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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2XMY
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.8
    Details 10% PEG 3350, NAF, PH 7.0
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.12 α = 90
    b = 71.5 β = 90
    c = 71.64 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 (RAXIS IV)
    Type RIGAKU
    Details BLUE MAX-FLUX CONFOCAL
    Collection Date 2004-10-10
     
    Diffraction Radiation
    Monochromator NI FILTER
    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) 1.9
    Resolution(Low) 21.78
    Number Reflections(Observed) 21623
    Percent Possible(Observed) 97.9
    R Merge I(Observed) 0.08
    Redundancy 3.13
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.42
    Mean I Over Sigma(Observed) 2.3
    Redundancy 3.08
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 40.64
    Number of Reflections(Observed) 20724
    Number of Reflections(R-Free) 897
    Percent Reflections(Observed) 97.78
    R-Factor(Observed) 0.19242
    R-Work 0.18913
    R-Free 0.27132
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 40.35
    Anisotropic B[1][1] -0.26
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.23
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.97
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.949
    Number of Reflections(R-Free) 60
    Number of Reflections(R-Work) 1522
    R-Factor(R-Work) 0.344
    R-Factor(R-Free) 0.402
    Percent Reflections(Observed) 99.68
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 7.92
    r_scbond_it 5.686
    r_mcangle_it 4.141
    r_mcbond_other 0.923
    r_mcbond_it 2.669
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.011
    r_chiral_restr 0.108
    r_dihedral_angle_4_deg 21.757
    r_dihedral_angle_3_deg 20.727
    r_dihedral_angle_2_deg 42.612
    r_dihedral_angle_1_deg 8.979
    r_angle_other_deg 0.905
    r_angle_refined_deg 1.694
    r_bond_other_d 0.0
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2372
    Nucleic Acid Atoms 0
    Heterogen Atoms 29
    Solvent Atoms 255
     
     
  •   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