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X-RAY DIFFRACTION
Materials and Methods page
4M9H
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7.5
    Temperature 291.0
    Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.61 α = 90
    b = 79.46 β = 105.63
    c = 54.96 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 104
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details mirrors
    Collection Date 2012-09-27
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.39
    Resolution(Low) 14
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.062
    B(Isotropic) From Wilson Plot 30.47
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.49
    Percent Possible(All) 95.3
    R Merge I(Observed) 0.26
    Number Unique Reflections(All) 1695
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method Isomorphous replacement
    reflnsShellList 2.394
    Resolution(Low) 13.737
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 33785
    Number of Reflections(R-Free) 3358
    Percent Reflections(Observed) 96.85
    R-Factor(Observed) 0.1822
    R-Work 0.1771
    R-Free 0.2276
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.3873
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3944
    Shell Resolution(Low) 2.4285
    Number of Reflections(R-Free) 90
    Number of Reflections(R-Work) 959
    R-Factor(R-Work) 0.2309
    R-Factor(R-Free) 0.2718
    Percent Reflections(Observed) 72.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4285
    Shell Resolution(Low) 2.4645
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 1132
    R-Factor(R-Work) 0.2323
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4645
    Shell Resolution(Low) 2.5028
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1187
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.3073
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5028
    Shell Resolution(Low) 2.5436
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1239
    R-Factor(R-Work) 0.23
    R-Factor(R-Free) 0.3011
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5436
    Shell Resolution(Low) 2.5871
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1240
    R-Factor(R-Work) 0.2377
    R-Factor(R-Free) 0.2792
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5871
    Shell Resolution(Low) 2.6339
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1285
    R-Factor(R-Work) 0.2153
    R-Factor(R-Free) 0.3321
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6339
    Shell Resolution(Low) 2.6842
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1289
    R-Factor(R-Work) 0.2072
    R-Factor(R-Free) 0.2443
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6842
    Shell Resolution(Low) 2.7385
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 1304
    R-Factor(R-Work) 0.2114
    R-Factor(R-Free) 0.2904
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7385
    Shell Resolution(Low) 2.7976
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 1222
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.3134
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7976
    Shell Resolution(Low) 2.8621
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 1368
    R-Factor(R-Work) 0.2083
    R-Factor(R-Free) 0.293
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8621
    Shell Resolution(Low) 2.933
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 1294
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2621
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.933
    Shell Resolution(Low) 3.0115
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1347
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.2981
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0115
    Shell Resolution(Low) 3.0991
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.2126
    R-Factor(R-Free) 0.2269
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0991
    Shell Resolution(Low) 3.1979
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1314
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2867
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1979
    Shell Resolution(Low) 3.3107
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1282
    R-Factor(R-Work) 0.1838
    R-Factor(R-Free) 0.2651
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3107
    Shell Resolution(Low) 3.4413
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 1346
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4413
    Shell Resolution(Low) 3.5952
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 1269
    R-Factor(R-Work) 0.1649
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5952
    Shell Resolution(Low) 3.781
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1295
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.2057
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.781
    Shell Resolution(Low) 4.0124
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1307
    R-Factor(R-Work) 0.1498
    R-Factor(R-Free) 0.1967
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0124
    Shell Resolution(Low) 4.3132
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1273
    R-Factor(R-Work) 0.1357
    R-Factor(R-Free) 0.1735
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3132
    Shell Resolution(Low) 4.7311
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 1311
    R-Factor(R-Work) 0.1361
    R-Factor(R-Free) 0.1575
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7311
    Shell Resolution(Low) 5.3794
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1344
    R-Factor(R-Work) 0.1462
    R-Factor(R-Free) 0.2001
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3794
    Shell Resolution(Low) 6.6471
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1282
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1805
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6471
    Shell Resolution(Low) 13.7369
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 1281
    R-Factor(R-Work) 0.1632
    R-Factor(R-Free) 0.1648
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.793
    f_plane_restr 0.002
    f_chiral_restr 0.04
    f_angle_d 0.632
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2429
    Nucleic Acid Atoms 627
    Heterogen Atoms 16
    Solvent Atoms 223
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Mar
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution isomorphous replacement
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO