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X-RAY DIFFRACTION
Materials and Methods page
2ONB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 290.0
    Details 30 mM ammonium sulfate, 30 mM 40% PEG 4K, 0.1 M Tris pH 8.5, 20 mM 2-ME, VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 95.69 α = 90
    b = 95.69 β = 90
    c = 82.5 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2004-03-20
     
    Diffraction Radiation
    Monochromator two passes, half degree
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength 0.97251
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.7
    Resolution(Low) 50
    Number Reflections(Observed) 12337
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.109
    Redundancy 18.2
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.8
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.334
    Redundancy 17.3
    Number Unique Reflections(All) 1226
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 41.44
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 12144
    Number of Reflections(R-Free) 1253
    Percent Reflections(Observed) 98.4
    R-Work 0.216
    R-Free 0.259
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 52.5
    Anisotropic B[1][1] -5.74
    Anisotropic B[1][2] 0.76
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -5.74
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 11.49
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7
    Shell Resolution(Low) 2.74
    Number of Reflections(Observed) 443
    Number of Reflections(R-Free) 35
    Number of Reflections(R-Work) 408
    R-Factor(R-Work) 0.282
    R-Factor(R-Free) 0.373
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.74
    Shell Resolution(Low) 2.78
    Number of Reflections(Observed) 464
    Number of Reflections(R-Free) 45
    Number of Reflections(R-Work) 419
    R-Factor(R-Work) 0.301
    R-Factor(R-Free) 0.388
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.78
    Shell Resolution(Low) 2.82
    Number of Reflections(Observed) 474
    Number of Reflections(R-Free) 43
    Number of Reflections(R-Work) 431
    R-Factor(R-Work) 0.267
    R-Factor(R-Free) 0.392
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.82
    Shell Resolution(Low) 2.86
    Number of Reflections(Observed) 461
    Number of Reflections(R-Free) 49
    Number of Reflections(R-Work) 412
    R-Factor(R-Work) 0.288
    R-Factor(R-Free) 0.336
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.86
    Shell Resolution(Low) 2.91
    Number of Reflections(Observed) 468
    Number of Reflections(R-Free) 47
    Number of Reflections(R-Work) 421
    R-Factor(R-Work) 0.278
    R-Factor(R-Free) 0.358
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.91
    Shell Resolution(Low) 2.96
    Number of Reflections(Observed) 471
    Number of Reflections(R-Free) 50
    Number of Reflections(R-Work) 421
    R-Factor(R-Work) 0.245
    R-Factor(R-Free) 0.265
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.96
    Shell Resolution(Low) 3.01
    Number of Reflections(Observed) 482
    Number of Reflections(R-Free) 44
    Number of Reflections(R-Work) 438
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.38
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.01
    Shell Resolution(Low) 3.07
    Number of Reflections(Observed) 474
    Number of Reflections(R-Free) 48
    Number of Reflections(R-Work) 426
    R-Factor(R-Work) 0.269
    R-Factor(R-Free) 0.315
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.07
    Shell Resolution(Low) 3.13
    Number of Reflections(Observed) 478
    Number of Reflections(R-Free) 50
    Number of Reflections(R-Work) 428
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.295
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.13
    Shell Resolution(Low) 3.2
    Number of Reflections(Observed) 477
    Number of Reflections(R-Free) 47
    Number of Reflections(R-Work) 430
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.283
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2
    Shell Resolution(Low) 3.28
    Number of Reflections(Observed) 480
    Number of Reflections(R-Free) 40
    Number of Reflections(R-Work) 440
    R-Factor(R-Work) 0.24
    R-Factor(R-Free) 0.34
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.28
    Shell Resolution(Low) 3.36
    Number of Reflections(Observed) 476
    Number of Reflections(R-Free) 52
    Number of Reflections(R-Work) 424
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.249
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.36
    Shell Resolution(Low) 3.45
    Number of Reflections(Observed) 499
    Number of Reflections(R-Free) 54
    Number of Reflections(R-Work) 445
    R-Factor(R-Work) 0.227
    R-Factor(R-Free) 0.292
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.45
    Shell Resolution(Low) 3.55
    Number of Reflections(Observed) 484
    Number of Reflections(R-Free) 38
    Number of Reflections(R-Work) 446
    R-Factor(R-Work) 0.225
    R-Factor(R-Free) 0.219
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.55
    Shell Resolution(Low) 3.66
    Number of Reflections(Observed) 481
    Number of Reflections(R-Free) 45
    Number of Reflections(R-Work) 436
    R-Factor(R-Work) 0.217
    R-Factor(R-Free) 0.275
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.66
    Shell Resolution(Low) 3.8
    Number of Reflections(Observed) 489
    Number of Reflections(R-Free) 55
    Number of Reflections(R-Work) 434
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.284
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8
    Shell Resolution(Low) 3.95
    Number of Reflections(Observed) 499
    Number of Reflections(R-Free) 56
    Number of Reflections(R-Work) 443
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.255
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.95
    Shell Resolution(Low) 4.13
    Number of Reflections(Observed) 485
    Number of Reflections(R-Free) 60
    Number of Reflections(R-Work) 425
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.218
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.13
    Shell Resolution(Low) 4.34
    Number of Reflections(Observed) 510
    Number of Reflections(R-Free) 56
    Number of Reflections(R-Work) 454
    R-Factor(R-Work) 0.155
    R-Factor(R-Free) 0.217
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.34
    Shell Resolution(Low) 4.62
    Number of Reflections(Observed) 485
    Number of Reflections(R-Free) 50
    Number of Reflections(R-Work) 435
    R-Factor(R-Work) 0.169
    R-Factor(R-Free) 0.195
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.62
    Shell Resolution(Low) 4.97
    Number of Reflections(Observed) 493
    Number of Reflections(R-Free) 53
    Number of Reflections(R-Work) 440
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.239
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.97
    Shell Resolution(Low) 5.47
    Number of Reflections(Observed) 504
    Number of Reflections(R-Free) 56
    Number of Reflections(R-Work) 448
    R-Factor(R-Work) 0.229
    R-Factor(R-Free) 0.307
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.47
    Shell Resolution(Low) 6.27
    Number of Reflections(Observed) 504
    Number of Reflections(R-Free) 68
    Number of Reflections(R-Work) 436
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.233
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.27
    Shell Resolution(Low) 7.89
    Number of Reflections(Observed) 516
    Number of Reflections(R-Free) 62
    Number of Reflections(R-Work) 454
    R-Factor(R-Work) 0.246
    R-Factor(R-Free) 0.262
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.99
    c_scbond_it 1.96
    c_mcangle_it 2.73
    c_mcbond_it 1.55
    c_improper_angle_d 1.03
    c_dihedral_angle_d 23.7
    c_angle_deg 1.3
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.32
    Luzzati Sigma A(Observed) 0.34
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.41
    Luzzati Sigma A(R-Free Set) 0.45
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2097
    Nucleic Acid Atoms 0
    Heterogen Atoms 20
    Solvent Atoms 85
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    data extraction pdb_extract version: 2.000
    refinement CNS
    data processing HKL