POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2YBN
  •   Crystallization Hide
    Crystallization Experiments
    pH 4.7
    Details 200 MM SODIUM ACETATE BUFFER PH 4.7, 10% W/V NACL.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.34 α = 90
    b = 78.34 β = 90
    c = 38.75 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Details MIRRORS
    Collection Date 2010-05-10
     
    Diffraction Radiation
    Monochromator EMG-T5 KOHZU DOUBLE CRYSTAL MONOCHROMATOR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength 0.939
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.1
    Resolution(High) 2
    Resolution(Low) 35
    Number Reflections(Observed) 8542
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.09
    B(Isotropic) From Wilson Plot 23.262
    Redundancy 6.0
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.1
    Percent Possible(All) 98.8
    R Merge I(Observed) 0.46
    Mean I Over Sigma(Observed) 1.1
    Redundancy 5.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 55.39
    Number of Reflections(Observed) 8078
    Number of Reflections(R-Free) 400
    Percent Reflections(Observed) 98.71
    R-Factor(Observed) 0.22027
    R-Work 0.21886
    R-Free 0.24969
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.569
    Anisotropic B[1][1] -0.65
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.65
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.3
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.052
    Number of Reflections(R-Free) 29
    Number of Reflections(R-Work) 586
    R-Factor(R-Work) 0.266
    R-Factor(R-Free) 0.296
    Percent Reflections(Observed) 98.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.319
    r_scbond_it 1.341
    r_mcangle_it 0.979
    r_mcbond_it 0.494
    r_gen_planes_refined 0.003
    r_chiral_restr 0.083
    r_dihedral_angle_4_deg 17.83
    r_dihedral_angle_3_deg 15.209
    r_dihedral_angle_2_deg 36.421
    r_dihedral_angle_1_deg 5.067
    r_angle_refined_deg 0.996
    r_bond_refined_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1001
    Nucleic Acid Atoms 0
    Heterogen Atoms 3
    Solvent Atoms 32
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building MOLREP