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X-RAY DIFFRACTION
Materials and Methods page
3VGW
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5
    Temperature 293.0
    Details 2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 116.01 α = 90
    b = 81.22 β = 92.47
    c = 74.41 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2010-04-24
     
    Diffraction Radiation
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.6
    Resolution(Low) 50
    Number Reflections(Observed) 176927
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.087
    Redundancy 5.5
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.66
    Percent Possible(All) 95.4
    R Merge I(Observed) 0.341
    Redundancy 5.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 35.85
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 176927
    Number of Reflections(R-Free) 8880
    Percent Reflections(Observed) 97.98
    R-Factor(Observed) 0.1908
    R-Work 0.1895
    R-Free 0.2148
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.6812
    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) 1.603
    Shell Resolution(Low) 1.645
    Number of Reflections(R-Free) 618
    Number of Reflections(R-Work) 11612
    R-Factor(R-Work) 0.227
    R-Factor(R-Free) 0.272
    Percent Reflections(Observed) 91.82
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 6.349
    r_scbond_it 4.228
    r_mcangle_it 3.05
    r_mcbond_it 1.845
    r_gen_planes_refined 0.016
    r_chiral_restr 0.222
    r_dihedral_angle_4_deg 25.112
    r_dihedral_angle_3_deg 15.555
    r_dihedral_angle_2_deg 32.518
    r_dihedral_angle_1_deg 6.58
    r_angle_refined_deg 2.925
    r_bond_refined_d 0.035
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7648
    Nucleic Acid Atoms 0
    Heterogen Atoms 324
    Solvent Atoms 572
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0110
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.5.0110
    molecular replacement MOLREP
    data reduction SCALEPACK