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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2XNB
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.8
    Details 10% PEG 3350, NAF, PH 7.0
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.01 α = 90
    b = 71.11 β = 90
    c = 72.03 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU
    Details BLUE MAX-FLUX CONFOCAL
    Collection Date 2004-07-30
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-D
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.8
    Resolution(Low) 31.88
    Number Reflections(Observed) 25565
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.08
    Redundancy 2.63
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.86
    Percent Possible(All) 99.1
    R Merge I(Observed) 0.48
    Mean I Over Sigma(Observed) 2.1
    Redundancy 2.56
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.85
    Resolution(Low) 30.0
    Number of Reflections(Observed) 22795
    Number of Reflections(R-Free) 766
    Percent Reflections(Observed) 98.74
    R-Factor(Observed) 0.21557
    R-Work 0.21279
    R-Free 0.29378
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.293
    Anisotropic B[1][1] -0.66
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.33
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.68
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.85
    Shell Resolution(Low) 1.898
    Number of Reflections(R-Free) 60
    Number of Reflections(R-Work) 1661
    R-Factor(R-Work) 0.45
    R-Factor(R-Free) 0.477
    Percent Reflections(Observed) 99.65
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 8.205
    r_scbond_it 6.294
    r_mcangle_it 4.61
    r_mcbond_other 1.146
    r_mcbond_it 3.229
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.017
    r_chiral_restr 0.126
    r_dihedral_angle_4_deg 24.623
    r_dihedral_angle_3_deg 21.963
    r_dihedral_angle_2_deg 41.472
    r_dihedral_angle_1_deg 8.852
    r_angle_other_deg 0.943
    r_angle_refined_deg 1.689
    r_bond_other_d 0.003
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2379
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 260
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) D*TREK
    Data Reduction (data scaling) D*TREK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building MOLREP