POP-OUT | CLOSE

An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2BYI
  •   Crystallization Hide
    Crystallization Experiments
    pH 5.5
    Details 25% PEG MME 2000, 0.1M NA CACODYLATE, PH6.5, 0.2M MGCL2, pH 5.50
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.3 α = 90
    b = 44.05 β = 115.28
    c = 54.18 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 IMAGE PLATE
    Type RIGAKU
    Details OSMIC BLUE MIRRORS
    Collection Date 2002-12-04
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.7
    Resolution(Low) 30
    Number Reflections(Observed) 27729
    Percent Possible(Observed) 97.7
    R Merge I(Observed) 0.04
    Redundancy 2.1
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.8
    Percent Possible(All) 99.1
    R Merge I(Observed) 0.31
    Mean I Over Sigma(Observed) 1.9
    Redundancy 1.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 48.8
    Number of Reflections(Observed) 26322
    Number of Reflections(R-Free) 1407
    Percent Reflections(Observed) 91.8
    R-Factor(Observed) 0.197
    R-Work 0.195
    R-Free 0.242
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.6
    Anisotropic B[1][1] -0.3
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.3
    Anisotropic B[2][2] -0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.06
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.64
    Number of Reflections(R-Free) 52
    Number of Reflections(R-Work) 1032
    R-Factor(R-Work) 0.395
    R-Factor(R-Free) 0.353
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.05
    r_scbond_it 2.444
    r_mcangle_it 1.573
    r_mcbond_it 0.909
    r_nbd_refined 0.199
    r_gen_planes_refined 0.007
    r_chiral_restr 0.106
    r_dihedral_angle_1_deg 5.99
    r_angle_refined_deg 1.48
    r_bond_refined_d 0.015
    r_xyhbond_nbd_refined 0.159
    r_symmetry_vdw_refined 0.161
    r_symmetry_hbond_refined 0.255
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1689
    Nucleic Acid Atoms 0
    Heterogen Atoms 28
    Solvent Atoms 261
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) D*TREK
    Data Reduction (data scaling) D*TREK
    Structure Solution AMORE
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24
    model building AMORE