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X-RAY DIFFRACTION
Materials and Methods page
3VOO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 293.0
    Details 50mM HEPES, 17.5% MPD, 25mM MES, 10% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 94.43 α = 90
    b = 94.43 β = 90
    c = 113.26 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU SATURN A200
    Collection Date 2010-05-21
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL26B1
    Wavelength List 1.000
    Site SPRING-8
    Beamline BL26B1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.34
    Resolution(Low) 50
    Number Reflections(Observed) 25136
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.058
    B(Isotropic) From Wilson Plot 49.5
    Redundancy 10.6
     
    High Resolution Shell Details
    Resolution(High) 2.34
    Resolution(Low) 2.42
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.364
    Redundancy 11.0
    Number Unique Reflections(All) 2474
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.34
    Resolution(Low) 19.64
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 24996
    Number of Reflections(R-Free) 1231
    Percent Reflections(Observed) 99.69
    R-Factor(Observed) 0.1975
    R-Work 0.1957
    R-Free 0.2336
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.9981
    Anisotropic B[1][1] 0.15
    Anisotropic B[1][2] 0.07
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.15
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.22
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.34
    Shell Resolution(Low) 2.4
    Number of Reflections(R-Free) 84
    Number of Reflections(R-Work) 1684
    R-Factor(R-Work) 0.195
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 99.27
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.775
    r_scbond_it 1.805
    r_mcangle_it 1.2
    r_mcbond_it 0.671
    r_gen_planes_refined 0.006
    r_chiral_restr 0.088
    r_dihedral_angle_4_deg 17.068
    r_dihedral_angle_3_deg 14.451
    r_dihedral_angle_2_deg 32.815
    r_dihedral_angle_1_deg 5.536
    r_angle_refined_deg 1.269
    r_bond_refined_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3223
    Nucleic Acid Atoms 0
    Heterogen Atoms 43
    Solvent Atoms 60
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction SCALEPACK
    data collection DENZO