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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VAX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 287.0
    Details 20% PEG3350, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 77.9 α = 90
    b = 67.28 β = 97.04
    c = 85.56 γ = 90
     
    Space Group
    Space Group Name:    P 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Collection Date 2011-01-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 1.000
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.4
    Resolution(Low) 84.92
    Number Reflections(All) 34563
    Number Reflections(Observed) 34563
    Percent Possible(Observed) 99.8
    Redundancy 7.3
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.53
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.41
    Mean I Over Sigma(Observed) 1.7
    R-Sym I(Observed) 0.41
    Redundancy 7.4
    Number Unique Reflections(All) 5026
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 45.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 34563
    Number of Reflections(R-Free) 1738
    Percent Reflections(Observed) 99.81
    R-Factor(Observed) 0.194
    R-Work 0.1918
    R-Free 0.2344
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.9579
    Anisotropic B[1][1] -1.18
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.82
    Anisotropic B[2][2] 1.94
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.97
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.462
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2415
    R-Factor(R-Work) 0.202
    R-Factor(R-Free) 0.288
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.35
    r_scbond_it 1.322
    r_mcangle_it 0.754
    r_mcbond_it 0.375
    r_gen_planes_refined 0.005
    r_chiral_restr 0.073
    r_dihedral_angle_4_deg 17.585
    r_dihedral_angle_3_deg 16.944
    r_dihedral_angle_2_deg 37.198
    r_dihedral_angle_1_deg 5.475
    r_angle_refined_deg 1.119
    r_bond_refined_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5438
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 269
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0102
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.5.0102
    molecular replacement Phaser
    data reduction SCALA version: 3.3.15
    data collection Mosflm