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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2BY7
  •   Crystallization Hide
    Crystallization Experiments
    Details 25% PEG 8000, 0.2 M AMMONIUM SULPHATE AND 0.1 M TRIS-HCL PH 8.0
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.22 α = 90
    b = 58.33 β = 90
    c = 66.75 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength 0.984
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.4
    Resolution(Low) 20
    Number Reflections(Observed) 52037
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.07
    B(Isotropic) From Wilson Plot 7.71
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 1.3
    Resolution(Low) 1.37
    Percent Possible(All) 93.4
    R Merge I(Observed) 0.25
    Mean I Over Sigma(Observed) 3.6
    Redundancy 2.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 1.3
    Resolution(Low) 19.86
    Number of Reflections(Observed) 49849
    Number of Reflections(R-Free) 2134
    Percent Reflections(Observed) 98.6
    R-Factor(Observed) 0.106
    R-Work 0.104
    R-Free 0.144
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 7.43
    Anisotropic B[1][1] 0.22
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.07
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.15
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3
    Shell Resolution(Low) 1.33
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 3291
    R-Factor(R-Work) 0.172
    R-Factor(R-Free) 0.247
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.974
    r_scbond_it 3.35
    r_mcangle_it 2.384
    r_mcbond_it 1.782
    r_nbd_refined 0.439
    r_gen_planes_other 0.007
    r_gen_planes_refined 0.013
    r_chiral_restr 0.127
    r_dihedral_angle_4_deg 20.534
    r_dihedral_angle_3_deg 11.247
    r_dihedral_angle_2_deg 40.432
    r_dihedral_angle_1_deg 7.318
    r_angle_other_deg 1.024
    r_angle_refined_deg 2.454
    r_bond_other_d 0.007
    r_bond_refined_d 0.018
    r_nbd_other 0.206
    r_nbtor_refined 0.189
    r_nbtor_other 0.092
    r_xyhbond_nbd_refined 0.216
    r_symmetry_vdw_refined 0.158
    r_symmetry_vdw_other 0.193
    r_symmetry_hbond_refined 0.243
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1629
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 422
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Refinement REFMAC 5.2.0003
     
    Software
    refinement REFMAC version: 5.2.0003