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X-RAY DIFFRACTION
Materials and Methods page
4F3T
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9
    Temperature 290.0
    Details microseeding in 100 mM Tris pH=9.0, 10% PEG 3350 (w/v), 8% 2-propanol (v/v), 0.12 M phenol, VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.43 α = 90
    b = 107.65 β = 106.69
    c = 68.72 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 ADSC QUANTUM 315
     
    Diffraction Radiation
    Monochromator Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Resolution(High) 2.25
    Resolution(Low) 50
    Number Reflections(All) 42106
    Number Reflections(Observed) 41096
    Percent Possible(Observed) 97.6
    R Merge I(Observed) 0.047
    Redundancy 2.7
     
    High Resolution Shell Details
    Resolution(High) 2.25
    Resolution(Low) 2.29
    Percent Possible(All) 92.6
    R Merge I(Observed) 0.359
    Redundancy 2.5
    Number Unique Reflections(All) 1945
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.25
    Resolution(Low) 47.438
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 41069
    Number of Reflections(Observed) 41069
    Number of Reflections(R-Free) 1295
    Percent Reflections(Observed) 97.44
    R-Factor(Observed) 0.208
    R-Work 0.207
    R-Free 0.254
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 57.952
    Anisotropic B[1][1] -0.76
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.883
    Anisotropic B[2][2] -2.289
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.049
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.247
    Shell Resolution(Low) 2.336
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 4233
    R-Factor(R-Work) 0.292
    R-Factor(R-Free) 0.354
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.336
    Shell Resolution(Low) 2.443
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 4476
    R-Factor(R-Work) 0.271
    R-Factor(R-Free) 0.342
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.443
    Shell Resolution(Low) 2.572
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 4469
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.572
    Shell Resolution(Low) 2.733
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 4495
    R-Factor(R-Work) 0.237
    R-Factor(R-Free) 0.295
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.733
    Shell Resolution(Low) 2.944
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 4430
    R-Factor(R-Work) 0.226
    R-Factor(R-Free) 0.318
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.944
    Shell Resolution(Low) 3.24
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 4486
    R-Factor(R-Work) 0.224
    R-Factor(R-Free) 0.275
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.24
    Shell Resolution(Low) 3.708
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 4442
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.24
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.708
    Shell Resolution(Low) 4.672
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 4401
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.213
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.672
    Shell Resolution(Low) 47.449
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 4342
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.231
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.762
    f_plane_restr 0.003
    f_chiral_restr 0.042
    f_angle_d 0.674
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6436
    Nucleic Acid Atoms 298
    Heterogen Atoms 14
    Solvent Atoms 136
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Solution SHARP
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.006
    refinement phenix
    density modification Solomon
    phasing SHARP
    data processing HKL