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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VWX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details 1.2 M sodium citrate, 0.1 M HEPES-NaOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 87.55 α = 90
    b = 87.55 β = 90
    c = 131.88 γ = 120
     
    Space Group
    Space Group Name:    P 31
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-01-17
     
    Diffraction Radiation
    Monochromator Numerical link type Si(111) double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-5A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline BL-5A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.8
    Resolution(Low) 75.8
    Number Reflections(All) 104764
    Number Reflections(Observed) 102983
    Percent Possible(Observed) 98.3
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 97.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 65.82
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 99532
    Number of Reflections(Observed) 97850
    Number of Reflections(R-Free) 5130
    Percent Reflections(Observed) 98.31
    R-Factor(Observed) 0.16532
    R-Work 0.16398
    R-Free 0.19052
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.7
    Anisotropic B[1][1] -0.86
    Anisotropic B[1][2] -0.86
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.86
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.79
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 7100
    R-Factor(R-Work) 0.229
    R-Factor(R-Free) 0.277
    Percent Reflections(Observed) 97.01
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.01
    r_chiral_restr 0.134
    r_dihedral_angle_4_deg 25.912
    r_dihedral_angle_3_deg 13.801
    r_dihedral_angle_2_deg 37.195
    r_dihedral_angle_1_deg 5.382
    r_angle_other_deg 0.983
    r_angle_refined_deg 1.719
    r_bond_other_d 0.005
    r_bond_refined_d 0.022
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6986
    Nucleic Acid Atoms 0
    Heterogen Atoms 80
    Solvent Atoms 934
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution Molrep
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.7.0029
    model building Molrep
    data collection ADSC version: Quantum