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X-RAY DIFFRACTION
Materials and Methods page
4JKD
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7.5
    Temperature 298.0
    Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.41 α = 90
    b = 77.74 β = 90
    c = 94.2 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-01-22
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.1158
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.55
    Resolution(Low) 50
    Number Reflections(All) 79587
    Number Reflections(Observed) 79587
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.05
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.61
    Percent Possible(All) 90.9
    R Merge I(Observed) 0.478
    Redundancy 2.6
    Number Unique Reflections(All) 7249
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 40.28
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 79523
    Number of Reflections(Observed) 79523
    Number of Reflections(R-Free) 3957
    Percent Reflections(Observed) 98.29
    R-Factor(Observed) 0.146
    R-Work 0.1438
    R-Free 0.1882
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.3857
    Anisotropic B[1][1] 0.15
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.33
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.18
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.55
    Shell Resolution(Low) 1.59
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 4791
    R-Factor(R-Work) 0.235
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 89.29
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 12.766
    r_sphericity_free 26.837
    r_rigid_bond_restr 2.677
    r_gen_planes_refined 0.006
    r_chiral_restr 0.084
    r_dihedral_angle_4_deg 14.231
    r_dihedral_angle_3_deg 12.488
    r_dihedral_angle_2_deg 39.787
    r_dihedral_angle_1_deg 5.541
    r_angle_refined_deg 1.323
    r_bond_refined_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3592
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 688
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution REFMAC 5.6.0117
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    data reduction SCALEPACK