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X-RAY DIFFRACTION
Materials and Methods page
4DPG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.7
    Temperature 291.0
    Details 22% PEG10000, 0.1 M MES pH 6.7, 0.1 M magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 79.2 α = 89.16
    b = 122.01 β = 85.58
    c = 149.2 γ = 89.71
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2011-07-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.9786
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.84
    Resolution(Low) 50
    Number Reflections(Observed) 128809
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.102
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.844
    Resolution(Low) 2.96
    Percent Possible(All) 98.6
    R Merge I(Observed) 0.487
    Redundancy 4.0
    Number Unique Reflections(All) 12750
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.844
    Resolution(Low) 46.836
    Cut-off Sigma(F) 1.98
    Number of Reflections(Observed) 128750
    Number of Reflections(R-Free) 6481
    Percent Reflections(Observed) 98.47
    R-Factor(Observed) 0.1866
    R-Work 0.1847
    R-Free 0.2229
     
    Temperature Factor Modeling
    Mean Isotropic B Value 42.3954
    Anisotropic B[1][1] -1.6703
    Anisotropic B[1][2] 0.023
    Anisotropic B[1][3] 0.129
    Anisotropic B[2][2] -0.0959
    Anisotropic B[2][3] 0.3519
    Anisotropic B[3][3] 1.7662
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.844
    Shell Resolution(Low) 2.8768
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3307
    R-Factor(R-Work) 0.2942
    R-Factor(R-Free) 0.3413
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8768
    Shell Resolution(Low) 2.9106
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4120
    R-Factor(R-Work) 0.2745
    R-Factor(R-Free) 0.3448
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9106
    Shell Resolution(Low) 2.9461
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 4115
    R-Factor(R-Work) 0.2587
    R-Factor(R-Free) 0.3212
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9461
    Shell Resolution(Low) 2.9834
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 4069
    R-Factor(R-Work) 0.2467
    R-Factor(R-Free) 0.3217
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9834
    Shell Resolution(Low) 3.0226
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4110
    R-Factor(R-Work) 0.2489
    R-Factor(R-Free) 0.2814
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0226
    Shell Resolution(Low) 3.064
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 4068
    R-Factor(R-Work) 0.2355
    R-Factor(R-Free) 0.2927
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.064
    Shell Resolution(Low) 3.1078
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 4106
    R-Factor(R-Work) 0.2258
    R-Factor(R-Free) 0.295
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1078
    Shell Resolution(Low) 3.1542
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 4124
    R-Factor(R-Work) 0.2145
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1542
    Shell Resolution(Low) 3.2034
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 4086
    R-Factor(R-Work) 0.2204
    R-Factor(R-Free) 0.2688
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2034
    Shell Resolution(Low) 3.2559
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4071
    R-Factor(R-Work) 0.2161
    R-Factor(R-Free) 0.2452
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2559
    Shell Resolution(Low) 3.3121
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4146
    R-Factor(R-Work) 0.2051
    R-Factor(R-Free) 0.2596
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3121
    Shell Resolution(Low) 3.3723
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4014
    R-Factor(R-Work) 0.2093
    R-Factor(R-Free) 0.2333
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3723
    Shell Resolution(Low) 3.4371
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 4124
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.3053
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4371
    Shell Resolution(Low) 3.5073
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 4047
    R-Factor(R-Work) 0.1981
    R-Factor(R-Free) 0.237
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5073
    Shell Resolution(Low) 3.5835
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 4134
    R-Factor(R-Work) 0.1943
    R-Factor(R-Free) 0.2275
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5835
    Shell Resolution(Low) 3.6668
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4079
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2245
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6668
    Shell Resolution(Low) 3.7585
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4124
    R-Factor(R-Work) 0.1798
    R-Factor(R-Free) 0.2257
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7585
    Shell Resolution(Low) 3.8601
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 4077
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.2081
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8601
    Shell Resolution(Low) 3.9736
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4142
    R-Factor(R-Work) 0.1616
    R-Factor(R-Free) 0.2121
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9736
    Shell Resolution(Low) 4.1018
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4072
    R-Factor(R-Work) 0.1637
    R-Factor(R-Free) 0.2086
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1018
    Shell Resolution(Low) 4.2483
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 4146
    R-Factor(R-Work) 0.1508
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2483
    Shell Resolution(Low) 4.4183
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4125
    R-Factor(R-Work) 0.1406
    R-Factor(R-Free) 0.1887
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4183
    Shell Resolution(Low) 4.6192
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.1375
    R-Factor(R-Free) 0.1756
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6192
    Shell Resolution(Low) 4.8625
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4112
    R-Factor(R-Work) 0.1385
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8625
    Shell Resolution(Low) 5.1668
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4068
    R-Factor(R-Work) 0.1527
    R-Factor(R-Free) 0.1826
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1668
    Shell Resolution(Low) 5.5651
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.1804
    R-Factor(R-Free) 0.2286
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5651
    Shell Resolution(Low) 6.124
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4115
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.2443
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.124
    Shell Resolution(Low) 7.0077
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 4113
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.1953
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0077
    Shell Resolution(Low) 8.8193
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4152
    R-Factor(R-Work) 0.1575
    R-Factor(R-Free) 0.1784
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.8193
    Shell Resolution(Low) 46.8421
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4063
    R-Factor(R-Work) 0.1685
    R-Factor(R-Free) 0.1682
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.893
    f_plane_restr 0.006
    f_chiral_restr 0.079
    f_angle_d 1.194
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 32869
    Nucleic Acid Atoms 0
    Heterogen Atoms 329
    Solvent Atoms 542
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution molrep
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction HKL