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An Information Portal to 110071 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1NDM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Details VAPOR DIFFUSION, HANGING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 90.68 α = 90
    b = 164.02 β = 90
    c = 40 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector IMAGE PLATE
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.1
    Number Reflections(Observed) 31484
    B(Isotropic) From Wilson Plot 5.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 8.45
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 31484
    Number of Reflections(Observed) 31484
    Number of Reflections(R-Free) 1564
    Percent Reflections(Observed) 89.5
    R-Factor(Observed) 0.2081
    R-Work 0.208
    R-Free 0.258
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 20.0
    Anisotropic B[1][1] -5.93
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.58
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 5.35
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.23
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4349
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.294
    R-Free Error 0.019
    Percent Reflections(Observed) 78.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 4.73
    c_scbond_it 3.94
    c_mcangle_it 3.45
    c_mcbond_it 2.61
    c_improper_angle_d 0.82
    c_bond_d 0.007
    c_angle_deg 1.4
    c_dihedral_angle_d 26.3
     
    Coordinate Error
    Luzzati ESD(R-Free Set) 0.31
    Luzzati Sigma A(R-Free Set) 0.27
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4258
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 598
     
     
  •   Software and Computing Hide
    Computing
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0