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X-RAY DIFFRACTION
Materials and Methods page
4DYY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 298.0
    Details 50 mM Tris, 5 mM calcium chloride, 8% PEG 1900 MME, 700 micro M cupric chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 179.59 α = 90
    b = 179.59 β = 90
    c = 179.59 γ = 90
     
    Space Group
    Space Group Name:    F 4 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2011-04-16
     
    Diffraction Radiation
    Monochromator Rh coated flat mirror, toroidal focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength List 0.98
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 1.9
    Resolution(Low) 103.69
    Number Reflections(All) 20095
    Number Reflections(Observed) 20095
    Percent Possible(Observed) 99.8
    Redundancy 27.1
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 2.0
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.492
    Mean I Over Sigma(Observed) 1.4
    R-Sym I(Observed) 0.492
    Redundancy 20.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 89.8
    Number of Reflections(all) 20087
    Number of Reflections(Observed) 18597
    Number of Reflections(R-Free) 1454
    Percent Reflections(Observed) 99.72
    R-Factor(Observed) 0.21935
    R-Work 0.21766
    R-Free 0.24072
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.864
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.951
    Number of Reflections(R-Free) 99
    Number of Reflections(R-Work) 1345
    R-Factor(R-Work) 0.321
    R-Factor(R-Free) 0.331
    Percent Reflections(Observed) 99.86
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.941
    r_scbond_it 1.191
    r_mcangle_it 0.718
    r_mcbond_it 0.439
    r_nbd_refined 0.179
    r_gen_planes_refined 0.003
    r_chiral_restr 0.068
    r_dihedral_angle_4_deg 18.424
    r_dihedral_angle_3_deg 12.027
    r_dihedral_angle_2_deg 36.392
    r_dihedral_angle_1_deg 4.454
    r_angle_refined_deg 0.886
    r_bond_refined_d 0.007
    r_nbtor_refined 0.291
    r_xyhbond_nbd_refined 0.275
    r_metal_ion_refined 0.073
    r_symmetry_vdw_refined 0.171
    r_symmetry_hbond_refined 0.12
    r_symmetry_metal_ion_refined 0.078
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1412
    Nucleic Acid Atoms 0
    Heterogen Atoms 17
    Solvent Atoms 164
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BluIce
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0005
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction SCALA version: 3.3.15
    data collection Mosflm