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X-RAY DIFFRACTION
Materials and Methods page
4DYX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 298.0
    Details 50 mM Tris, 5 mM calcium chloride, 200 microM cupric chloride , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 179.27 α = 90
    b = 179.27 β = 90
    c = 179.27 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 AREA DETECTOR
    Type MARMOSAIC 325 mm CCD
    Collection Date 2012-01-23
     
    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) 1.85
    Resolution(Low) 103.5
    Number Reflections(All) 21660
    Number Reflections(Observed) 21660
    Percent Possible(Observed) 100.0
    Redundancy 15.2
     
    High Resolution Shell Details
    Resolution(High) 1.85
    Resolution(Low) 1.95
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.215
    Mean I Over Sigma(Observed) 3.2
    R-Sym I(Observed) 0.215
    Redundancy 15.2
    Number Unique Reflections(All) 3115
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.85
    Resolution(Low) 51.78
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 21641
    Number of Reflections(Observed) 21639
    Number of Reflections(R-Free) 1573
    Percent Reflections(Observed) 99.98
    R-Factor(All) 0.1709
    R-Factor(Observed) 0.1709
    R-Work 0.1688
    R-Free 0.1968
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.5534
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.851
    Shell Resolution(Low) 1.899
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 1470
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.234
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.762
    r_scbond_it 1.076
    r_mcangle_it 0.587
    r_mcbond_it 0.356
    r_symmetry_metal_ion_refined 0.045
    r_symmetry_hbond_refined 0.09
    r_symmetry_vdw_refined 0.185
    r_bond_refined_d 0.006
    r_angle_refined_deg 0.842
    r_dihedral_angle_1_deg 4.429
    r_dihedral_angle_2_deg 36.803
    r_dihedral_angle_3_deg 11.114
    r_dihedral_angle_4_deg 17.995
    r_chiral_restr 0.069
    r_gen_planes_refined 0.003
    r_nbd_refined 0.175
    r_nbtor_refined 0.29
    r_xyhbond_nbd_refined 0.081
    r_metal_ion_refined 0.082
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1416
    Nucleic Acid Atoms 0
    Heterogen Atoms 7
    Solvent Atoms 215
     
     
  •   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