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X-RAY DIFFRACTION
Materials and Methods page
4JDY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 10.5
    Temperature 295.0
    Details PEG 8000, CAPS, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 110.75 α = 90
    b = 126.08 β = 90
    c = 180.82 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2010-11-20
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PAL/PLS BEAMLINE 6C1
    Wavelength List 1.23985
    Site PAL/PLS
    Beamline 6C1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.8
    Resolution(Low) 50
    Number Reflections(Observed) 115287
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.072
    Redundancy 5.3
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.86
    Percent Possible(All) 97.0
    R Merge I(Observed) 0.328
    Redundancy 3.8
    Number Unique Reflections(All) 11228
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 50.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 153419
    Number of Reflections(Observed) 115269
    Number of Reflections(R-Free) 5765
    Percent Reflections(Observed) 99.0
    R-Factor(Observed) 0.1843
    R-Work 0.1829
    R-Free 0.2106
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.2308
    Anisotropic B[1][1] 0.58
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.56
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.802
    Shell Resolution(Low) 1.849
    Number of Reflections(R-Free) 396
    Number of Reflections(R-Work) 7803
    R-Factor(R-Work) 0.278
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 95.98
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 6.249
    r_scbond_it 4.024
    r_mcangle_it 2.71
    r_mcbond_it 1.605
    r_gen_planes_refined 0.013
    r_chiral_restr 0.181
    r_dihedral_angle_4_deg 16.987
    r_dihedral_angle_3_deg 14.138
    r_dihedral_angle_2_deg 32.277
    r_dihedral_angle_1_deg 6.439
    r_angle_refined_deg 2.202
    r_bond_refined_d 0.03
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5841
    Nucleic Acid Atoms 0
    Heterogen Atoms 18
    Solvent Atoms 445
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction HKL