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X-RAY DIFFRACTION
Materials and Methods page
4DYZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 298.0
    Details 50 mM Tris, 10 mM calcium chloride, 4% PEG 400, soaked in 20 mM EDTA, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 181.07 α = 90
    b = 181.07 β = 90
    c = 181.07 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 2011-04-17
     
    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) 2.3
    Resolution(Low) 104.54
    Number Reflections(All) 11848
    Number Reflections(Observed) 11848
    Percent Possible(Observed) 100.0
    Redundancy 42.0
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.42
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.397
    Mean I Over Sigma(Observed) 1.9
    R-Sym I(Observed) 0.397
    Redundancy 42.9
    Number Unique Reflections(All) 1680
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 90.54
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 11848
    Number of Reflections(Observed) 11847
    Number of Reflections(R-Free) 819
    Percent Reflections(Observed) 99.97
    R-Factor(Observed) 0.2231
    R-Work 0.2194
    R-Free 0.2715
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.9923
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(R-Free) 61
    Number of Reflections(R-Work) 797
    R-Factor(R-Work) 0.253
    R-Factor(R-Free) 0.303
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.162
    r_scbond_it 1.316
    r_mcangle_it 0.896
    r_mcbond_it 0.541
    r_symmetry_hbond_refined 0.096
    r_symmetry_vdw_refined 0.159
    r_bond_refined_d 0.008
    r_angle_refined_deg 0.996
    r_dihedral_angle_1_deg 4.949
    r_dihedral_angle_2_deg 39.299
    r_dihedral_angle_3_deg 14.999
    r_dihedral_angle_4_deg 19.504
    r_chiral_restr 0.074
    r_gen_planes_refined 0.003
    r_nbd_refined 0.175
    r_nbtor_refined 0.289
    r_xyhbond_nbd_refined 0.156
    r_metal_ion_refined 0.246
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1413
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 93
     
     
  •   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