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X-RAY DIFFRACTION
Materials and Methods page
4KLF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 8
    Temperature 291.0
    Details 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 50.75 α = 90
    b = 79.96 β = 107.52
    c = 55.32 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 2012-08-09
     
    Diffraction Radiation
    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) 1.85
    Resolution(Low) 50
    Number Reflections(All) 36019
    Number Reflections(Observed) 35045
    Percent Possible(Observed) 97.3
    R Merge I(Observed) 0.053
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.85
    Resolution(Low) 1.92
    Percent Possible(All) 87.9
    R Merge I(Observed) 0.318
    Mean I Over Sigma(Observed) 2.778
    R-Sym I(Observed) 0.318
    Redundancy 1.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.85
    Resolution(Low) 24.198
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 33042
    Number of Reflections(R-Free) 3285
    Percent Reflections(Observed) 91.78
    R-Factor(Observed) 0.1842
    R-Work 0.179
    R-Free 0.2312
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.1664
    Anisotropic B[1][1] 1.1109
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.5379
    Anisotropic B[2][2] 0.3114
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.4223
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.85
    Shell Resolution(Low) 1.8774
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 960
    R-Factor(R-Work) 0.2601
    R-Factor(R-Free) 0.3389
    Percent Reflections(Observed) 69.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8774
    Shell Resolution(Low) 1.9067
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 1086
    R-Factor(R-Work) 0.2353
    R-Factor(R-Free) 0.3387
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9067
    Shell Resolution(Low) 1.938
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 1074
    R-Factor(R-Work) 0.2173
    R-Factor(R-Free) 0.2939
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.938
    Shell Resolution(Low) 1.9714
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1171
    R-Factor(R-Work) 0.2133
    R-Factor(R-Free) 0.303
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9714
    Shell Resolution(Low) 2.0072
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1224
    R-Factor(R-Work) 0.1883
    R-Factor(R-Free) 0.2829
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0072
    Shell Resolution(Low) 2.0458
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1287
    R-Factor(R-Work) 0.2019
    R-Factor(R-Free) 0.2855
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0458
    Shell Resolution(Low) 2.0875
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1263
    R-Factor(R-Work) 0.1899
    R-Factor(R-Free) 0.2553
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0875
    Shell Resolution(Low) 2.1329
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 1321
    R-Factor(R-Work) 0.1837
    R-Factor(R-Free) 0.2456
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1329
    Shell Resolution(Low) 2.1825
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1305
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2428
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1825
    Shell Resolution(Low) 2.237
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 1355
    R-Factor(R-Work) 0.1894
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.237
    Shell Resolution(Low) 2.2974
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1335
    R-Factor(R-Work) 0.1821
    R-Factor(R-Free) 0.2472
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2974
    Shell Resolution(Low) 2.365
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1312
    R-Factor(R-Work) 0.184
    R-Factor(R-Free) 0.2275
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.365
    Shell Resolution(Low) 2.4413
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 1330
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2628
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4413
    Shell Resolution(Low) 2.5284
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1338
    R-Factor(R-Work) 0.1955
    R-Factor(R-Free) 0.2298
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5284
    Shell Resolution(Low) 2.6295
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1355
    R-Factor(R-Work) 0.2061
    R-Factor(R-Free) 0.2698
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6295
    Shell Resolution(Low) 2.7491
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1358
    R-Factor(R-Work) 0.1993
    R-Factor(R-Free) 0.2595
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7491
    Shell Resolution(Low) 2.8938
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 1335
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8938
    Shell Resolution(Low) 3.0747
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1390
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2571
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0747
    Shell Resolution(Low) 3.3116
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1373
    R-Factor(R-Work) 0.1876
    R-Factor(R-Free) 0.2132
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3116
    Shell Resolution(Low) 3.6438
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1416
    R-Factor(R-Work) 0.1793
    R-Factor(R-Free) 0.2357
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6438
    Shell Resolution(Low) 4.1688
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1368
    R-Factor(R-Work) 0.1417
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1688
    Shell Resolution(Low) 5.2434
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1358
    R-Factor(R-Work) 0.1374
    R-Factor(R-Free) 0.1698
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2434
    Shell Resolution(Low) 24.2
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1443
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2006
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.907
    f_plane_restr 0.005
    f_chiral_restr 0.062
    f_angle_d 1.124
    f_bond_d 0.017
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2612
    Nucleic Acid Atoms 651
    Heterogen Atoms 43
    Solvent Atoms 407
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL