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X-RAY DIFFRACTION
Materials and Methods page
2IAG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 277.0
    Details The native recombinant PGIS (25 mg/ml in the buffer containing 20 mM Tris, pH 8.0 and 150 mM NaCl) was found to crystallize spontaneously into needle clusters in the Eppendorf tube when stored at 4 C for about a week. A combination of microseeding technique and the hanging-drop vapor-diffusion method was then used to improve crystal quality. Specifically, seed stock was prepared by crushing these initial PGIS needle clusters with the Seed Bead Kit (Hampton Research). Following four 10-fold serial dilutions of the seed stock using the gel filtration buffer, 1 micro-l of diluted seeds was added into a 10 micro-l drop of freshly concentrated PGIS sample, and equilibrated at 4 C against 450 micro-l of the gel filtration buffer. High quality single crystals of PGIS were most often obtained using 100- or 1000-fold diluted seed stock, and reached suitable size (~ 0.05,0.05 ~ 0.1 mm3) within one week., VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 67.73 α = 90
    b = 105.6 β = 92.01
    c = 73.95 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2006-05-15
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2006-06-29
     
    Diffraction Radiation
    Diffraction Protocol MAD
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL12B2
    Wavelength List 0.9537, 0.9793
    Site SPRING-8
    Beamline BL12B2
    Source SYNCHROTRON
    Type NSRRC BEAMLINE BL13B1
    Wavelength List 0.980127
    Site NSRRC
    Beamline BL13B1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.15
    Resolution(Low) 30
    Number Reflections(All) 56459
    Number Reflections(Observed) 51322
    Percent Possible(Observed) 90.9
    Redundancy 2.8
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.23
    Percent Possible(All) 93.5
    Mean I Over Sigma(Observed) 3.1
    R-Sym I(Observed) 0.35
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.15
    Resolution(Low) 20.15
    Number of Reflections(Observed) 48702
    Number of Reflections(R-Free) 2601
    Percent Reflections(Observed) 90.96
    R-Factor(Observed) 0.20407
    R-Work 0.2009
    R-Free 0.26313
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.948
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.151
    Shell Resolution(Low) 2.206
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3616
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.318
    Percent Reflections(Observed) 93.29
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.987
    r_scbond_it 1.961
    r_mcangle_it 1.213
    r_mcbond_it 0.642
    r_nbd_refined 0.205
    r_gen_planes_refined 0.005
    r_chiral_restr 0.095
    r_dihedral_angle_4_deg 18.433
    r_dihedral_angle_3_deg 17.588
    r_dihedral_angle_2_deg 32.256
    r_dihedral_angle_1_deg 6.177
    r_angle_refined_deg 1.38
    r_bond_refined_d 0.011
    r_nbtor_refined 0.304
    r_xyhbond_nbd_refined 0.16
    r_symmetry_vdw_refined 0.192
    r_symmetry_hbond_refined 0.154
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7611
    Nucleic Acid Atoms 0
    Heterogen Atoms 87
    Solvent Atoms 435
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019