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X-RAY DIFFRACTION
Materials and Methods page
4IHS
  •   Crystallization Hide
    Crystallization Experiments
    Method MICROBATCH UNDER OIL
    pH 6
    Temperature 288.0
    Details Equal volumes of precipitant, protein solution and DNA. Precipitant: sodium malonate Crystal Screen C4- 2.4 M sodium malonate pH 6.0. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 156.49 α = 90
    b = 156.49 β = 90
    c = 141.52 γ = 90
     
    Space Group
    Space Group Name:    P 42 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2008-07-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 0.99999
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.1
    Resolution(Low) 200
    Number Reflections(Observed) 30569
    Percent Possible(Observed) 92.7
    R Merge I(Observed) 0.114
    B(Isotropic) From Wilson Plot 99.4
    Redundancy 8.2
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.21
    Percent Possible(All) 72.5
    R Merge I(Observed) 0.399
    Redundancy 3.0
    Number Unique Reflections(All) 2350
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.1
    Resolution(Low) 48.95
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 30320
    Number of Reflections(R-Free) 1523
    Percent Reflections(Observed) 91.97
    R-Factor(Observed) 0.1794
    R-Work 0.1782
    R-Free 0.2029
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 108.173
    Anisotropic B[1][1] 0.85
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.85
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.7
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1
    Shell Resolution(Low) 3.165
    Number of Reflections(R-Free) 68
    Number of Reflections(R-Work) 1481
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.294
    Percent Reflections(Observed) 67.406
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.165
    Shell Resolution(Low) 3.252
    Number of Reflections(R-Free) 102
    Number of Reflections(R-Work) 1607
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 78.215
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.252
    Shell Resolution(Low) 3.346
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 1662
    R-Factor(R-Work) 0.229
    R-Factor(R-Free) 0.263
    Percent Reflections(Observed) 84.451
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.346
    Shell Resolution(Low) 3.449
    Number of Reflections(R-Free) 80
    Number of Reflections(R-Work) 1802
    R-Factor(R-Work) 0.228
    R-Factor(R-Free) 0.254
    Percent Reflections(Observed) 91.715
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.449
    Shell Resolution(Low) 3.562
    Number of Reflections(R-Free) 94
    Number of Reflections(R-Work) 1753
    R-Factor(R-Work) 0.206
    R-Factor(R-Free) 0.241
    Percent Reflections(Observed) 94.283
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.562
    Shell Resolution(Low) 3.687
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 1695
    R-Factor(R-Work) 0.196
    R-Factor(R-Free) 0.239
    Percent Reflections(Observed) 94.904
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.687
    Shell Resolution(Low) 3.826
    Number of Reflections(R-Free) 70
    Number of Reflections(R-Work) 1686
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 95.591
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.826
    Shell Resolution(Low) 3.982
    Number of Reflections(R-Free) 85
    Number of Reflections(R-Work) 1620
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 96.765
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.982
    Shell Resolution(Low) 4.159
    Number of Reflections(R-Free) 78
    Number of Reflections(R-Work) 1532
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 96.234
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.159
    Shell Resolution(Low) 4.361
    Number of Reflections(R-Free) 82
    Number of Reflections(R-Work) 1465
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 97.418
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.361
    Shell Resolution(Low) 4.597
    Number of Reflections(R-Free) 75
    Number of Reflections(R-Work) 1401
    R-Factor(R-Work) 0.132
    R-Factor(R-Free) 0.143
    Percent Reflections(Observed) 96.534
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.597
    Shell Resolution(Low) 4.875
    Number of Reflections(R-Free) 77
    Number of Reflections(R-Work) 1290
    R-Factor(R-Work) 0.149
    R-Factor(R-Free) 0.161
    Percent Reflections(Observed) 96.471
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.875
    Shell Resolution(Low) 5.211
    Number of Reflections(R-Free) 64
    Number of Reflections(R-Work) 1236
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.177
    Percent Reflections(Observed) 96.654
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.211
    Shell Resolution(Low) 5.628
    Number of Reflections(R-Free) 57
    Number of Reflections(R-Work) 1139
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 96.374
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.628
    Shell Resolution(Low) 6.163
    Number of Reflections(R-Free) 49
    Number of Reflections(R-Work) 1045
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 95.713
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.163
    Shell Resolution(Low) 6.888
    Number of Reflections(R-Free) 50
    Number of Reflections(R-Work) 929
    R-Factor(R-Work) 0.182
    R-Factor(R-Free) 0.206
    Percent Reflections(Observed) 96.169
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.888
    Shell Resolution(Low) 7.949
    Number of Reflections(R-Free) 38
    Number of Reflections(R-Work) 816
    R-Factor(R-Work) 0.135
    R-Factor(R-Free) 0.175
    Percent Reflections(Observed) 94.784
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.949
    Shell Resolution(Low) 9.722
    Number of Reflections(R-Free) 47
    Number of Reflections(R-Work) 658
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.149
    Percent Reflections(Observed) 94.504
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.722
    Shell Resolution(Low) 13.697
    Number of Reflections(R-Free) 16
    Number of Reflections(R-Work) 503
    R-Factor(R-Work) 0.162
    R-Factor(R-Free) 0.155
    Percent Reflections(Observed) 92.844
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 13.697
    Shell Resolution(Low) 110.657
    Number of Reflections(R-Free) 6
    Number of Reflections(R-Work) 244
    R-Factor(R-Work) 0.276
    R-Factor(R-Free) 0.291
    Percent Reflections(Observed) 82.508
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.005
    r_chiral_restr 0.062
    r_dihedral_angle_4_deg 14.37
    r_dihedral_angle_3_deg 17.221
    r_dihedral_angle_2_deg 35.28
    r_dihedral_angle_1_deg 5.336
    r_angle_other_deg 0.843
    r_angle_refined_deg 0.994
    r_bond_other_d 0.001
    r_bond_refined_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2922
    Nucleic Acid Atoms 2038
    Heterogen Atoms 15
    Solvent Atoms 20
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molecular Replacement
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: refmac_5.6.0117
    data reduction SCALEPACK
    data collection DENZO