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X-RAY DIFFRACTION
Materials and Methods page
3EK8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 298.0
    Details 0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 120.8 α = 90
    b = 120.8 β = 90
    c = 97.35 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU SATURN 92
    Collection Date 2008-05-12
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.8
    Resolution(Low) 29.3
    Number Reflections(Observed) 18310
    Percent Possible(Observed) 100.0
    Redundancy 11.94
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.9
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 3.5
    R-Sym I(Observed) 0.573
    Redundancy 12.04
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 29.3
    Number of Reflections(Observed) 17372
    Number of Reflections(R-Free) 934
    Percent Reflections(Observed) 99.97
    R-Factor(Observed) 0.22569
    R-Work 0.22359
    R-Free 0.26553
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.663
    Anisotropic B[1][1] 0.36
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.36
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.72
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 2.872
    Number of Reflections(R-Free) 70
    Number of Reflections(R-Work) 1258
    R-Factor(R-Work) 0.291
    R-Factor(R-Free) 0.32
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.346
    r_scbond_it 1.383
    r_mcangle_it 1.18
    r_mcbond_it 0.654
    r_nbd_refined 0.217
    r_gen_planes_refined 0.004
    r_chiral_restr 0.081
    r_dihedral_angle_4_deg 20.433
    r_dihedral_angle_3_deg 20.256
    r_dihedral_angle_2_deg 38.686
    r_dihedral_angle_1_deg 6.144
    r_angle_refined_deg 1.355
    r_bond_refined_d 0.011
    r_nbtor_refined 0.306
    r_xyhbond_nbd_refined 0.147
    r_metal_ion_refined 0.109
    r_symmetry_vdw_refined 0.155
    r_symmetry_hbond_refined 0.139
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3148
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 24
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) d*TREK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.006
    refinement REFMAC5 version: 5.2.0019
    molecular replacement Phaser
    data processing D*trek
    collection/data indexing D*trek