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X-RAY DIFFRACTION
Materials and Methods page
3G5G
  •   Crystallization Hide
    Crystallization Experiments
    Method precipitation
    pH 8
    Temperature 277.0
    Details 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 128.72 α = 90
    b = 128.72 β = 90
    c = 137.51 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2008-11-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.9330
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.8
    Resolution(Low) 46.98
    Number Reflections(All) 31845
    Number Reflections(Observed) 31686
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.135
    B(Isotropic) From Wilson Plot 32.789
    Redundancy 11.17
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 3.0
    Percent Possible(All) 93.7
    R Merge I(Observed) 0.372
    Mean I Over Sigma(Observed) 7.7
    Number Unique Reflections(All) 5569
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 46.984
    Cut-off Sigma(I) 7.7
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 31845
    Number of Reflections(Observed) 30225
    Number of Reflections(R-Free) 1606
    Percent Reflections(Observed) 99.96
    R-Factor(All) 0.239
    R-Factor(Observed) 0.239
    R-Work 0.237
    R-Free 0.269
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.078
    Anisotropic B[1][1] -0.04
    Anisotropic B[1][2] -0.02
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.06
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 2.873
    Number of Reflections(Observed) 2223
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2223
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.346
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.273
    r_scbond_it 1.303
    r_mcangle_it 0.78
    r_mcbond_it 0.487
    r_symmetry_hbond_refined 0.249
    r_bond_refined_d 0.015
    r_angle_refined_deg 1.579
    r_dihedral_angle_1_deg 5.647
    r_dihedral_angle_2_deg 34.601
    r_dihedral_angle_3_deg 19.524
    r_dihedral_angle_4_deg 19.086
    r_chiral_restr 0.162
    r_gen_planes_refined 0.005
    r_nbd_refined 0.225
    r_nbtor_refined 0.312
    r_xyhbond_nbd_refined 0.146
    r_symmetry_vdw_refined 0.333
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8689
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 4
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MX-CUBE
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.006
    refinement REFMAC5
    molecular replacement Phaser
    data processing Xscale