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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1LGD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.8
    Temperature 298.0
    Details PEG 2000 or 3350, Tris-HCl, BME. Crystals are soaked in BME-free solution in the presence of bicarbonate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.01 α = 90
    b = 44.59 β = 92.82
    c = 76.64 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 298
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAC Science DIP-2030H
    Details MIRRORS
    Collection Date 1998-02-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type ENRAF-NONIUS FR591
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.9
    Resolution(Low) 20
    Number Reflections(All) 16497
    Number Reflections(Observed) 16497
    Percent Possible(Observed) 88.6
    R Merge I(Observed) 0.089
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 87.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 20.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 16497
    Number of Reflections(Observed) 16497
    Number of Reflections(R-Free) 894
    Percent Reflections(Observed) 88.65
    R-Factor(All) 0.18909
    R-Factor(Observed) 0.18909
    R-Work 0.18771
    R-Free 0.2141
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.463
    Anisotropic B[1][1] -0.27
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.54
    Anisotropic B[2][2] 0.7
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.49
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.949
    Number of Reflections(R-Free) 54
    Number of Reflections(R-Work) 1185
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.282
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_nbd_refined 0.233
    r_gen_planes_refined 0.005
    r_chiral_restr 0.108
    r_dihedral_angle_3_deg 19.336
    r_dihedral_angle_1_deg 3.938
    r_angle_refined_deg 1.443
    r_bond_refined_d 0.011
    r_xyhbond_nbd_refined 0.15
    r_symmetry_vdw_refined 0.259
    r_symmetry_hbond_refined 0.15
    r_mcbond_it 0.786
    r_mcangle_it 1.464
    r_scbond_it 2.188
    r_scangle_it 3.569
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2049
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 161
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution X-PLOR
    Structure Refinement REFMAC 5
     
    Software
    refinement REFMAC version: 5.0
    model building X-PLOR