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An Information Portal to 108124 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2XTH
  •   Crystallization Hide
    Crystallization Experiments
    pH 4.7
    Details 10% SODIUM CHLORIDE W/V; PH 4.7 0.04M SODIUM ACETATE BUFFER; 80MG OF LYSOZYME PROTEIN 2ML AQUEOUS.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.64 α = 90
    b = 78.64 β = 90
    c = 36.45 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE (R-AXIS IV)
    Type RIGAKU
    Details OSMIC CONFOCAL MAX-FLUX
    Collection Date 2008-12-09
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type MICROMAX 007
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.53
    Resolution(Low) 55.6
    Number Reflections(Observed) 12866
    Percent Possible(Observed) 87.2
    R Merge I(Observed) 0.08
    Redundancy 6.17
     
    High Resolution Shell Details
    Resolution(High) 1.53
    Resolution(Low) 1.58
    Percent Possible(All) 23.2
    R Merge I(Observed) 0.29
    Mean I Over Sigma(Observed) 2.2
    Redundancy 1.89
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 1.8
    Resolution(Low) 55.64
    Number of Reflections(Observed) 10509
    Number of Reflections(R-Free) 556
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.2
    R-Work 0.198
    R-Free 0.249
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.91
    Anisotropic B[1][1] -0.48
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.48
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.96
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.85
    Number of Reflections(R-Free) 50
    Number of Reflections(R-Work) 740
    R-Factor(R-Work) 0.288
    R-Factor(R-Free) 0.381
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.522
    r_scbond_it 2.188
    r_mcangle_it 1.397
    r_mcbond_it 0.862
    r_nbd_refined 0.202
    r_gen_planes_refined 0.005
    r_chiral_restr 0.104
    r_dihedral_angle_4_deg 23.598
    r_dihedral_angle_3_deg 14.592
    r_dihedral_angle_2_deg 33.973
    r_dihedral_angle_1_deg 6.137
    r_angle_refined_deg 1.336
    r_bond_refined_d 0.013
    r_nbtor_refined 0.298
    r_xyhbond_nbd_refined 0.248
    r_symmetry_vdw_refined 0.186
    r_symmetry_hbond_refined 0.197
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1001
    Nucleic Acid Atoms 0
    Heterogen Atoms 13
    Solvent Atoms 129
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) D*TREK
    Data Reduction (data scaling) D*TREK
    Structure Solution REFMAC5
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building REFMAC5