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X-RAY DIFFRACTION
Materials and Methods page
4GXJ
  •   Crystallization Hide
    Crystallization Experiments
    pH 8
    Temperature 291.0
    Details 50mM Imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.08 α = 90
    b = 77.43 β = 114.45
    c = 55.12 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU SATURN 92
    Details MIRRORS
    Collection Date 2011-07-13
     
    Diffraction Radiation
    Monochromator MIRRORS VARIMAXHF
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength 1.54178
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.2
    Resolution(Low) 50
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.097
    B(Isotropic) From Wilson Plot 36.87
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.28
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.579
    Mean I Over Sigma(Observed) 2.95
    Redundancy 5.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 21.06
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 36585
    Number of Reflections(Observed) 36585
    Number of Reflections(R-Free) 3623
    Percent Reflections(Observed) 86.5
    R-Factor(Observed) 0.237
    R-Work 0.231
    R-Free 0.292
     
    Temperature Factor Modeling
    Isotropic Thermal Model Restrained
    Anisotropic B[1][1] -0.3399
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.9778
    Anisotropic B[2][2] 0.388
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.0481
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1957
    Shell Resolution(Low) 2.2246
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1237
    R-Factor(R-Work) 0.2965
    R-Factor(R-Free) 0.3568
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2246
    Shell Resolution(Low) 2.255
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1233
    R-Factor(R-Work) 0.3004
    R-Factor(R-Free) 0.3865
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.255
    Shell Resolution(Low) 2.2872
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1223
    R-Factor(R-Work) 0.3259
    R-Factor(R-Free) 0.412
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2872
    Shell Resolution(Low) 2.3213
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1223
    R-Factor(R-Work) 0.3122
    R-Factor(R-Free) 0.3884
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3213
    Shell Resolution(Low) 2.3575
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1158
    R-Factor(R-Work) 0.298
    R-Factor(R-Free) 0.3938
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3575
    Shell Resolution(Low) 2.3961
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1256
    R-Factor(R-Work) 0.3239
    R-Factor(R-Free) 0.356
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3961
    Shell Resolution(Low) 2.4374
    Number of Reflections(R-Free) 95
    Number of Reflections(R-Work) 1173
    R-Factor(R-Work) 0.3053
    R-Factor(R-Free) 0.3987
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4374
    Shell Resolution(Low) 2.4816
    Number of Reflections(R-Free) 107
    Number of Reflections(R-Work) 1120
    R-Factor(R-Work) 0.3347
    R-Factor(R-Free) 0.3557
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4816
    Shell Resolution(Low) 2.5293
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 1146
    R-Factor(R-Work) 0.3149
    R-Factor(R-Free) 0.3964
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5293
    Shell Resolution(Low) 2.5808
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1122
    R-Factor(R-Work) 0.3361
    R-Factor(R-Free) 0.4282
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5808
    Shell Resolution(Low) 2.6368
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 1188
    R-Factor(R-Work) 0.3097
    R-Factor(R-Free) 0.3558
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6368
    Shell Resolution(Low) 2.6981
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 1113
    R-Factor(R-Work) 0.3131
    R-Factor(R-Free) 0.3792
    Percent Reflections(Observed) 76.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6981
    Shell Resolution(Low) 2.7654
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1025
    R-Factor(R-Work) 0.3291
    R-Factor(R-Free) 0.3787
    Percent Reflections(Observed) 71.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7654
    Shell Resolution(Low) 2.84
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 1046
    R-Factor(R-Work) 0.2858
    R-Factor(R-Free) 0.333
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.84
    Shell Resolution(Low) 2.9233
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 1100
    R-Factor(R-Work) 0.2749
    R-Factor(R-Free) 0.3447
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9233
    Shell Resolution(Low) 3.0174
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1171
    R-Factor(R-Work) 0.2573
    R-Factor(R-Free) 0.3732
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0174
    Shell Resolution(Low) 3.1249
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1321
    R-Factor(R-Work) 0.2478
    R-Factor(R-Free) 0.2998
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1249
    Shell Resolution(Low) 3.2496
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1510
    R-Factor(R-Work) 0.2456
    R-Factor(R-Free) 0.2847
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2496
    Shell Resolution(Low) 3.3969
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1441
    R-Factor(R-Work) 0.2521
    R-Factor(R-Free) 0.29
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3969
    Shell Resolution(Low) 3.5752
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1461
    R-Factor(R-Work) 0.2224
    R-Factor(R-Free) 0.3019
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5752
    Shell Resolution(Low) 3.798
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1490
    R-Factor(R-Work) 0.193
    R-Factor(R-Free) 0.2644
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.798
    Shell Resolution(Low) 4.0893
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1463
    R-Factor(R-Work) 0.1615
    R-Factor(R-Free) 0.2369
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0893
    Shell Resolution(Low) 4.4972
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 1428
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.2213
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4972
    Shell Resolution(Low) 5.1397
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1425
    R-Factor(R-Work) 0.1772
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1397
    Shell Resolution(Low) 6.4445
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 1434
    R-Factor(R-Work) 0.2061
    R-Factor(R-Free) 0.2628
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4445
    Shell Resolution(Low) 21.0567
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 1455
    R-Factor(R-Work) 0.2151
    R-Factor(R-Free) 0.245
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.061
    f_dihedral_angle_d 21.716
    f_angle_d 1.153
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2514
    Nucleic Acid Atoms 633
    Heterogen Atoms 39
    Solvent Atoms 102
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution CNS
    Structure Refinement PHENIX (PHENIX.REFINE: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building CNS
    data collection StructureStudio