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X-RAY DIFFRACTION
Materials and Methods page
4KHP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.15
    Details 100 mM Mes-KOH (pH 6.5), 200 mM KCl, 75 mM NH4Cl, 15 mM MgCl2, and 26% (vol/vol) 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 401 α = 90
    b = 401 β = 90
    c = 176 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04
    Wavelength List 0.99
    Site DIAMOND
    Beamline I04
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.1
    Resolution(Low) 29.7
    Number Reflections(All) 234683
    Number Reflections(Observed) 234683
    Percent Possible(Observed) 91.4
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.2
    Percent Possible(All) 95.1
    Mean I Over Sigma(Observed) 1.47
    R-Sym I(Observed) 0.691
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.1
    Resolution(Low) 29.67
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 234682
    Number of Reflections(Observed) 234682
    Number of Reflections(R-Free) 11726
    Percent Reflections(Observed) 91.35
    R-Factor(All) 0.1873
    R-Factor(Observed) 0.1873
    R-Work 0.1852
    R-Free 0.2262
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 83.2593
    Anisotropic B[1][1] 0.01
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1
    Shell Resolution(Low) 3.18
    Number of Reflections(R-Free) 869
    Number of Reflections(R-Work) 16852
    R-Factor(R-Work) 0.296
    R-Factor(R-Free) 0.319
    Percent Reflections(Observed) 95.14
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_mcangle_it 10.609
    r_mcbond_other 6.718
    r_bond_refined_d 0.01
    r_bond_other_d 0.003
    r_angle_refined_deg 1.751
    r_angle_other_deg 1.26
    r_dihedral_angle_1_deg 8.601
    r_dihedral_angle_2_deg 34.871
    r_dihedral_angle_3_deg 23.112
    r_dihedral_angle_4_deg 20.012
    r_chiral_restr 0.101
    r_gen_planes_refined 0.008
    r_gen_planes_other 0.001
    r_mcbond_it 6.718
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19120
    Nucleic Acid Atoms 32485
    Heterogen Atoms 427
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHENIX
    Structure Refinement REFMAC 5.8.0031
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.8.0031