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X-RAY DIFFRACTION
Materials and Methods page
4F5N
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 291.0
    Details 50mM Imidazole, 350mM Sodium Acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.32 α = 90
    b = 79.18 β = 105.53
    c = 54.86 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 2011-09-26
     
    Diffraction Radiation
    Monochromator mirrors VarimaxHF
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.54178
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.8
    Resolution(Low) 28
    Number Reflections(All) 209537
    Number Reflections(Observed) 209537
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.047
    B(Isotropic) From Wilson Plot 28.5
    Redundancy 5.2
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.86
    Percent Possible(All) 90.8
    R Merge I(Observed) 0.229
    Mean I Over Sigma(Observed) 3.0
    Redundancy 1.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 22.098
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 39766
    Number of Reflections(Observed) 39766
    Number of Reflections(R-Free) 4016
    Percent Reflections(Observed) 95.47
    R-Factor(All) 0.202
    R-Factor(Observed) 0.1903
    R-Work 0.1871
    R-Free 0.2196
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Restrained
    Mean Isotropic B Value 28.0
    Anisotropic B[1][1] 2.641
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 2.2336
    Anisotropic B[2][2] 0.738
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.379
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7981
    Shell Resolution(Low) 1.8193
    Number of Reflections(R-Free) 107
    Number of Reflections(R-Work) 974
    R-Factor(R-Work) 0.2572
    R-Factor(R-Free) 0.3263
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8193
    Shell Resolution(Low) 1.8415
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 1028
    R-Factor(R-Work) 0.2454
    R-Factor(R-Free) 0.3267
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8415
    Shell Resolution(Low) 1.8648
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 1067
    R-Factor(R-Work) 0.2323
    R-Factor(R-Free) 0.295
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8648
    Shell Resolution(Low) 1.8893
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1154
    R-Factor(R-Work) 0.2277
    R-Factor(R-Free) 0.289
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8893
    Shell Resolution(Low) 1.9152
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 1115
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.2178
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9152
    Shell Resolution(Low) 1.9425
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1212
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.293
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9425
    Shell Resolution(Low) 1.9715
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1185
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9715
    Shell Resolution(Low) 2.0023
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1238
    R-Factor(R-Work) 0.2007
    R-Factor(R-Free) 0.2779
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0023
    Shell Resolution(Low) 2.0351
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1232
    R-Factor(R-Work) 0.1935
    R-Factor(R-Free) 0.2374
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0351
    Shell Resolution(Low) 2.0701
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1266
    R-Factor(R-Work) 0.1923
    R-Factor(R-Free) 0.2494
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0701
    Shell Resolution(Low) 2.1078
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1256
    R-Factor(R-Work) 0.195
    R-Factor(R-Free) 0.2339
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1078
    Shell Resolution(Low) 2.1483
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1254
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.2783
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1483
    Shell Resolution(Low) 2.1921
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1282
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.2553
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1921
    Shell Resolution(Low) 2.2397
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1259
    R-Factor(R-Work) 0.1957
    R-Factor(R-Free) 0.2524
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2397
    Shell Resolution(Low) 2.2917
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1267
    R-Factor(R-Work) 0.1906
    R-Factor(R-Free) 0.2361
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2917
    Shell Resolution(Low) 2.349
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1261
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2369
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.349
    Shell Resolution(Low) 2.4124
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1266
    R-Factor(R-Work) 0.1998
    R-Factor(R-Free) 0.2348
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4124
    Shell Resolution(Low) 2.4833
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 1289
    R-Factor(R-Work) 0.2006
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4833
    Shell Resolution(Low) 2.5634
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1252
    R-Factor(R-Work) 0.209
    R-Factor(R-Free) 0.2479
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5634
    Shell Resolution(Low) 2.6548
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1269
    R-Factor(R-Work) 0.2016
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6548
    Shell Resolution(Low) 2.7609
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1262
    R-Factor(R-Work) 0.2005
    R-Factor(R-Free) 0.2493
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7609
    Shell Resolution(Low) 2.8863
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1277
    R-Factor(R-Work) 0.1915
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8863
    Shell Resolution(Low) 3.0381
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 1265
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.2248
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0381
    Shell Resolution(Low) 3.228
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 1272
    R-Factor(R-Work) 0.1917
    R-Factor(R-Free) 0.2194
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.228
    Shell Resolution(Low) 3.4763
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1303
    R-Factor(R-Work) 0.1746
    R-Factor(R-Free) 0.1825
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4763
    Shell Resolution(Low) 3.8245
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1305
    R-Factor(R-Work) 0.1659
    R-Factor(R-Free) 0.1871
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8245
    Shell Resolution(Low) 4.3742
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1302
    R-Factor(R-Work) 0.152
    R-Factor(R-Free) 0.1774
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3742
    Shell Resolution(Low) 5.497
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1300
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.1676
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.497
    Shell Resolution(Low) 22.1
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1338
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.057
    f_dihedral_angle_d 19.131
    f_angle_d 1.027
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2577
    Nucleic Acid Atoms 632
    Heterogen Atoms 33
    Solvent Atoms 563
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    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