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X-RAY DIFFRACTION
Materials and Methods page
1YXT
  •   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 = 95.57 α = 90
    b = 95.57 β = 90
    c = 80.86 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 2002-06-21
     
    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) 82.76
    Number Reflections(All) 0
    Number Reflections(Observed) 28420
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.057
    Redundancy 4.2
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.11
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.715
    Mean I Over Sigma(Observed) 1.0
    R-Sym I(Observed) 0.715
    Redundancy 4.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 81.65
    Cut-off Sigma(F) 1.5
    Number of Reflections(all) 28435
    Number of Reflections(Observed) 26945
    Number of Reflections(R-Free) 1435
    Percent Reflections(Observed) 99.81
    R-Factor(All) 0.183
    R-Factor(Observed) 0.183
    R-Work 0.181
    R-Free 0.216
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.228
    Anisotropic B[1][1] 1.24
    Anisotropic B[1][2] 0.62
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.24
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.86
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.052
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 2004
    R-Factor(R-Work) 0.289
    R-Factor(R-Free) 0.334
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.118
    r_scbond_it 1.899
    r_mcangle_it 1.362
    r_mcbond_it 0.723
    r_symmetry_hbond_refined 0.299
    r_symmetry_vdw_other 0.346
    r_symmetry_vdw_refined 0.338
    r_bond_refined_d 0.013
    r_bond_other_d 0.0
    r_angle_refined_deg 1.568
    r_angle_other_deg 0.735
    r_dihedral_angle_1_deg 3.178
    r_chiral_restr 0.094
    r_gen_planes_refined 0.005
    r_gen_planes_other 0.002
    r_nbd_refined 0.26
    r_nbd_other 0.287
    r_nbtor_other 0.085
    r_xyhbond_nbd_refined 0.177
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2230
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 123
     
     
  •   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