f_plane_restr 0.002
    f_chiral_restr 0.036
    f_angle_d 0.598
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2316
    Nucleic Acid Atoms 627
    Heterogen Atoms 33
    Solvent Atoms 234
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO