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X-RAY DIFFRACTION
Materials and Methods page
3VAZ
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7.5
    Temperature 298.0
    Details 22% PEG 400, 0.2M CaCl2, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 155.39 α = 90
    b = 155.39 β = 90
    c = 317.85 γ = 120
     
    Space Group
    Space Group Name:    P 62 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Collection Date 2011-09-25
     
    Diffraction Radiation
    Monochromator Varimax optics
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.19
    Resolution(Low) 29.74
    Number Reflections(Observed) 38297
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.315
    B(Isotropic) From Wilson Plot 17.228
     
    High Resolution Shell Details
    Resolution(High) 3.19
    Resolution(Low) 3.39
    Percent Possible(All) 99.0
    R Merge I(Observed) 0.733
    Mean I Over Sigma(Observed) 5.35
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.19
    Resolution(Low) 29.74
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 38297
    Number of Reflections(R-Free) 1915
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.2059
    R-Work 0.2022
    R-Free 0.277
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.828
    Anisotropic B[1][1] -1.77
    Anisotropic B[1][2] -0.88
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.77
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.65
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.194
    Shell Resolution(Low) 3.276
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.37
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 0.122
    r_scbond_it 0.057
    r_mcangle_it 0.291
    r_mcbond_it 0.163
    r_gen_planes_refined 0.003
    r_chiral_restr 0.064
    r_dihedral_angle_4_deg 19.342
    r_dihedral_angle_3_deg 15.637
    r_dihedral_angle_2_deg 39.934
    r_dihedral_angle_1_deg 5.018
    r_angle_refined_deg 0.995
    r_bond_refined_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14999
    Nucleic Acid Atoms 0
    Heterogen Atoms 308
    Solvent Atoms 414
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser
    data reduction Xscale