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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YXU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 277.0
    Details Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 195.74 α = 90
    b = 195.74 β = 90
    c = 80.56 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2002-05-21
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.5
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2
    Resolution(Low) 72.55
    Number Reflections(All) 84753
    Number Reflections(Observed) 84733
    Percent Possible(Observed) 97.3
     
    High Resolution Shell Details
    Resolution(High) 2.24
    Resolution(Low) 2.36
    Percent Possible(All) 96.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.24
    Resolution(Low) 72.55
    Cut-off Sigma(F) 1.5
    Number of Reflections(all) 84753
    Number of Reflections(Observed) 78366
    Number of Reflections(R-Free) 4111
    Percent Reflections(Observed) 97.34
    R-Factor(All) 0.231
    R-Factor(Observed) 0.228
    R-Work 0.228
    R-Free 0.276
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.785
    Anisotropic B[1][1] 2.22
    Anisotropic B[1][2] 1.11
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.22
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.34
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.24
    Shell Resolution(Low) 2.298
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5750
    R-Factor(R-Work) 0.3
    R-Factor(R-Free) 0.336
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.233
    r_scbond_it 1.375
    r_mcangle_it 0.875
    r_mcbond_it 0.484
    r_symmetry_hbond_refined 0.151
    r_symmetry_vdw_other 0.283
    r_symmetry_vdw_refined 0.084
    r_bond_refined_d 0.013
    r_bond_other_d 0.003
    r_angle_refined_deg 1.515
    r_angle_other_deg 0.98
    r_dihedral_angle_1_deg 3.093
    r_chiral_restr 0.104
    r_gen_planes_refined 0.005
    r_gen_planes_other 0.004
    r_nbd_refined 0.205
    r_nbd_other 0.233
    r_nbtor_other 0.084
    r_xyhbond_nbd_refined 0.191
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8889
    Nucleic Acid Atoms 0
    Heterogen Atoms 112
    Solvent Atoms 384
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.1.25
     
    Software
    data extraction pdb_extract version: 1.600
    refinement REFMAC5 version: 5.1.25
    data processing SCALA