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X-RAY DIFFRACTION
Materials and Methods page
3CFM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 291.0
    Details Mother liquor: 100 mM tris pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop 1 uL mother liquor + 1 uL TTR 10 mg/mL; crystals appeared in about 5 days, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 43.17 α = 90
    b = 86.11 β = 90
    c = 63.76 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details Osmic
    Collection Date 2005-05-10
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU ULTRAX 18
    Wavelength List 1.542
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.6
    Resolution(Low) 86.11
    Number Reflections(All) 32087
    Number Reflections(Observed) 32073
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.046
    B(Isotropic) From Wilson Plot 20.5
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.69
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.398
    Mean I Over Sigma(Observed) 1.9
    R-Sym I(Observed) 0.398
    Redundancy 6.7
    Number Unique Reflections(All) 4565
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 17.87
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 32061
    Number of Reflections(Observed) 32042
    Number of Reflections(R-Free) 1624
    Percent Reflections(Observed) 99.96
    R-Factor(All) 0.192
    R-Factor(Observed) 0.192
    R-Work 0.191
    R-Free 0.218
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.203
    Anisotropic B[1][1] -0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.641
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2153
    R-Factor(R-Work) 0.328
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_symmetry_hbond_refined 0.103
    r_bond_refined_d 0.007
    r_angle_refined_deg 1.057
    r_dihedral_angle_1_deg 5.758
    r_dihedral_angle_2_deg 30.885
    r_dihedral_angle_3_deg 13.435
    r_dihedral_angle_4_deg 15.355
    r_chiral_restr 0.072
    r_gen_planes_refined 0.003
    r_nbd_refined 0.181
    r_nbtor_refined 0.301
    r_xyhbond_nbd_refined 0.119
    r_symmetry_vdw_refined 0.18
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1785
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 282
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.004
    refinement REFMAC5
    molecular replacement MOLREP
    data processing SCALA
    collection/data indexing Mosflm