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X-RAY DIFFRACTION
Materials and Methods page
3V8D
  •   Crystallization Hide
    Crystallization Experiments
    pH 5.6
    Temperature 291.0
    Details 30% PEG-400, 0.2M lithium sulfate, 0.1M trisodium citrate, pH 5.6, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.62 α = 66.33
    b = 74.22 β = 75.53
    c = 87.93 γ = 69.62
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2011-09-22
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.97625
    Site CLSI
    Beamline 08ID-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.9
    Resolution(Low) 50
    Number Reflections(Observed) 92430
    Percent Possible(Observed) 97.6
    R Merge I(Observed) 0.074
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 96.4
    R Merge I(Observed) 0.848
    Redundancy 3.7
    Number Unique Reflections(All) 9089
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 50.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 92179
    Number of Reflections(R-Free) 2066
    Percent Reflections(Observed) 97.601
    R-Factor(Observed) 0.186
    R-Work 0.1852
    R-Free 0.225
    R-Free Selection Details THIN SHELLS (SFTOOLS)
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.151
    Anisotropic B[1][1] -0.613
    Anisotropic B[1][2] -0.549
    Anisotropic B[1][3] -0.243
    Anisotropic B[2][2] 0.26
    Anisotropic B[2][3] 0.72
    Anisotropic B[3][3] 0.279
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.949
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 6751
    R-Factor(R-Work) 0.287
    Percent Reflections(Observed) 96.264
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.949
    Shell Resolution(Low) 2.003
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 6555
    R-Factor(R-Work) 0.267
    Percent Reflections(Observed) 96.624
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.003
    Shell Resolution(Low) 2.061
    Number of Reflections(R-Free) 400
    Number of Reflections(R-Work) 6036
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.272
    Percent Reflections(Observed) 96.782
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.061
    Shell Resolution(Low) 2.124
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 6199
    R-Factor(R-Work) 0.233
    Percent Reflections(Observed) 96.92
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.124
    Shell Resolution(Low) 2.193
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 6014
    R-Factor(R-Work) 0.215
    Percent Reflections(Observed) 96.906
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.193
    Shell Resolution(Low) 2.27
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 5446
    R-Factor(R-Work) 0.208
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 97.109
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.27
    Shell Resolution(Low) 2.356
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 5679
    R-Factor(R-Work) 0.197
    Percent Reflections(Observed) 97.293
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.356
    Shell Resolution(Low) 2.452
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 5173
    R-Factor(R-Work) 0.2
    R-Factor(R-Free) 0.241
    Percent Reflections(Observed) 97.658
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.452
    Shell Resolution(Low) 2.56
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 5260
    R-Factor(R-Work) 0.199
    Percent Reflections(Observed) 97.715
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.56
    Shell Resolution(Low) 2.685
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4759
    R-Factor(R-Work) 0.194
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 98.083
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.685
    Shell Resolution(Low) 2.83
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4785
    R-Factor(R-Work) 0.193
    Percent Reflections(Observed) 98.154
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.83
    Shell Resolution(Low) 3.001
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 4296
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 98.34
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.001
    Shell Resolution(Low) 3.207
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4283
    R-Factor(R-Work) 0.185
    Percent Reflections(Observed) 98.392
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.207
    Shell Resolution(Low) 3.463
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 3841
    R-Factor(R-Work) 0.17
    R-Factor(R-Free) 0.216
    Percent Reflections(Observed) 98.544
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.463
    Shell Resolution(Low) 3.792
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3489
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 98.457
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.792
    Shell Resolution(Low) 4.236
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 3319
    R-Factor(R-Work) 0.144
    Percent Reflections(Observed) 98.487
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.236
    Shell Resolution(Low) 4.886
    Number of Reflections(R-Free) 85
    Number of Reflections(R-Work) 2840
    R-Factor(R-Work) 0.139
    R-Factor(R-Free) 0.182
    Percent Reflections(Observed) 98.651
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.886
    Shell Resolution(Low) 5.97
    Number of Reflections(R-Free) 76
    Number of Reflections(R-Work) 2411
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.192
    Percent Reflections(Observed) 99.4
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.97
    Shell Resolution(Low) 8.383
    Number of Reflections(R-Free) 77
    Number of Reflections(R-Work) 1862
    R-Factor(R-Work) 0.194
    R-Factor(R-Free) 0.199
    Percent Reflections(Observed) 99.538
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.383
    Shell Resolution(Low) 50.0
    Number of Reflections(R-Free) 14
    Number of Reflections(R-Work) 1068
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 98.723
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.002
    r_gen_planes_refined 0.004
    r_chiral_restr 0.061
    r_dihedral_angle_4_deg 15.459
    r_dihedral_angle_3_deg 11.886
    r_dihedral_angle_2_deg 34.518
    r_dihedral_angle_1_deg 5.408
    r_angle_other_deg 0.808
    r_angle_refined_deg 1.407
    r_bond_other_d 0.003
    r_bond_refined_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7479
    Nucleic Acid Atoms 0
    Heterogen Atoms 188
    Solvent Atoms 354
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution phaser
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.6.0117
    molecular replacement Phaser
    data reduction HKL