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X-RAY DIFFRACTION
Materials and Methods page
3VNO
  •   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 = 94.54 α = 90
    b = 94.54 β = 90
    c = 113 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 2010-11-24
     
    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) 2.17
    Resolution(Low) 20
    Number Reflections(Observed) 31376
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.048
    B(Isotropic) From Wilson Plot 42.762
    Redundancy 10.5
     
    High Resolution Shell Details
    Resolution(High) 2.17
    Resolution(Low) 2.25
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.339
    Redundancy 10.9
    Number Unique Reflections(All) 3106
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.17
    Resolution(Low) 19.79
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 31226
    Number of Reflections(R-Free) 1516
    Percent Reflections(Observed) 99.57
    R-Factor(Observed) 0.2006
    R-Work 0.1993
    R-Free 0.2271
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.1839
    Anisotropic B[1][1] 0.11
    Anisotropic B[1][2] 0.06
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.11
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.17
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.17
    Shell Resolution(Low) 2.226
    Number of Reflections(R-Free) 101
    Number of Reflections(R-Work) 2139
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 99.47
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.685
    r_scbond_it 1.703
    r_mcangle_it 1.177
    r_mcbond_it 0.641
    r_gen_planes_refined 0.006
    r_chiral_restr 0.084
    r_dihedral_angle_4_deg 18.423
    r_dihedral_angle_3_deg 14.821
    r_dihedral_angle_2_deg 32.234
    r_dihedral_angle_1_deg 5.539
    r_angle_refined_deg 1.25
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3218
    Nucleic Acid Atoms 0
    Heterogen Atoms 51
    Solvent Atoms 81
     
     
  •   Software and Computing Hide
    Computing
    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