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X-RAY DIFFRACTION
Materials and Methods page
3VB2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 293.0
    Details 5% Tacsimate,0.1M HEPES, 10% PEG 5000MME, 0.3M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.8 α = 90
    b = 62.8 β = 90
    c = 173.06 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 130 mm
    Collection Date 2011-01-05
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97915
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.6
    Resolution(Low) 59.03
    Number Reflections(All) 10837
    Number Reflections(Observed) 10837
    Percent Possible(Observed) 95.9
    B(Isotropic) From Wilson Plot 59.8
    Redundancy 6.0
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.74
    Percent Possible(All) 97.6
    R Merge I(Observed) 0.493
    Mean I Over Sigma(Observed) 1.3
    R-Sym I(Observed) 0.493
    Redundancy 6.2
    Number Unique Reflections(All) 1557
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 30.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 10739
    Number of Reflections(R-Free) 511
    Percent Reflections(Observed) 94.83
    R-Factor(Observed) 0.2448
    R-Work 0.2429
    R-Free 0.2834
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 77.1884
    Anisotropic B[1][1] 0.05
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.05
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.11
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.667
    Number of Reflections(R-Free) 34
    Number of Reflections(R-Work) 631
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.321
    Percent Reflections(Observed) 96.1
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.008
    r_chiral_restr 0.057
    r_dihedral_angle_4_deg 16.054
    r_dihedral_angle_3_deg 17.896
    r_dihedral_angle_2_deg 40.638
    r_dihedral_angle_1_deg 6.869
    r_angle_refined_deg 0.681
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2104
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 18
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser
    data reduction SCALA version: 3.3.16