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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3V5K
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details 25 mM MES pH6.5 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.77 α = 90
    b = 87.08 β = 90.04
    c = 79.68 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2011-10-12
     
    Diffraction Radiation
    Monochromator graphite
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 1.0
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.3
    Resolution(Low) 30
    Number Reflections(All) 37378
    Number Reflections(Observed) 35327
    Percent Possible(Observed) 94.2
    R Merge I(Observed) 0.079
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 98.6
    R Merge I(Observed) 0.294
    Redundancy 4.0
    Number Unique Reflections(All) 3693
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.31
    Resolution(Low) 29.39
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 37523
    Number of Reflections(Observed) 35266
    Number of Reflections(R-Free) 1754
    Percent Reflections(Observed) 93.53
    R-Factor(All) 0.1876
    R-Factor(Observed) 0.1876
    R-Work 0.1855
    R-Free 0.228
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.631
    Anisotropic B[1][1] 2.8937
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.2817
    Anisotropic B[2][2] -12.4557
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 9.562
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.31
    Shell Resolution(Low) 2.38
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2664
    Percent Reflections(Observed) 93.53
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    t_other_torsion 17.92
    t_omega_torsion 3.41
    t_angle_deg 1.07
    t_bond_d 0.009
    t_ideal_dist_contact 0.0
    t_chiral_improper_torsion 0.0
    t_it 0.0
    t_gen_planes 0.0
    t_trig_c_planes 0.0
    t_dihedral_angle_d 0.0
     
    Coordinate Error
    Luzzati ESD(Observed) 0.305
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6326
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 289
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement BUSTER 2.10.0
     
    Software
    data extraction pdb_extract version: 3.10
    refinement BUSTER-TNT
    molecular replacement Phaser version: 2.3.0
    data reduction SCALEPACK