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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VHS
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.0
    Details 28% PEG 400, 0.1M HEPES, 0.2M calcium chrolide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 36.48 α = 90
    b = 73.46 β = 90
    c = 34.65 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2007-12-05
     
    Diffraction Radiation
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-17A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline BL-17A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.9
    Resolution(Low) 100
    Number Reflections(Observed) 3816
    Percent Possible(Observed) 97.6
    R Merge I(Observed) 0.063
    B(Isotropic) From Wilson Plot 32.4
    Redundancy 5.5
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.93
    Percent Possible(All) 89.5
    R Merge I(Observed) 0.384
    Mean I Over Sigma(Observed) 3.3
    Redundancy 3.5
    Number Unique Reflections(All) 187
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.9
    Resolution(Low) 23.77
    Number of Reflections(Observed) 3605
    Number of Reflections(R-Free) 175
    Percent Reflections(Observed) 96.97
    R-Factor(Observed) 0.21526
    R-Work 0.21282
    R-Free 0.26151
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.8
    Anisotropic B[1][1] -0.48
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.96
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.48
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.901
    Shell Resolution(Low) 1.95
    Number of Reflections(R-Free) 15
    Number of Reflections(R-Work) 247
    R-Factor(R-Work) 0.337
    R-Factor(R-Free) 0.325
    Percent Reflections(Observed) 90.97
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.484
    r_scbond_it 2.688
    r_mcangle_it 1.683
    r_mcbond_it 0.897
    r_gen_planes_refined 0.006
    r_chiral_restr 0.1
    r_dihedral_angle_4_deg 15.208
    r_dihedral_angle_3_deg 17.483
    r_dihedral_angle_2_deg 48.557
    r_dihedral_angle_1_deg 5.328
    r_angle_refined_deg 1.584
    r_bond_refined_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 403
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 16
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building SOLVE
    data collection ADSC version: Quantum