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X-RAY DIFFRACTION
Materials and Methods page
4K4Z
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 289.0
    Details sitting drop, temperature 289K, VAPOR DIFFUSION, SITTING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.64 α = 89.98
    b = 60.63 β = 89.92
    c = 194.68 γ = 78.68
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type NOIR-1
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength 1.00
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.17
    Resolution(Low) 45.6
    Number Reflections(Observed) 140661
    Percent Possible(Observed) 97.8
    R Merge I(Observed) 0.055
    Redundancy 1.95
     
    High Resolution Shell Details
    Resolution(High) 2.17
    Resolution(Low) 2.25
    Percent Possible(All) 97.1
    R Merge I(Observed) 0.474
    Mean I Over Sigma(Observed) 1.5
    Redundancy 1.94
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.17
    Resolution(Low) 45.58
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 140232
    Number of Reflections(R-Free) 7082
    Percent Reflections(Observed) 97.5
    R-Factor(Observed) 0.206
    R-Work 0.204
    R-Free 0.244
     
    Temperature Factor Modeling
    Mean Isotropic B Value 40.96
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.17
    Shell Resolution(Low) 2.1947
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4341
    R-Factor(R-Work) 0.3206
    R-Factor(R-Free) 0.3866
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1947
    Shell Resolution(Low) 2.2205
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4433
    R-Factor(R-Work) 0.3184
    R-Factor(R-Free) 0.3987
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2205
    Shell Resolution(Low) 2.2476
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4515
    R-Factor(R-Work) 0.309
    R-Factor(R-Free) 0.3858
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2476
    Shell Resolution(Low) 2.276
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4289
    R-Factor(R-Work) 0.3081
    R-Factor(R-Free) 0.3659
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.276
    Shell Resolution(Low) 2.306
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4398
    R-Factor(R-Work) 0.2867
    R-Factor(R-Free) 0.3128
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.306
    Shell Resolution(Low) 2.3376
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4520
    R-Factor(R-Work) 0.27
    R-Factor(R-Free) 0.307
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3376
    Shell Resolution(Low) 2.371
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4234
    R-Factor(R-Work) 0.2703
    R-Factor(R-Free) 0.3158
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.371
    Shell Resolution(Low) 2.4063
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 4536
    R-Factor(R-Work) 0.2553
    R-Factor(R-Free) 0.3291
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4063
    Shell Resolution(Low) 2.4439
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 4354
    R-Factor(R-Work) 0.2697
    R-Factor(R-Free) 0.3282
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4439
    Shell Resolution(Low) 2.484
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4451
    R-Factor(R-Work) 0.2731
    R-Factor(R-Free) 0.3617
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.484
    Shell Resolution(Low) 2.5268
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4507
    R-Factor(R-Work) 0.2553
    R-Factor(R-Free) 0.3089
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5268
    Shell Resolution(Low) 2.5728
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 4396
    R-Factor(R-Work) 0.2471
    R-Factor(R-Free) 0.2895
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5728
    Shell Resolution(Low) 2.6223
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 4427
    R-Factor(R-Work) 0.2576
    R-Factor(R-Free) 0.3017
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6223
    Shell Resolution(Low) 2.6758
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4432
    R-Factor(R-Work) 0.2467
    R-Factor(R-Free) 0.301
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6758
    Shell Resolution(Low) 2.7339
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4502
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.2992
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7339
    Shell Resolution(Low) 2.7975
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4409
    R-Factor(R-Work) 0.2286
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7975
    Shell Resolution(Low) 2.8675
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4522
    R-Factor(R-Work) 0.2268
    R-Factor(R-Free) 0.3145
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8675
    Shell Resolution(Low) 2.945
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4378
    R-Factor(R-Work) 0.2383
    R-Factor(R-Free) 0.2837
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.945
    Shell Resolution(Low) 3.0316
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 4566
    R-Factor(R-Work) 0.2297
    R-Factor(R-Free) 0.2738
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0316
    Shell Resolution(Low) 3.1295
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4352
    R-Factor(R-Work) 0.2227
    R-Factor(R-Free) 0.2958
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1295
    Shell Resolution(Low) 3.2413
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4469
    R-Factor(R-Work) 0.2153
    R-Factor(R-Free) 0.2279
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2413
    Shell Resolution(Low) 3.371
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4526
    R-Factor(R-Work) 0.2008
    R-Factor(R-Free) 0.2525
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.371
    Shell Resolution(Low) 3.5244
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4385
    R-Factor(R-Work) 0.1838
    R-Factor(R-Free) 0.2229
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5244
    Shell Resolution(Low) 3.7101
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4428
    R-Factor(R-Work) 0.1734
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7101
    Shell Resolution(Low) 3.9425
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4475
    R-Factor(R-Work) 0.1639
    R-Factor(R-Free) 0.2233
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9425
    Shell Resolution(Low) 4.2467
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4502
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.1877
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2467
    Shell Resolution(Low) 4.6736
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4519
    R-Factor(R-Work) 0.1451
    R-Factor(R-Free) 0.157
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6736
    Shell Resolution(Low) 5.349
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4451
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.2013
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.349
    Shell Resolution(Low) 6.7357
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 4496
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2097
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7357
    Shell Resolution(Low) 45.592
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4337
    R-Factor(R-Work) 0.1784
    R-Factor(R-Free) 0.2042
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.048
    f_dihedral_angle_d 13.559
    f_angle_d 1.102
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14756
    Nucleic Acid Atoms 2877
    Heterogen Atoms 4
    Solvent Atoms 1266
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DTREK
    Data Reduction (data scaling) DTREK
    Structure Solution PHENIX
    Structure Refinement PHENIX (PHENIX.REFINE: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction D*trek version: 9.9.9.4D
    data collection D*trek